Musings: archive for July-December 2010

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December 29, 2010

Blast detector

December 29, 2010

That's it. The color change shows that a blast occurred.

The purpose? One stated goal is to monitor soldiers. The problem is that they may survive the immediate blast event, but suffer delayed brain damage -- called traumatic brain injury (TBI). The blast detector described here could document the blast, thus serving as a warning that the soldier needs medical attention for a condition that might not be visible. The detectors are small -- the size of a small button. The soldier could wear several of them, including on or in the helmet. Detectors could be calibrated, so that the color change would effectively measure the size of the blast; this would give more specific information to guide the need for treatment.

How does it work? On the principle that the color of very small materials depends on the size. So the detector contains materials that will change color if "broken". The result is visible to the naked eye. It's based on the structure of the material; no power is needed.

News story: Color-Changing 'Blast Badge' Detects Exposure to Explosive Shock Waves. (Science Daily, December 4, 2010.) The figure above is from this story.

The article, via abstract at PubMed: Color changing photonic crystals detect blast exposure. (D K Cullen et al, NeuroImage 54(Supplement 1):S37, January 2011.)

More on shock waves... Aerospace engineers develop explosive device for supersonic delivery of vaccines (August 2, 2011).

What is it?

December 28, 2010

This is what happens when one puts together an animal from spare parts.

What is it?

For the story: The source. (National Geographic News, November 24, 2010.) (The figure above is reduced from the main figure of this story.)

For more: the article. (K J Osborn et al, Biology Letters 7:449, June 23, 2011.) An interesting and largely readable article. It starts with an intriguing title that is a plea to look for more. Much of the article discusses the critter -- how they found it and what it is like. Many nice pictures. The "Data Supplement" at that link includes a video. The video is also available at video.

For more from the deep sea, see the book The Deep - The Extraordinary Creatures of the Abyss, by Claire Nouvian. It is listed on my page of Book suggestions.

Other "What is it?" features include...
* Next: What is it? (February 7, 2011).
* Previous: What is it? (December 14, 2010).

Musings also notes Nouvian's book in another post featuring a strange and beautiful creature of the sea: Quiz: What is it? (October 31, 2012). See the answer.

The following post is not exactly related, but... Captain Nemo anyone? -- Giant squid sighting (January 15, 2013).

December 20, 2010

A candle for Christmas

December 20, 2010

Musings posts items of historical interest from time to time. This one is a book: a book about what happens when a candle burns, a book about chemistry -- premised on the observations of the candle.

Whoa! How did we go from "a candle for Christmas" to chemistry? Well, it really is a chem book, and the content has nothing to do with the holidays -- beyond any connection you would like to make. But the book itself does have a connection to the holidays. It's a famous book, by a famous chemist, with a famous connection to the Christmas holidays.

The book is: Michael Faraday, The chemical history of a candle: a course of lectures delivered before a juvenile audience at the Royal Institution. These lectures were given during the Christmas holidays of 1860-1; Faraday instituted this series of Christmas lectures for youngsters. The lectures were edited by William Crookes, and originally published in 1861. (Also included is a Lecture on platinum, delivered to the Royal Institution, February 1861.) Numerous editions have been published since. The one I read was an 1894 book, published by Chatto & Windus, in the UC Berkeley library.

Michael Faraday's public lectures are legendary, and this book will show you why. The topic is simple: how a candle burns -- and related issues. If only we could have been there! But just reading the lectures makes clear how he enraptured a youthful audience for six lectures on this one seemingly simple topic. Highly recommended, as chemistry and history. No particular background is required to read it.

The book is available online at various sites, including:
*;idno=ALQ5362.0001.001 and
The first of those includes the illustrations, but can only be displayed one page at a time. The second offers several options, with or without the figures.

There is an abridged version of the Candle lectures, with some beautiful pictures, at The Chemical History of a Candle. This could serve as a good introduction.

I have noted this book on my pages of Books: Suggestions for general science reading and Internet resources: Chemistry - Miscellaneous; History section.

More Faraday... Lyell on fossil rain-prints (May 6, 2012).

More Christmas: More resin for Christmas through better use of Boswellia (December 17, 2012).

Added October 25, 2016. More about the science of combustion: How easy is it to destroy any traces of 43 students by burning them? (October 25, 2016).

Robot uses coffee as a picker-upper

December 17, 2010

Just look over the following news story; I can't do much better: Robotic Gripper Runs on Coffee ... and Balloons. (Science Daily, October 26, 2010.)

Here are a couple of pictures. (Both are parts of Figure 1 of the paper.)

Fig 1D. A diagram of how the robotic gripper works. Fig 1B. An example of the robotic gripper in action, on an irregular object.
Figure 1D. A cartoon of how the robotic gripper works. Figure 1B. An example of the robotic gripper in action, on an irregular object.

There are some good materials posted by the authors. They include overview, pictures, and videos. To get you started...
* News story from one of the source universities: Balloon filled with ground coffee makes ideal robotic gripper. (Cornell University, October 25, 2010.) The movie here includes some demonstration of how the device works, along with a good explanation.
* Lab page: Universal robotic gripper based on the jamming of granular material. (Cornell Computational Synthesis Laboratory.)

The article: Universal robotic gripper based on the jamming of granular material. (E Brown et al, PNAS 107:18809, November 2, 2010.) The movie here, under Supporting Information, is a sequence of examples of the coffee-based gripper in action. It includes the egg scene that you will hear about; I guess this shows how to break an egg using coffee. You might want to look at their conflict of interest statement.

A recent post on another approach to developing a robotic "hand"... eSkin: Developing better sense of touch for artificial skin (November 29, 2010). I hope that you can see advantages and disadvantages of the two approaches. They may have merit for different uses. In designing a robot, we want to think about the intended function. We should not be too biased by our understanding of how we do it now.

Think about... The price of coffee fluctuates, based on supply and demand. This work, sponsored by the US Department of Defense (specifically, DARPA, the Defense Advanced Research Projects Agency), raises the possibility of coffee prices rising because of increased use by robots.

* * * * *

Another good news story on this... Get a grainy grip -- Robot hands may work better if they look more like beanbags than fingers. (American Scientist 99:29, January 2011.)

* * * * *

More on robots... Robots should learn to crawl first, then walk (February 27, 2011).

More DARPA robotics: See cat run (March 14, 2012).

For more on coffee...
* Added May 29, 2016. Why you should freeze the coffee beans before grinding them (May 29, 2016).
* How caffeine interferes with sleep (December 11, 2015).
* Your desire for caffeine: It may be in your genes (May 31, 2011).

More about balloons: How balloons burst (December 20, 2015).

December 15, 2010

What is it?

December 14, 2010

What is it? (Ignore the baby.)

For the story: The source. (Mail Online, December 6, 2010.) (The figure at left is trimmed from the first figure of this story.)

Previous panda post: The panda genome (January 11, 2010).

Other "What is it?" features include...
* Next: What is it? (December 28, 2010).
* Previous: What is it? (November 20, 2009).

Thanks to Thien for this item.

Designing a probiotic that fights cholera

December 13, 2010

We have had a range of posts on how the microbes that are normally associated with our body can be beneficial or even essential. An example is Can the Staph solve the Staph problem? (July 12, 2010); this post not only shows that one strain of "staph" bacteria may protect us from another, but begins to explain how that might occur. In addition to our natural bacteria, we sometimes take in bacteria intentionally; the use of such probiotics is supposed to promote health, though there is also much folklore about them. The post How probiotics work: a clue? (October 11, 2010) at least begins to hint how they might work.

Can we design a "good bacterium" -- a probiotic? That is exactly what the current paper does -- and with a noble cause: controlling cholera.

For our purposes, the cholera infection has two main parts. In the first part, the cholera bug enters the system, grows rapidly, and makes a toxin that makes you sick -- very sick. But then the bacteria realize that it is getting crowded, and they stop -- and leave. How do they know it is crowded? Because they have a system for counting bacteria, and determining when the cell density is high. The system is known as quorum sensing; it was first discovered in bacteria that make light, but only when the cell density is high, such as packed together in the "light organ" of a fish or squid. These quorum sensing systems are now known to be common in bacteria, and the details of how they work have been worked out in many cases. So the idea is simple... why not make a probiotic to confuse the cholera bacteria: design another bacterium to make the quorum sensing signal that tells the cholera bacteria their time is up. If this works, the cholera bacteria would enter -- and immediately receive the signal that it is time to go, before doing any harm. Since the cholera signaling system has been worked out, the scientists knew how to design the probiotic; they have tested it, and it works (in mice).

Effect of engineered E coli on cholera. Fig 2. The figure shows the key results. This is Figure 2 of the paper.

Bars A-I show the survival of the mice, after various "pretreatments" and infection with cholera (except for a control). The various pretreatment conditions A-I are shown by the pattern of dots below the bars.

Bars A & B are really most important. Bar A shows no survival; all the mice died of cholera. Bar B shows 90% survival. What's the difference? Look at the dots below. The first (top) set of dots shows the time of the pretreatment; both A & B were treated 8 hr before the cholera infection. The second set of dots shows how many bacteria were used -- for the protective pretreatment; both A & B were given the highest dose, 109 bacteria. The final (bottom) set of dots shows what the pretreatment was: for A it was ordinary E coli bacteria (called "Nissle"), but for B it was the engineered E coli carrying the cqsA gene. The cqsA gene is the gene that is supposed to make the signal to combat the cholera infection; it did. That's really the heart of the story.

The other bars are for various conditions. (Skip them if you just want the highlights.) For example, Bars B-D differ only in the pretreatment dose; the smaller the dose, the less effective it is. Bars F-G show what happens if the time of the pretreatment is less (compare with B); later treatment is not as good. Bars H-I are controls, with no pre-treatment; in I, there is also no infection with cholera.

It's almost too good to be true. Take a strain of E coli known to be safe, add a gene that is predicted to cause interference with the cholera infection. It works, almost remarkably well. It should be rather inexpensive to make. Simple to use: just eat it, 8 hours before getting infected. Now, for many diseases that might seem like an impractical requirement. But cholera tends to come in bursts. Haiti has an epidemic of cholera; treatment of people in problem areas with this engineered bacteria may be a reasonable proposition. [Musings post on the cholera epidemic in Haiti: Cholera in Haiti (November 22, 2010).]

What are the limitations of this story? The big one for now is that this has been tested only in mice. There is no particular reason it shouldn't work in humans, but the only way to know is to test it. Testing anything in humans is a big deal, but I suspect this will get tested. Also, we don't know for sure what the long term effects of this probiotic might be -- in mice or humans. The parental E coli strain is known to be safe, but we do not know the long term effect of the altered bacterium. It has been designed to specifically interfere with signaling of cholera bacteria, but we do not know what else it might do over the long term.

News story: Bioengineered 'Bacterial Communication' Blocks Cholera Spread. (Planetsave, June 29, 2010.) It's a little more political than our usual news story, but the presentation of the science is fine.

The article: Engineered bacterial communication prevents Vibrio cholerae virulence in an infant mouse model. (F Duan & J C March, PNAS 107:11260, June 22, 2010.)

Also see:
* When life imitates art... Bacteria blink for arsenic (April 15, 2012).
* Gut bacteria affect the brain (March 18, 2011).

For more on quorum sensing, see my page Unusual microbes: Bacteria that can count -- and talk.

A virus with an immune system -- stolen from a host? (March 25, 2013).

What color is your rice? Rice, diabetes, and arsenic.

December 12, 2010

An intriguing paper on rice and diabetes showed up a few months ago. One thing led to another, and so much information popped up that I once again managed to set it aside. Now, back to it... Because there is quite a bit, I have moved the main discussion to a supplemental page. There are two main topics there, both about white vs brown rice. One relates to diabetes and the other to arsenic. There is also some general background information.
* The supplemental page is: What color is your rice? Rice, diabetes, and arsenic -- supplemental page.

* A previous item on rice: What to do if you are about to drown (September 23, 2009).
* A previous item on diabetes: Making replacement insulin-producing cells: another way (May 14, 2010).
* A previous item on arsenic: NASA: Life with arsenic (December 7, 2010).

Also see:
* A smart insulin patch that rapidly responds to glucose level (October 26, 2015).
* Golden rice as a source of vitamin A: a clinical trial and a controversy (November 2, 2012).
* The rice-arsenic issue: Consumer Reports and the FDA weigh in (September 25, 2012).
* Rice and arsenic: rice syrup, baby food, and energy bars (April 23, 2012).
* Rice and arsenic: a follow-up (January 8, 2012).

More on diabetes is on my page Biotechnology in the News (BITN) -- Other topics under Diabetes.

December 8, 2010

NASA: Life with arsenic

December 7, 2010

Last week, in a much publicized news conference, NASA announced the discovery of a bacterium that can use arsenic instead of phosphorus. The news media covered it with a flourish -- and produced much nonsense. The paper was posted at the Science magazine web site, so we can look at what was really shown. Whatever the hype that the news media added, it is an interesting -- but incomplete -- story.

Growth of bacteria on arsenic. The figure at left shows a key experiment; this is Figure 1B of the paper.

The graph shows the growth of the bacteria under different conditions. Number of cells on the y-axis (log scale); time on the x-axis. The three conditions are, from the top: with added phosphate (circles), added arsenate (squares), or neither (open triangles).

Importantly, if there is no addition, the bacteria grow very little, if at all (lower curve). Then, arsenic (in the form of arsenate) does indeed stimulate growth (middle curve). So does phosphate; in fact, it is better (upper curve).

The above experiment (along with other measurements) does seem to establish the basic point: they have a bacterium that can use As instead of P. But now let's look at some of the limitations of the story -- as we have it so far.

First, the bug prefers P to As: it grows better if P is added than if As is added. You can see this in the graph above. Ok, no problem. They explicitly do not claim that the bug requires or prefers As, merely that it can use it.

Second and more importantly, the growth medium with no added P contains a trace level of P. (This probably comes from low levels of P contaminating other chemicals they use.) It's not enough to support growth alone (lower curve in the graph), but it does mean that when the bugs are growing on As, they also have a small amount of P available. In fact, analysis of the bacteria grown on As shows a weight ratio of about 7 As : 1 P. (On a mole basis, the ratio would be about half that.) Thus there still is considerable P in the bacteria. They cannot claim a total replacement of As for P. The paper recognizes this limitation, but some of the news coverage does not. (The total of As + P is rather low. This may be interesting, too.)

So, where is the As in the cell? This becomes particularly important since the replacement is incomplete. And this is where the paper gets rather weak. They hand-wave that it is everywhere, but there is little specific information. They do provide some data to show that the DNA contains As; I don't know how good that story is.

Where did this bacterium come from? It was isolated from Mono Lake -- a highly alkaline lake (in the Sierras of eastern California), with a high As level. Thus it is likely that the starting bug was quite resistant to As. All the reported work was done under lab conditions. There has been an opportunity for both physiological and genetic adaptation. Thus we do not know whether the bug uses As in nature. This does not minimize the importance of the work as a proof of principle. It is whatever it is, and it could exist naturally.

Did the "adaptation" to growing on As in the lab require genetic changes? There is not enough information given to tell. From what the paper said, the adaptation did not seem very difficult, so it is unlikely that extensive genetic changes were needed.

A concern about this work deals with the chemistry of As. It's true that As and P are in the same chemical family -- but family members are not identical. Esters and anhydrides of arsenate are relatively unstable. The paper notes this. DNA with As instead of P may well be no big deal -- at least structurally. But ATP with As instead of P seems a big deal. It's really important to establish which specific molecules have As -- and to find how high a replacement of P can occur. (I saw news stories suggesting that the bug uses adenosine triarsenate instead of adenosine triphosphate. However, the paper makes no such claim. They may hint at it, but there really is no evidence on the matter.)

Announcement: Discovery of "Arsenic-bug" Expands Definition of Life. (NASA, December 2, 2010.) Hype-alert -- starting with a dreadful title. But it is an interesting page.

* News story accompanying the article: Biochemistry: What Poison? Bacterium Uses Arsenic To Build DNA and Other Molecules. (E Pennisi, Science 330:1302, December 3, 2010.) Excellent. A good place to start.
* The article: A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. (F Wolfe-Simon et al, Science 332:1163, June 3, 2011.) A pdf file of Supporting Online Material is also there, freely available; it contains considerably more information.

Some background notes...

Previous work has shown that some marine microbes can replace the P in their lipids with S. I think that replacement with N has also been reported. This occurs under P-limitation. The argument has been that this substitution is "easy", and it spares the P for the more essential use in nucleic acids and such. See the Musings post: How do you make phospholipid membranes if you are short of phosphorus? (November 1, 2009).

In 2008 there was a report of a bacterium that seems to be able to use arsenite as the reductant in photosynthesis. Interestingly, this bug was also from Mono Lake. See the Musings post: Arsenic and photosynthesis (September 9, 2008).

There have been various other reports of specific biological uses of As, including specific As-containing biochemicals being made. The point of the new work is the substitution of As for P in the primary metabolic pathways. It is important to establish how extensive this substitution is; the hype says it is very extensive, but the actual data so far is very limited.

On a lighter note, a look at the author affiliations for the new paper shows that one author is from BEYOND.

Thanks to several people for useful discussions of this work over recent days. That includes both public and private discussion following my post of this in the chemed group.

For more about arsenic...
* Humans resistant to arsenic? (June 16, 2015).
* What color is your rice? Rice, diabetes, and arsenic. (December 12, 2010). [And Rice and arsenic: a follow-up (January 8, 2012).]

Other posts on phosphorus include...
* Phosphorus long long ago... The origin of reactive phosphorus on Earth? (July 5, 2013).

* * * * *

There is a major follow-up post, as the paper finally appeared in print: NASA: Life with arsenic -- follow-up (June 7, 2011). I have updated the listing for the article, above. Otherwise, please see the follow-up post for more discussion of this story.

More follow-up, as "rebuttal" papers appear: NASA: Life with arsenic -- Follow-up #2 (August 20, 2012).

What's a dia? Bumblebees and reindeer don't agree.

December 6, 2010

The daily cycle is a dominant feature of the lives of organisms on the surface of the earth. Light-dark-light-dark -- in a predictable but complex pattern. The daily cycle is so important that it is "built in" to our biology -- and operates even if we don't get the usual light and dark cues. That is, our bodies have a built-in circadian rhythm, which operates with but also independently from the daily light-dark cycles. The word circadian literally means about (circa) a day (dia). The common phenomenon of jet lag results from a conflict between our intrinsic circadian rhythm and the immediate light-dark cues.

So, what happens when we lose the light-dark cues? For example, what happens in the arctic during the summer, when there is 24 hours of daylight?

There have been two recent reports on this in recent months, one with reindeer and one with bumblebees. The results are very different with the two animals.

a reindeer a bumblebee A reindeer and a bumblebee.

Not to scale.

The reindeer is from the news story listed below. The bumblebee is from A to Z of a Wildlife Garden: Bumblebee. (Royal Society for the Protection of Birds)

The reindeer seem to turn off their circadian clock during the eternal summer; they are out and about, foraging, at all hours. On the other hand, the bumblebees turn in around midnight, despite the continuing daylight. Interestingly, substantially the same results were obtained with a bumblebee species native to the arctic and a species imported from lower latitude.

Incidentally, the first step in the bumblebee work is to get a thousand bumblebees, and attach a radio-frequency identification (RFID) tag to each one. (Recall Radio-tagged ants (May 13, 2009) for another example of using RFID to track insects.)

For the bumblebee story...
* News story: Bees stick to working hours. (University World News, July 4, 2010.)
* The article, which is freely available: Bumblebee foraging rhythms under the midnight sun measured with radiofrequency identification. (R J Stelzer & L Chittka, BMC Biology 8:93, June 29, 2010.)

For the reindeer story...
* News story: Reindeer body clock switched off. (BBC, March 15, 2010.)
* The article, via abstract at PubMed: A Circadian Clock Is Not Required in an Arctic Mammal. (W Lu et al, Current Biology 20:533, March 23, 2010.) (This is reference #41 of the bumblebee article listed above.) This paper is actually more on the biochemical aspects of the body rhythms.

The following post is about daily rhythms in lab mice, and it links to another dealing with humans: Does it matter when you eat? Or whether you leave a light on at night? (December 1, 2010).

The following post is about the effect of circadian rhythms on pregnancy: Light-dark (day-night) cycles affect pregnancy (August 10, 2012).

Next bumblebee post: The traveling bumblebee problem (January 11, 2011).

Other arctic posts include:
* Mammoth hemoglobin (February 1, 2011).
* Inuk, a 4000 year old Saqqaq from Qeqertasussuk (March 1, 2010).

Do your genes affect your politics?

December 5, 2010

This is the first Musings post where the opening paragraph of the paper notes that the work builds on the ideas of Karl Marx. It is also the first Musings post that is based on an article in Journal of Politics.

The work here is good science, in the broad area of behavioral genetics. The question asked is good and the model suggested is reasonable. There are two big cautions about this work. One is that we must understand that the results are quite preliminary. Second, the model proposed is not a simple relationship between genes and politics, but an "effect"; they do not propose that there is a gene for liberalism, but rather that a certain gene may make one somewhat more prone to be liberal. The authors explain these points at some length, but some of the media coverage is less careful.

The question they ask is reflected in the tittle of this post. In fact, they have a specific gene in mind: a receptor for the neurotransmitter dopamine. They already know that people have different forms of this receptor, and they know that people with one form of the receptor have a tendency toward "novelty-seeking behavior". The receptor affects how a person reacts to novelty, but is not in itself a source of novelty. They hypothesize that the distinction between what we commonly call conservative and liberal politics is related to novelty-seeking. They suggest that being exposed to a wide range of views can be considered a source of novelty. They use "number of friends" as a measure of this exposure.

The allele in question is called DRD4-7R. DR = dopamine receptor. D4 refers to one particular dopamine receptor. 7R refers to one particular allele (form).

Fig 1: Political characterization vs number of friends, for 2 or 0 copies of the allele being tested. The figure shows a key set of results. This is Figure 1 of the paper.

The left hand frame is for people who have two copies of the R7 allele of the dopamine receptor gene DRD4; this is the allele that is associated with novelty seeking. The graph shows their politics vs their number of friends. You can see that there is a trend: the more friends they report, the more likely they are to report being liberal. In contrast, the right frame is for people with no copies of the novelty-seeking receptor; these people show no such trend.

There are numerous limitations to the study. They start with the parameters being measured. Using one simple parameter to measure political views is a simplification. Using the number of friends is a stand-in for the intended variable of exposure to multiple views. Importantly, finding an effect that tests as statistically significant does not mean it is true. They discuss these limitations and more. But it is a step: they find some evidence for a gene that affects political views, and have an idea how it might work. Further work will confirm this -- or not. Even if it is true, it is only one part of the picture -- but determining one part of a complex story is progress.

See Mission Improbable (November 10, 2009) for more about p values.

News story: Researchers Find a 'Liberal Gene'. (Science Daily, October 28, 2010.)

The article: Friendships Moderate an Association between a Dopamine Gene Variant and Political Ideology. (J E Settle et al, Journal of Politics 72:1189, October 2010.) (There is also a pdf copy freely available at the author web site: author copy of pdf. I encourage you to look over the article. Much of it is a clearly written and well balanced overview of the role of "nature vs nurture" in behavior. Even the work itself is described very clearly, for the most part.

For more politics... The political leapfrog (January 24, 2011).

Water: a bat's view

December 3, 2010

To a bat, a body of water is a horizontal acoustical mirror.

Bats rely primarily on echolocation for navigation. Water is a smooth reflective surface. The figure shows what happens to the call signals from the bat at such a surface; the major black arrows give the main idea. Most of the signal is reflected away from the bat.

The figure is Figure 2 of the paper.
Reflection patterns for a bat signal on a water body. Figure 2.

If that is right, then an echolocating bat might try to drink from other acoustically reflective surfaces. That's the basic idea behind a new paper -- and the results substantially confirm the hypothesis. They tested the bats using metal plates with smooth surfaces and similar plates with roughened surfaces. The bats completely ignored the roughened surfaces; these bounced enough signal back to the bat to make it clear they were not water. But the bats repeatedly tried to drink from the metal plates (and from similarly reflective plates of other materials tested). The bats seemed not to learn from experience that diving at a metal plate was not a good way to quench their thirst. The same behavior was seen with naive juveniles, suggesting that the behavior is innate.

In nature, it is likely that the only horizontal reflective surface that bats encounter is water. Thus their approach to characterizing water probably serves them well.

Are bats confused by manmade water-mimics? The authors raise the question but have no evidence on the matter. A previous Musings post dealt with the issue of animals detecting water surface by light polarization, and some work suggests that such animals may indeed be confused by manmade objects: Aedes aegypti mosquitoes do not respond to polarized light when trying to land on water (May 22, 2010).

I'd like to see them test the bats directly with water and smooth metal surfaces. Can the bats tell the difference, in a direct comparison? Either possible result would be interesting. If the bats cannot tell the difference, can they learn to do so? If they can tell the difference, either initially or upon learning, what factors are involved?

News story: For Bats, All Smooth, Horizontal Surfaces Are Water -- Even When They Look, Smell and Feel Differently. (Science Daily, November 4, 2010.)

The article is freely available at: Innate recognition of water bodies in echolocating bats. (S Greif & B M Siem, Nature Communications 1:107, November 2010.) Two movie files are available there under "Supplementary Information"; they show a bat seeking a drink from a body of water -- and from a metal plate.

More about bats: How to find the blood (August 29, 2011).

Also see:
* A plant that communicates with bats (September 7, 2011). This is about attracting echolocating bats.
* On a similarity of bats and dolphins (September 15, 2013).

December 1, 2010

Does it matter when you eat? Or whether you leave a light on at night?

December 1, 2010


And then we might ask if the two questions in the title are related. And again the answer is maybe.

Those are the lessons from a recent paper. But we need to be cautious about the interpretation.

Let's start by looking at what they actually did -- the facts of the story. They took lab mice, subjected them to different light-dark cycles (different types of "days"), and measured their weight gain.

Mouse weights, with various light-dark and feeding regimes. Figure 4A. The figure at left summarizes some of the key results. It is Figure 4A of the paper.

Caution... Some of the labeling is a bit confusing, so let's go through this slowly.

The two main parts of the graph are for different types of days. LD means light-dark; LD is essentially a normal day. DM stands for dim; what this means is that at night there was dim lighting, rather than total darkness. That is, the two types of days are light-dark (on the left, dark bars) and light-dim (on the right, dim bars).

For each type of day, three feeding cycles were used. These are denoted by the F labels at the bottom. More about them in a moment.

First, let's look at the basic observation. Mice grown with the two day types, but with food always available. FA = food always. So look at the first (left) bar for each day type. The y-axis shows the average weight of the mice grown under each condition. (The axis is labeled body mass gain, but it really should be body mass.) For the FA condition, you can see that DM mice are heavier than LD mice. That is, dim light at night leads to the mice gaining more weight.

That point confirms previous observations. Further, they had noted that LD and DM mice ate about the same amount of food, but that the timing was different: DM mice ate more during the day. So, the rest of this experiment was designed to test the effect of food timing. In addition to the usual FA (food always), they had two additional food regimens: FD (food dark) or FL (food light), with food available for only part of the day.

The next key result, then, is what the DM mice do when the timing of their food is varied. Remember, with FA (food always), the DM mice were heavier. But if food is available only at night (FD), they are not heavier.

You can also see that mice fed only during the day (FL) are heavier than mice fed only during the night (FD) -- regardless of the details of lighting.

Thus it seems that two things are happening. First, mice fed during the day gain more weight than mice fed at night. Second, dim light at night causes the mice to shift some of their eating to daytime -- and thus leads to more weight.

They measured the amount of food eaten in the various parts of this experiment; interestingly, the amount of food eaten was about the same under all conditions. Thus greater weight gain seems to reflect a shift in metabolism rather than a shift in eating habits. Food eaten during the day is more likely to be stored at fat (weight gain).

What are we supposed to make of this? Let's assume that the basic findings as reported are correct. For the mice reading this post, the implications are clear enough: leave the lights off at night. But what are the implications for humans? That is much less clear. What the report does show is that light cycles may affect feeding habits and that feeding habits may affect our metabolism, and hence affect weight. Ok, good. But why should we accept any of the details as being relevant to humans? Mice have a very different daily rhythm than we do. It is one thing to suggest -- and show -- that daily rhythm may be important, but quite another to suggest that the mouse daily rhythm is directly relevant to the human daily rhythm.

Despite the reservations, it is important to remember that the natural environment for humans did not include artificial lighting. Obviously, we have some ability to adapt to altered light cycles, but it is hard to know our limits. The possibility that people do not do well with altered light-dark cycles has been raised before. We also know that people vary in their natural body rhythms -- just as they do in most any property. These are general comments, which open us to these issues being worth considering, but they do not lead to any specific conclusions. If you can live relying on your natural body rhythm, that is good. For sleeping, that is easy enough in principle: try to live without an alarm clock. That would let your natural rhythm, determine your sleep cycle -- and remember that other people may have quite different natural rhythms. It is less obvious what a natural eating cycle should be, but it is reasonable enough for individuals to experiment to see what works for them.

News story: Nighttime Light Ups Weight in Mice. (MedPage Today, October 12, 2010.)

The article: Light at night increases body mass by shifting the time of food intake. (L K Fonken et al, PNAS 107:18664, October 26, 2010.)

Also see:
* Added July 29, 2016. A world atlas of darkness (July 29, 2016).
* Effect of artificial lighting on the environment (September 3, 2015).
* When is waste removed from the brain? Sleep and the brain drain (November 17, 2013).
* A recent post on body rhythms: Sleepy teenagers (July 23, 2010).
* Daily rhythms in the long arctic day: What's a dia? Bumblebees and reindeer don't agree. (December 6, 2010).

How many human genomes have been sequenced?

November 30, 2010

In an earlier post I noted that the number of sequenced human genomes was nine. That was earlier this year -- about nine months ago: Inuk, a 4000 year old Saqqaq from Qeqertasussuk (March 1, 2010).

Nature now reports that the number of sequenced human genomes is "at least 2700" -- as of October. They expect it to be ten times that by the end of 2011.

That is in a Nature news feature, which is a nice overview of the status of determining human genomes. It's a two page spread, with lots of graphics. It shows the worldwide distribution of sequencing machines, and gives some indication of how many genomes they are doing, and the racial representation. Genomes by the thousand. (Nature 467:1026, October 28, 2010.) You could milk this for lots of information, but I think the main point is to have a look -- and be impressed. This is a revolutionary development; we are witness -- if not participants.

For more perspective on the human genome: The human genome - 10 years on (April 16, 2010).

The cost of genome sequencing: The $1000 genome: Are we there yet? (March 14, 2011).

Ancient DNA: an overview (August 22, 2015). Now, a perspective on the emerging field of ancient genomes.

There is more about genome sequencing on my page Biotechnology in the News (BITN) - DNA and the genome. It includes a list of Musings posts on sequencing and genomes.

eSkin: Developing better sense of touch for artificial skin

November 29, 2010

What does it take to hold an egg between thumb and forefinger -- without either dropping or crushing it? Answer: a good sense of touch, well integrated into your neuromuscular system for operating "hand". If the task seems easy, think about doing it holding the egg with a pair of tongs (or such device). Even with the tongs in your hand, I bet the task seems much harder.

A previous post on prosthetic limbs noted the need for such devices to have a sense of touch, that is, to be able to sense pressure. [Prosthetic arms (September 16, 2009)] Development of pressure-sensing skin has been challenging. Here is a report of a new development, in part from UC Berkeley, and featured in the university news.

This is really about technology development. The goal is clear enough: the development of a better sense of touch, for both prosthetic and robotic applications. The artificial skin should be "like" human skin: it should be able to respond to varying degrees of pressure, with good spatial resolution. It should be durable, even with common exposure -- including folding. And it should have reasonable cost. The approaches involve modern electronics.

A photo of the Berkeley e-skin.

You can see that the piece here is about the size of a hand; it contains an 18x19 array of pressure-sensitive pixels. The folding does not affect performance.

This is Figure 1b of the Berkeley paper listed below.
E-skin photo

News story: Engineers make artificial skin out of nanowires. (UC Berkeley, September 12, 2010.) Good overview of the issues, and an introduction to the Berkeley approach.

Although I first learned about this from the Berkeley news release, there are actually two papers on the topic together in the journal, along with a News and Views article. The two papers, from Berkeley and Stanford, are independent, with different approaches. The News article is an excellent overview of both, including the issues that need to be addressed in developing an electronic sense of touch that is human-like.

* News story accompanying the article: Flexible electronics: Within touch of artificial skin. (J J Boland, Nature Materials 9:790, October 2010.) "Flexible arrays of transducers can now be fabricated with pressure sensitivity and response times approaching those of natural human skin."

The articles:
* Nanowire active-matrix circuitry for low-voltage macroscale artificial skin. (K Takei et al, Nature Materials 9:821, October 2010.) The Berkeley paper.
* Highly sensitive flexible pressure sensors with microstructured rubber dielectric layers. (S C B Mannsfeld et al, Nature Materials 9:859, October 2010.) The Stanford paper.

Another approach to developing a robotic "hand"...: Robot uses coffee as a picker-upper (December 17, 2010).

Added January 3, 2017. and, perhaps more seriously... An artificial hand that can tell if a tomato is ripe (January 3, 2017).

More from the same Berkeley lab (as the current post)... A box that will fold up upon command -- heat- or light-actuated switches (September 3, 2011).

More about skin: A virus that could treat acne? (October 21, 2012)

More about the sense of touch: Crocodilians: Thick-skinned but very touch-sensitive (January 2, 2013).

Can genes be patented? The Myriad case -- legal issues

November 28, 2010

* Original post: Can genes be patented? The Myriad case (April 2, 2010).
* Follow-up: Can genes be patented? The Myriad case -- follow-up (November 8, 2010).
* Can genes be patented? The Myriad case: The Last Word (June 26, 2013).

These posts have stimulated some combination of interest and curiosity, perhaps even concern, about the legal issues. From his own follow-up, Borislav sends the following item, which is an analysis of the case by a pair of biotech lawyers: Pigs Fly: Federal Court Invalidates Myriad's Patent Claims. (J Conley & D Vorhaus, Genomics Law Report, March 30, 2010.) I found it to be an excellent analysis, at various levels. Some of it may not be easy reading, but I encourage you to at least look it over for the big ideas if you have any interest in the legal issues. The article is not only a good analysis of this case, but a useful insight into how the legal system operates.

The article refers to a patent issue regarding the chemical adrenaline (epinephrine). Adrenaline was patented by Parke-Davis (now Pfizer) in 1900, and the patent was upheld in 1911 -- despite it being a natural product. As you can see, the adrenaline case is relevant to the current case of the BRCA genes.

November 23, 2010


November 23, 2010

This post is about an essay -- a broad-ranging essay. Among its issues is how one approaches solving a problem; among the specific problems addressed is carbon emissions. Interestingly, the essay connected to a private discussion the day I read it, so it seems worth sharing, despite some reservations.

One of the issues is the merits of addressing a problem with incremental small improvements versus thinking through a bold new strategy that will really be better in the long run. We sometimes call this evolution versus revolution -- but don't make much of a possible biology analogy. The author makes it an issue of engineers versus politicians or policy planners, though of course that is stereotyped. His context for bringing this up is solving the C-emissions problem. Whether his answer is right in this case we can leave as an open point; what he does is to raise the question, and make the case for one approach.

One of his specific concerns is about wind energy. Wind energy has appeal, since it is not based on fossil fuels and does not result in CO2 emissions. However, he properly notes that the intermittent nature of wind energy creates a new type of problem; as a result, the benefit of replacing coal by wind for generation of electricity is less than expected. (The same point can be made for solar energy.) Ok, good, and if you had not thought about the problem of intermittent energy sources, then this is worthwhile. But it is a known issue, and various approaches are being studied to deal with it. It is good that he raises it, but his discussion of dealing with it is weak.

Overall, the essay seems worth a good look. It raises some good issues and some good questions. I don't buy all his answers, but that is not the main point here. It's not so much that his answers are wrong, but that there is more to the story. But surely you do not expect one person in a three-page article to present a complete analysis?

The essay is freely available: Strategy versus evolution - Reaching President Obama's CO2 emissions goal for 2050 will require strategic planning. (A Pavlak, American Scientist 98:448, November 2010.)

Other posts on climate change or energy development include:
* Windmills for your cell phone? (January 21, 2014).
* A Christmas present: Using concentrated sunlight to split water and CO2 (February 18, 2011).
* Where is the control knob for global warming? (November 16, 2010).

There is more about energy on my page Internet Resources for Organic and Biochemistry under Energy resources. It includes a list of some related Musings posts.

Cholera in Haiti

November 22, 2010

Among its problems, Haiti is now dealing with an emerging epidemic of cholera -- a disease not confirmed there for decades. Among the stories associated with this Haitian cholera outbreak is the possibility that the cholera was introduced by United Nations peace-keepers. True or not, the story is having an effect; some of the locals believe it, and this is interfering with aid.

Here are a couple of articles about the Haitian cholera; both include some about the possible origin. Although their dates are two weeks apart, I suspect that they deal with the same facts at this point. As to the possibility of import, the short answer is that there is insufficient information to say what happened. Interestingly, cholera experts have different ideas about what is likely. Both stories are quite readable. I encourage you to at least browse through both, then read more as suits you.

Article, freely available: Update: Cholera Outbreak --- Haiti, 2010. (Morbidity and Mortality Weekly Report (MMWR) 59:1473, November 19, 2010. Authorship is given as "Ministry of Public Health and Population, Haiti. Pan American Health Organization. CDC".) This is a formal scientific article on the initial analyses that have been done. It will give you an idea how a disease outbreak is handled. As usual in MMWR, the main article is followed by an "editorial note", broadly putting the article in perspective. You may find this part more readable and more interesting.

News story: Infectious diseases: Haiti's Outbreak Is Latest in Cholera's New Global Assault. (Science 330:738, November 5, 2010.) This is a lively news story, with much discussion of cholera transmission, including the origin of this outbreak. This is interesting to read, but emphasize that there are few hard facts at this point.

Cholera is caused by a bacterium, called Vibrio cholerae. However, the cholera toxin is coded for by a virus. Only bacteria carrying the virus can make the toxin.

The disease is self-limiting. After some period of replication, the bacteria "clear out". Thus, treatment emphasizes treating the symptoms, mainly by rehydration.

For more about cholera, specifically about the possibility of inducing the bacteria to "clear out" early, see the post: Designing a probiotic that fights cholera (December 13, 2010).

Checking mosquito saliva

November 19, 2010

If a mosquito is about to bite you, can you tell if it carries a disease agent? Sure, just check its saliva.

The problem of course is catching the mosquito, so you can test it. And what we have now is a proposed method for "catching" mosquitoes, so they can be tested. Actually, we don't even need to "catch" them; the proposed method sets up a station where the mosquitoes can just drop off their samples, on their own. This isn't about testing the one that is about to bite you, but testing a local population; it is a surveillance system.

The general idea is simple enough; it's just a matter of working out a procedure that is practical in the field. The heart of the method is a "honey trap" -- a card impregnated with honey, and giving off CO2 to help attract the mosquitoes. The mosquitoes are attracted to the "nectar", drop by for a little meal, and leave some saliva on the card. The card is then sent in to a high-tech lab and analyzed for virus molecules.

The trap A picture of the trap, from Figure 1A of the paper.

Mosquitoes are attracted to the CO2 flow at the bottom, and enter the trap in an upward draft (driven by a small battery-operated fan at the top). Once in the main chamber, they may feed on the honey-impregnated "FTA cards" -- and leave some saliva. (FTA stands for a brand name; an FTA card is a filter paper that has been treated to preserve bio-molecules, such as the RNA of the viruses.)

How useful is this? They discuss how it compares with alternative surveillance systems now in use, and they think it is good. They do not go into any economic considerations, such as the cost of the device. We'll see whether they -- or others -- continue with this and make a practical real-world device.

If you haven't thought much about mosquito expectoration, you'll learn something from this work.

News story: Honey Trap to Detect Mosquito Pathogens. (The Naked Scientists, June 13, 2010.) Good introduction to the ideas; includes an overview of competing methods.

The article: Exploiting mosquito sugar feeding to detect mosquito-borne pathogens. (S Hall-Mendelin et al, PNAS 107:11255, June 22, 2010.)

Also see:
* Why don't black African mosquitoes bite humans? (December 19, 2014).
* Malaria-infected mosquitoes have greater attraction for people (May 28, 2013).
* Using genetically engineered mosquitoes in the real world (October 18, 2010).

More on disease-causing mosquitoes (and malaria) is on my page Biotechnology in the News (BITN) -- Other topics under Malaria.

November 17, 2010

Death-grip scars from zombie ants, 48 million years ago -- Follow-up

November 17, 2010

Original post: Death-grip scars from zombie ants, 48 million years ago (November 9, 2010).

Borislav adds a video... Cordyceps: attack of the killer fungi. (From the BBC series Planet Earth, narrated by David Attenborough.)

The fungal genus is given here as Cordyceps. In the earlier work, it is given as Ophiocordyceps. Those two names are synonyms.

More from David Attenborough: Frozen Planet (November 14, 2011).

Using genetically engineered mosquitoes in the real world -- Update

November 17, 2010

Original post: Using genetically engineered mosquitoes in the real world (October 18, 2010).

This post seems to be jinxed. I originally offered a news story; a few days later, that story was no longer available. So I posted another; a few days later, it was no longer available. So I have now posted two more. All of these -- the original and replacement links -- are the same basic story. It is simply an announcement that a real-world test of genetically engineered mosquitoes is imminent.

Where is the control knob for global warming?

November 16, 2010

The general idea behind the greenhouse effect and global warming is simple: The sun's energy reaches the earth. Some of the solar energy is radiated back into space -- at longer wavelengths, in the infrared (IR). Certain gases in the atmosphere can absorb this IR radiation; the more of such greenhouse gases in the atmosphere, the more IR radiation gets absorbed, and the warmer is the Earth.

So, which is the most important greenhouse gas? That would seem to be a simple question, but it actually causes considerable confusion. There are two gases that are "most important" -- but they are most important in different ways.

One way to look at it would be to ask which atmospheric gas absorbs the most IR energy. That would be water. But the other way to look at it is to ask which gas is most important in determining the overall IR absorption. And that would be carbon dioxide.

How can that be? Because the CO2 level affects the H2O level. Why? Because water in the atmosphere -- water vapor -- can condense into liquid water. The more CO2 there is, the warmer the atmosphere -- and more H2O vaporizes, thus making the atmosphere even warmer. That is, the amount of water vapor in the atmosphere responds to the CO2 level -- and magnifies changes in CO2. Thus we see that CO2 is "in charge"; CO2 is the control knob for the greenhouse effect.

The figure below, Figure 2 from the paper, shows how CO2 serves as the controller. Caution... The labeling of the graph is confusing!

Figure 2, showing various parameters over time after setting CO2 (and other non-condensing greenhouse gasses) to zero. The graph was generated by a computer model of climate change. At time 0, they set the CO2 level to 0. (More precisely, they set the level of all of the non-condensing greenhouse gases to 0 -- but the major one is CO2.) Then the computer calculates various parameters that will result over 50 years. A key parameter is the water vapor -- the blue curve, which is the bottom curve for most of the graph. This curve starts at "100%", meaning the current amount of water vapor, and drops quickly. After about 10 years the water vapor has dropped to about 10% of the current amount. Remember, the water vapor is the major greenhouse gas. In this model, they remove the CO2 -- and the water vapor is largely lost. That is, CO2 controls the water vapor. The other curve of particular interest is the one for surface temperature -- the black curve, which should be read using the y-axis scale at the left. It gets cold!

(If you want to understand the other curves, be sure to read what is said in the text about them. As noted, the labeling of the graph is confusing. I think the lines themselves are fine, but labeling many lines on one graph can be difficult, and they did not do it well.)

News story: Carbon Dioxide Controls Earth's Temperature, New Modeling Study Shows. (Science Daily, October 15, 2010.)

The article: Atmospheric CO2: Principal Control Knob Governing Earth's Temperature. (A A Lacis et al, Science 330:356, October 15, 2010.)

There is a second article referred to in the news story, another new paper from the same group. It sorts through the contributions of individual atmospheric components to the overall greenhouse effect. For those trying to follow the story in detail, this may be useful. It deals with various estimates from the literature, as well as semantic confusions. Attribution of the present-day total greenhouse effect. (G A Schmidt et al, Journal of Geophysical Research 115:D20106, October 16, 2010.) If you can't access that... there is a draft of the paper freely available from the author: author copy; draft.

Other posts on climate change include:
* Why isn't the temperature rising? (September 12, 2011).
* Planning (November 23, 2010).
* CO2 emissions: What if we just stopped making new CO2-emitters? (October 5, 2010).

Also see: How graphs can mislead (May 24, 2015).

One health

November 15, 2010

"One Health is a paradigm that encompasses the health of humans, animals, and their environment, recognizing that the health of each domain is inextricably interconnected." This is the opening sentence of the paper listed below.

The One Health idea emphasizes interconnections. This includes straightforward interconnections such as diseases being transmitted between different types of animals. It's straightforward, but the importance is often not fully appreciated. Look at a list of diseases that have emerged recently, and see where they come from. Further, One Health makes the connection to the environment. For example, climate variation -- natural or otherwise -- leads to changes in the distribution of mosquitoes, and therefore to changes in the distribution of mosquito-transmitted diseases such as dengue fever.

We noted the One Health idea in the post Q     or     Beware of goats bearing infections     or     It's one health. (February 20, 2010). The immediate context there was the sharing of a disease (Q fever) between goats and humans. The proponents of the One Health idea would say that it is relevant to many of our posts dealing with diseases, of humans or of other animals, or the "health" of the environment.

At times, One Health may seem to be a political movement. Resist that, and look at individual points that are made. That is, try to focus on the scientific reasons behind the One Health idea, rather than the political decisions made as a result. The One Health idea should encourage you to look at the big picture of how we are all interconnected; it does not mean that you blindly accept any particular connection that anyone suggests. One Health is not an end in itself, but a way of looking at things. That is, the point of reading about One Health is not to judge it as being right or wrong, but to see the connections that it suggests.

The paper is a very readable "news feature" type article, written for a general audience. It is freely available: One Health -- Attaining Optimal Health for People, Animals, and the Environment. Adopting the One Health paradigm is crucial for understanding emerging diseases and meeting future challenges in global health. (R Atlas et al, Microbe 5:383, September 2010.) Some of it is "political", but much deals with the core scientific issues; it discusses numerous specific diseases (including Q fever). Browse as you wish.

The "one health" idea emphasizes the flow of diseases among various organisms. The following post is about the flow of diseases among countries. Of course, those are related issues. International relations: sharing flu viruses (May 28, 2011).

For a broad overview of public health... Ten Great Public Health Achievements, 2001-2010 (June 26, 2011).

Schmallenberg virus (January 20, 2012). A new disease is emerging.

Also see: Disease outbreaks: Trends and perspective (March 31, 2015).

Also see my page BITN: Emerging diseases. That discusses disease transmission among types of animals.

How humans form bureaucracies

November 13, 2010

Some human societies are simple, some are complex. How did we get from one to the other? Anthropologists have long debated this -- often with little evidence. A new paper opens a new approach to addressing this question.

The basic approach here is, in part, quite simple. They considered a group of isolated but related societies, for which they had considerable information. As a key part of the work, they analyzed the relatedness of the languages -- using the type of computer analysis used for analyzing the relatedness of genomes. That is, they made a family tree of the languages. This family tree based on languages presumably reflects how the societies are related.

Further, they classified each society as to its "structure" -- basically, how many levels of bureaucracy it has. Then, by looking at the pattern of the society structures on the family tree (based on the languages), they could see what kinds of transitions from one structure to another were common. Figure 4 of the paper, below, summarizes the findings.

Figure 4: rates of the various possible transitions. The four ovals represent the four societal structures they studied, in order of complexity, left to right. (The simplest, rather egalitarian, societies have no bureaucracy; these are called acephalous -- literally, headless.)

In principle, a society at any of these levels might transition to any other level. So, there are lots of arrows, showing all those possible transitions. But the width of the arrow reflects how common each type of transition is, according to their analysis. The dotted arrows are for cases where the rate seems to be zero.

The main conclusions...
* If you look at rightward arrows, forming a more complex society: only short arrows are found at any measurable rates. Apparently, they would conclude, societies become more complex in small steps.
* If you look at leftward arrows, forming a less complex society: all the possible arrows are found. Apparently, they would conclude, societies become less complex in small or large steps.

The article will get criticized at various levels. The classification of society structure is too simple, and sometimes controversial. The language data may or may not be complete enough to be showing the true family tree of the societies. The set of models they tested can probably be extended. But the main point of the paper is introducing the approach. They try the approach on one set of data and models. If people find merit in their approach, it can be extended as more data and more models surface.

News story: Societies evolve slowly, just like biological species. (PhysOrg, October 14, 2010.) Don't take the "just like" in the title too literally. What they mean is that the same tools can be used to analyze the two processes, not that the processes per se are similar.

* News story accompanying the article: Sociology: Political evolution. (J Diamond, Nature 467:798, October 14, 2010.) A good overview of the work.
* The article: Rise and fall of political complexity in island South-East Asia and the Pacific. (T E Currie et al, Nature 467:801, October 14, 2010.) Much of this is surprisingly readable. They do a good job of describing what they do, what some of the assumptions are, and the basic findings. Of course, the real work is highly mathematical, but that part is largely hidden from the reader.

The turtle that plays basketball

November 12, 2010

Would that title be any less disconcerting if it simply said "The turtle that plays"?

There is a delightful news article in a recent issue of The Scientist about play. What is play? Why do we do it? It seems that many other animals appear to play. How do we understand that? The article presents a range of evidence, and a range of views on what it means. As you read it, keep separate seeing what the animals do and interpreting it. Overall, a fun article -- well worth some of your time for mental play.

Recess. (J Akst, The Scientist, October 2010, p 44.)

For more about play: Do young chimpanzees play with dolls? (January 28, 2011).

For more about turtles: Where is turtle #92587? (February 22, 2011).

For more about sports: Baseball physics (July 31, 2011).

November 10, 2010

Death-grip scars from zombie ants, 48 million years ago

November 9, 2010

This paper deals with fossil evidence for a bizarre behavior seen in a modern fungus-ant-plant association. As you read it, be sure to distinguish what the modern association is, and what the new evidence is for its occurrence in ancient times.

The figure at right shows an example of what actually happens now -- real biology. The figure shows an ant attached to a leaf, at a vein. A fungus is growing out of the head of the ant.

The news story listed below describes how this comes about. The key point is that the fungus modifies the behavior of the ant, so that the ant attaches to the leaf, in what is known as a death-grip.

The figure is reduced from one in the news story. Figure 1f of the paper is similar.
Ant attached to leaf, at vein; fungus growing out of ant head.

Image of scar on fossil leaf

This figure, based on photographs of a fossil leaf, shows a dumbbell-shaped scar near a major leaf vein.

This is part of Figure 1b of the paper. The white box (whose contents are magnified in another part) is about 2 mm across. The full figure shows pictures of fossil scars and scars from known modern ant "death-grips" at various magnifications.

Their interpretation of the fossil scar, with this unusual type of damage, is that it is likely due to the same type of death-grip seen with modern fungus-infected ants. Note that they have no direct evidence that a fungus is involved with this fossil leaf phenomenon.

News story: 'Zombie ants' controlled by parasitic fungus for 48m years -- Earliest evidence of fungus that takes over ants' behaviour for its own ends found by scientists. (Guardian, August 18, 2010.) Good description of the modern fungus-ant interaction.

Zombie? In popular usage, the word refers to mind control. An organism is a zombie if its mind has been taken over by another. In this case, the fungus controls the behavior of the ant, causing it to make the death-grip attachment to the leaf. We infer that the fungus is controlling the mind of the ant, thus making the ant a zombie.

The article: Ancient death-grip leaf scars reveal ant-fungal parasitism. (D P Hughes et al, Biology Letters 7:67, February 23, 2011.)

Other posts about ants:
* Why a tree cultivates ants (October 3, 2010).
* How to survive flooding by making a waterproof raft (May 27, 2011).
* TIGER discovers smallest known fly; does it live in the head of tiny ants? (July 31, 2012).
* The advantage of washing with formic acid (August 8, 2014).

More about zombies:
* Wasp hides under ladybug (January 3, 2012).
* Halloween special: The largest (known) pumpkin (October 31, 2011).
* Dr. Smith? (September 5, 2009).

Other posts featuring pictures of fossils include:
* The oldest known plants (November 2, 2010).
* Paleobioboron (January 26, 2011).

* * * * *

More, November 17, 2010...

Borislav adds a video... Cordyceps: attack of the killer fungi. (From the BBC series Planet Earth, narrated by David Attenborough.)

The fungal genus is given here as Cordyceps. In the earlier work, it is given as Ophiocordyceps. Those two names are synonyms.

Can genes be patented? The Myriad case -- follow-up

November 8, 2010

Among the posts in this story...
* Can genes be patented? The Myriad case (April 2, 2010). Original post.
* Can genes be patented? The Myriad case: The Last Word (June 26, 2013).

As expected, Myriad has appealed the original decision, discussed in the above post. There has been an interesting development... The US government has filed a brief opposing the patenting of "natural" genes. This is a change in the government position. (Whether the change is due to the different politics of the current administration or to the evolution of the field -- or some combination -- is beyond my scope.)

For a short introduction to this development: U.S. Says Genes Should Not Be Eligible for Patents. (New York Times, October 29, 2010.) It includes a link to the legal brief, for those who want the legalese.

Fructose; soft drinks vs fruit juices

November 7, 2010


Another item on food. Like others, it is murky -- but interesting. A draft of this item proved so controversial that I ended up holding it. Here is a revised version. I hope the clear breakdown into short sections helps make clear how each part should be looked at.

We have an epidemic of obesity and metabolic diseases such as Type II diabetes. Somehow, these seem related to diet -- and perhaps to the high consumption of soft drinks. Or perhaps to the high consumption of high fructose corn syrup (HFCS), the major sweetening agent in soft drinks (and in some other processed foods). Perhaps. Or perhaps not. One would think that collecting data would resolve this, but it has not. For one thing, the rise of consumption of HFCS may correlate with an overall rise in consumption of sugar; separating these two possible causes is not easy.

Fructose: some basic facts

Fructose is closely related to the more common sugar glucose. In fact, they are isomers of each other: the same atoms, arranged a bit differently. The industrial production of HFCS is done using the enzyme glucose isomerase, to convert about half of the glucose to the fructose isomer. A similar enzyme is part of glycolysis, a major pathway for digesting sugar in your body. (This enzyme actually works on the phosphorylated forms of the sugars.) However, despite this close connection, the simple notion that glucose and fructose are equivalent in the body is not correct. That opens up the possibility that one is better for you -- but of course does not prove it.

A fructose resource

The immediate stimulus for this post was an item on the Nutrigenomics list, highlighting a major review article on fructose.
* The Nutrigenomics item is short, consists largely of the abstract of the paper, and makes clear the ambiguity of our current state of knowledge. More on High Fructose Corn Syrup. (NutriAlerts, April 11, 2010.) [Update... This page is no longer available. The original URL was: ]
* The paper is quite lengthy and detailed. It is full of information -- but not clear conclusions. However, it is well organized, with a clear listing of the contents at the start. You can find some interesting historical material in the Introduction, and can look at specific aspects of the fructose story as you wish. Or just jump ahead to the Perspectives -- and get the disappointing bottom line. It's freely available at: Metabolic Effects of Fructose and the Worldwide Increase in Obesity. (L Tappy & K-A Le, Physiol Rev 90:23-46, January 2010.)

Fruit juice vs soft drinks?

The fructose article reminded me of a news story that a reader sent a few months ago. It dealt with the merits of fruit juice vs soft drinks -- a related issue, since soft drinks are typically sweetened with HFCS. Some of us batted it around a bit, but I never got around to posting it. So let's bring it in here. The news story is: It's time fruit juice loses its wholesome image, some experts say. (Los Angeles Times, November 8, 2009.) Their lead-in: "Compared with soda, juice carries more calories and as much sugar. There's also evidence that high consumption increases the risk of obesity, especially among kids."

The basic question here is whether fruit juice is "just as bad" for you as soda (soft drinks). One instinct we have is to reject that, because fruit juice is supposedly a healthful food, with vitamins. True enough. But that misses the point. Whatever benefit fruit juice may have is likely satisfied by having a glass or two. The point of concern is about large amounts. Some people drink lots of soda. Simply replacing that with an equivalent amount of juice (same amount of sugar) may result in about the same health effects. At large amounts (doses!), the sugar is probably the main concern; if the sugar is high in fructose, it may be a greater concern. High consumption of vitamins is of questionable value.


With my usual disclaimer that I do not give nutritional (or medical) advice, here is my "advice"... I think a key problem with soda is that people drink it in addition to a full diet of food. Thus the soda is extra calories -- and mostly sugar. Replacing it with a different but equivalent source of extra calories is probably just as bad. Thus I discourage large scale use of any sugar-rich drink. Typical amounts of drinks consumed with meals are probably fine; it is the regular consumption of drinks during the day, separate from meals, that is the (potential) problem. Drink water. Or coffee or tea -- without additions.

Those are my opinions. Please don't act on this simply because I said a conclusion, but I would encourage you to look into this, and reach your own conclusions. If you find some good sources with other views, let me know. I think you will find that the subject is indeed murky, and you will be forced to make personal choices without full information. In that case, I suggest that reducing caloric intake is probably a good guiding point, and reducing consumption of sugar-rich drinks -- soda or juice -- is probably a safe choice.

More on fructose... Fructose and your brain (January 28, 2013).

More on sugary drinks...
* Added August 30, 2016. The Berkeley soda tax: does a "fat tax" work? (August 30, 2016).
* Soft drinks (sugar) and blood pressure (April 1, 2011).

More on sweeteners...
* Artificial sweeteners: Saccharin and high blood sugar levels (December 7, 2014).
* Rice and arsenic: rice syrup, baby food, and energy bars (April 23, 2012).

Responses of other animals to sugars... Why and how some cockroaches avoid glucose (October 11, 2013).

Other posts related to nutrition include...
* Breeding plants to be more nutritious (May 11, 2010).
* Is folic acid good for you or bad for you? (April 10, 2010).

More on how sugars are metabolized: A better way to divide 6 by 2: A more efficient way to use sugar (November 10, 2013).

Other posts related to obesity include...
* A gene for obesity (May 7, 2011).

My page Internet resources: Biology - Miscellaneous contains a section on Nutrition; Food safety.

Polio: progress toward eradication

November 5, 2010

Mankind has, we think, eradicated two diseases. One is smallpox, an ancient scourge of humanity. The other is the major cattle disease rinderpest. For the latter, see the Musings post: Another disease has been eradicated. GREP. (February 2, 2010). That post also includes some general information about disease eradication programs, and an introduction to the polio problem.

In 1988 the world medical community declared a goal of eradicating polio -- by 2000. That goal was not met. However, tremendous progress has been made: the number of countries with endemic polio is now only four (down from over 100), and the number of cases reported annually is down by 99%. How to achieve total eradication, so that the number of cases is zero without vaccination, is a continuing challenge. Part of the approach is new vaccines; a big news story a few days ago noted major progress, so let's look at it.

The polio story actually involves three viruses, known as Types 1, 2 and 3. The viruses cause very similar disease but are antigenically somewhat distinct, and require separate antibodies. Type 2 polio has in fact been pretty much eradicated -- a fact that is now affecting the approach. The traditional vaccine is trivalent -- made against all three polio types. But with Type 2 polio essentially gone, it is reasonable to consider eliminating it from the vaccine mix. Thus people are now exploring the use of monovalent vaccines, against Type 1 or Type 3, or bivalent vaccines, against Type 1 and Type 3.

The other basic background that is needed may be more familiar. There are polio vaccines that are administered by injection, and there are polio vaccines administered orally. (These are sometimes referred to as Salk or Sabin vaccines, respectively, in recognition of key scientists who developed them.) There is debate in the medical community about their relative merits. However, the present work involves only oral vaccines, so we won't go into that here.

This background lets us classify the polio vaccines -- and follow the terminology used to describe them. All of the vaccines described here are OPV = oral polio vaccine. There is a prefix telling us whether the vaccine is mono- (m), bi- (b), or tri- (t) valent -- telling us how many poliovirus Types it is targeted against. For monovalent vaccines, the type is indicated at the end. Thus, mOPV1 is a monovalent oral polio vaccine against Type 1 poliovirus. Although there might be various types of bivalent vaccines, the only one of interest is the one against Types 1 and 3, since Type 2 seems no longer a problem; thus the type numbers are not shown with the bOPV.

The new work compares the effectiveness of the various vaccines. Here is an example of the new results, taken from Figure 2 of the paper.

Antibody titers achieved with various vaccines The graph shows the amount of antibody that resulted from each of the five vaccines tested (60 days after giving the vaccine). More specifically, it shows the antibody measurement as a percentage of infants who have the indicated amount of antibody -- or more. For example, look at the red curve which is for one vaccine (bOPV)... About 95% of the infants have an antibody titer of at least 10, about 80% have at least 100, and about 40% have at least 1000.

This graph is for Type 1 poliovirus. The best results (highest or right-most curve) are for mOPV1 -- the monovalent vaccine against this particular virus. Next -- and fairly close -- is the bivalent vaccine, bOPV. Next is the trivalent vaccine, with all three virus types. The two lowest curves are for two vaccines that do not contain Type 1 virus at all.

The main conclusion from this figure is that the bivalent vaccine and the appropriate monovalent vaccine are both considerably more effective than the commonly used trivalent vaccine. It seems that the Type 2 virus may actually be interfering with vaccine effectiveness; dropping Type 2 from the vaccine program may be advantageous. Further, the bivalent vaccine is almost as good as the monovalent vaccines. The full Figure 2 in the paper shows the results for the other types; they follow the same pattern.

Figure 3 of the paper summarizes the effectiveness of the various vaccines. But caution... the x-axis runs "backwards": the better vaccines are to the left.

This work is from India. In fact, bivalent vaccine is now being used there, and there is a considerable reduction in polio cases this year. That is, the higher level of antibody reported in the new paper seems to be resulting in reduced disease. A similar story is developing in Nigeria. These are encouraging results; it remains to be seen whether they hold over an extended period.

News story: Bivalent Oral Polio Vaccine Produces Better Immune Response Than Trivalent Vaccine, Study Says. (Kaiser Daily Global Health Policy Report, October 26, 2010.)

* Commentary accompanying the article, via PubMed: Poliomyelitis eradication: another step forward. (N W Crawford & J P Buttery, Lancet 376:1624, November 13, 2010.)
* The article, via PubMed: Immunogenicity of bivalent types 1 and 3 oral poliovirus vaccine: a randomised, double-blind, controlled trial. (R W Sutter et al, Lancet 376:1682, November 13, 2010.)

Also see:
* WHO certifies "South-East Asia" free of polio (November 1, 2014).
* Poliovirus eradication: an update, with some good news and some bad news (May 22, 2011).
* Making a wimpy virus (July 23, 2008). A different approach toward making a vaccine virus.
* The Cutter Incident: How America's First Polio Vaccine Led to the Growing Vaccine Crisis. A book listed on my page of Book Suggestions. The book, by Paul Offit, 2005, is on historical aspects of polio vaccine, focusing on the Cutter incident, involving defective batches of vaccine.

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Polio.

November 3, 2010

Haystack -- Follow-up

November 3, 2010

Original post: Haystack (October 6, 2009).

Haystack was a software intended to allow users to use the Internet anonymously. The motivation was to allow Internet use for people in countries with government restrictions on Internet usage. Such programs are difficult to implement, and typically require high maintenance -- to keep them ahead of the authorities. A reader expressed considerable skepticism about Haystack when I posted it initially; turns out he may have been right. Haystack has now been withdrawn, with allegations that it did not work very well in the first place.

The Wikipedia page provides very brief coverage, but is likely to be updated if there are further developments. As of now, I also recommend the BBC news story of September 14, 2010; this is currently reference 8. Wikipedia: Haystack (software).

The oldest known plants

November 2, 2010

This paper makes a small advance in our knowledge of plants, but is an interesting story with some nice pictures.

The big story is that plants developed from algae. Plants and algae are the two big groups of oxygen-evolving photosynthetic eukaryotic organisms. Plants grow on land, and algae grow in water; strictly speaking, they are distinct groups. Common usage does not always agree, and the term land plants is sometimes used for clarity.

The simplest modern plants -- the simplest photosynthetic eukaryotes on land -- are thought to be the liverworts; there is a picture of them in the news story listed below. Liverworts do not fossilize well, but their spores do. Therefore, modern work on the oldest plants is largely the observation of spores from organisms similar to liverworts.

What's new here is finding such fossil spores in formations in Argentina dated to about 472 million years (Ma) ago. That is about 10 Ma older than the previous oldest known plants. Issues in determining the validity of the work are in the dating of the geological formations and the identification of the spores.

Examples of the spores that were found. The Figure at right shows examples of the spores that were found. The scale bars are 20 µm.

In parts e and h, you can see that the structure shown contains 4 spores.

This is reduced from Fig S3 in the online supplemental materials (which are freely available). The pdf of the article contains the same figure (Figure 2) -- but without color. The news story also includes a version of this figure.

An interesting tidbit is that the previous oldest spores were from Saudi Arabia and the Czech Republic -- all of which were at about the same latitude, 35° S, at the time of the plants. If it surprises you to hear of Saudi Arabia being in the southern hemisphere -- actually south of Argentina... Remember, this was nearly a half billion years ago, on the continent of Gondwana. Figure S4, again in the freely available online supplement, has a map.

News story: Fossils of earliest land plants discovered in Argentina. (BBC, October 12 , 2010.)

* Commentary accompanying the article: The invasion of the land by plants: when and where?. (C H Wellman, New Phytologist 188:306-309, October 2010.)
* The article: Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana). (C V Rubinstein et al, New Phytologist 188:365-369, October 2010.)

Other posts featuring pictures of fossils include:
* Death-grip scars from zombie ants, 48 million years ago (November 9, 2010).
* Paleobioboron (January 26, 2011).

More from Saudi Arabia: Where is the MERS virus coming from? (September 22, 2013).

More from Gondwana: How were the Gamburtsevs formed? (December 7, 2011).

Cancer in the ancient world

November 1, 2010

Borislav sent a news story about an interesting "Perspectives" article in the Nature journals -- and included a big caution. Indeed! The article is an exploration of cancer in the ancient world -- focusing on Greek and Egyptian cultures of 2-4 thousand years ago. These are cultures for which we have both writings and biological materials. Modern techniques allow rather sophisticated examination of the ancient bones and mummies; what do we learn about cancer from them? And what do we learn from reading the medical texts of those cultures? So, in this short article (only about four pages of text), they open up this ancient world of cancer with lots of interesting information. The article may well be worth a look simply for the overview of how we learn about ancient medical issues.

In one section of the article, they raise the question of whether cancer was rare in those days, thus has increased markedly in modern times. Ok, good question. But they present no data. Cancer is not one disease, but many; cancer incidence depends on the type of cancer. And it varies with environment. They address some of these concerns, but largely ignore them; then they end up suggesting a blanket conclusion. Frankly, I think they look rather foolish at that point. It is not news to suggest that some aspects of modern society, such as "pollution", may enhance cancer. What we need is data. But no matter. This is something of an essay, and they can state their opinions. The article is still full of interesting information -- and good questions; it also includes a huge reference list for more.

Here is the news story that first came up. How the ancient world dealt with cancer. (CNN, October 14, 2010.) If you will read through the whole article, it ends up giving a reasonable overview of the issues.

Here is a blog entry by a scientist. I know nothing about him, but the article seems good. Is Cancer A Disease of the Modern World? (Derek Lowe, October 20, 2010.)

So far, we have not seen any coverage of the article in the serious scientific news media, so the above items will do for now.

The article: Cancer: an old disease, a new disease or something in between?. (A R David & M R Zimmerman, Nature Reviews Cancer 10:728, October 2010.)

Other posts about cancer include:
* A tumor in a Neandertal (July 8, 2013).
* Diagnosis of prostate cancer in a 2100 year old man (November 8, 2011). A new example of a cancer found by high resolution CT scan of a mummy.
* Targeting cancers (January 15, 2011).
* A cancer drug with a switch: it acts only in a cancer cell (September 26, 2010).

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Cancer.

Cellulosics for energy: an update

October 30, 2010

Here is a news feature with a nice update on the status of making biofuels (such as ethanol) from cellulosics -- either agricultural waste materials, or plants grown for that purpose.

Making biofuel from corn (starch) works, but competes with the food use of the corn. Using cellulose has appeal, but there is a barrier: cellulose is not easily degraded -- reflecting, after all, its natural role. Now, cellulose is biodegradable, and some organisms even use it as a major food. The problem is not the basic idea, but actually implementing it in a practical -- and economical -- manner. Bottom line... No one has really succeeded yet, and goals for cellulose-derived biofuels are being scaled back. This doesn't mean that cellulose won't work. However, it will likely require new discoveries to achieve better degradation, not simply implementation of what is already known.

The news feature: Is There a Road Ahead for Cellulosic Ethanol?. (R F Service, Science 329:784, August 13, 2010.) A short, readable overview; a useful status report. It is part of a feature section on "Scaling Up Alternative Energy".

Also see:
* Engineering E coli bacteria to convert cellulose to biofuel (December 13, 2011). A milestone. Not an economic process, but an interesting technical achievement.
* Another degradation issue... Degradable polyethylene isn't (October 17, 2011).
* Cellulose: improved processing (February 25, 2011). This post offers two improvements in cellulose processing. Caution... The practical importance of these improvements -- their effect on the economics -- is unknown.
* A Christmas present: Using concentrated sunlight to split water and CO2 (February 18, 2011).
* Making biofuels from cellulose (May 17, 2010). Discussion of a process involving chemical degradation of cellulose, after dissolving it in an ionic liquid. Includes some discussion of the economics.
* Alternative energy for a sustainable future (May 7, 2009).

There is more about energy on my page Internet Resources for Organic and Biochemistry under Energy resources. It includes a list of some related Musings posts.

An anti-freeze story: Why a tick carries a human pathogen

October 29, 2010

We're used to the idea that insects serve as vectors for disease agents. We're also getting used to the idea that organisms carry microbes for their own benefit. Now we have a story that ties these two ideas together: a tick that carries bacteria that causes human disease -- and the tick benefits from the bacteria! In this case, the bacteria help the ticks survive the cold, by promoting formation of an anti-freeze protein.

In looking for a news story on this, I came across a blog entry that does a pretty good job of telling the story. So I'll be brief, and just aim you to the blog: Of Ticks and Bacteria. (Benjamin Tseng, October 4, 2010. The figure here is reduced from one on this page.) tick

* Commentary accompanying the article, freely available via PubMed: Fitness and freezing: vector biology and human health. (G Neelakanta et al, Journal of Clinical Investigation 120:3087, September 2010.)
* The article, freely available via PubMed: Anaplasma phagocytophilum induces Ixodes scapularis ticks to express an antifreeze glycoprotein gene that enhances their survival in the cold. (J S Dumler, Journal of Clinical Investigation 120:3179, September 2010.)

Here are some recent Musings posts related to the points made in the opening paragraph...
* Using genetically engineered mosquitoes in the real world (October 18, 2010). About disease transmission by insects.
* Plants need bacteria, too (October 9, 2010). Organisms carrying microbes for their benefit.
* Developing improved degradation of organophosphate pesticides (September 7, 2010). This post dealt with organisms promoting ice-formation, but some organisms do exactly the opposite.

October 27, 2010

The first truly habitable exoplanet? Follow-up.

October 26, 2010

Original post: The first truly habitable exoplanet? (October 12, 2010). The content of this follow-up has been integrated into that post.

Apparently the basic finding of that work has been called into question. We don't have much to go on. The critique of the initial finding was done at a meeting, and we have a newspaper account. I'm sure the two groups will be working together in analyzing the existing data. Perhaps it will take more data to reach a better conclusion. For now, it must remain an open question. Such uncertainties about new planets are common; the detection methods are pushing the limits of the technologies.

News story: Gliese 581g: 'Goldilocks' planet might not exist after all -- Gliese 581g, a newly discovered, first-of-its-kind planet thought to exist in its star's habitable zone, might just be 'noise,' astronomers say. (Christian Science Monitor, October 13, 2010.) A good overview both of the original report and of the doubts that have been raised. It seems to be by someone quite knowledgeable in the field.

* * * * *

More, July 27, 2012... Further information has been added to the original post (which is noted at the start of this post).

Bird theater -- follow-up

October 26, 2010

Original post: Bird theater (October 19, 2010).

Darsh notes three videos on bowerbirds. They are now added to the original post. I encourage you to check at least the first one. Note that there are different kinds of bowerbirds, so you will see similarities and differences.

US Army attacks colony collapse problem -- and an ethics story

October 25, 2010

For background on the problem, see Why are the bees dying? (January 26, 2010). That post also presents a proposed explanation for the problem. Now we have another. (Abbreviation: CCD = colony collapse disorder.)

The approach here is something of the ultimate in brute force. I exaggerate only slightly by saying that they inject infected bees into their mass spectrometer (MS) -- and measure everything. Seriously, this is an emerging powerful approach for analyzing the proteome -- the entire set of proteins. It makes use of top-of-the-line MS machines, with cost approaching a million dollars. The results are analyzed by sophisticated software, using reference databases that have been built up. In some ways, it is the ultimate black box science. Although the logic of the methodology is straightforward, almost all the work is hidden by complex software.

Ok, it is a black box. Did they find something? Indeed. Their analysis uncovered two organisms which, they suggest, may act together to cause the CCD. One is a (microsporidian) fungus, one that had previously been implicated in CCD -- though the supporting data were inconsistent. The other is a novel virus. Their claim, from the protein analysis with the MS, is that the disease is characterized by having these two agents together. Taken alone, that is an association, and does not show causality. However, they do one lab experiment, which shows that the two agents together are more lethal to bees than either alone. It's not a big effect, and it is hard to know how relevant the conditions of this experiment are, but at least there is something that further work can build on.

Effect of fungus and virus on bee survival. Here are the results of that experiment.

The graph shows survival curves for four groups of bees, with various treatments. Nosema is the fungus. The curves for fungus and for virus are very similar, at least past the first few days. The curve for fungus plus virus shows the poorest survival.

This is Figure 3 of the paper.

I think that the most important part of this work is finding the new virus. That virus now becomes a candidate that can be explored further, along with the fungus -- and whatever else comes up. For now, we should remain open about what causes CCD.

News story: Scientists and Soldiers Solve a Bee Mystery. (New York Times, October 6, 2010.) A somewhat whimsical overview of the work. Despite the hyped title, overall it gives a good sense of the work and its significance.

The article, which is freely available: Iridovirus and Microsporidian Linked to Honey Bee Colony Decline. (J J Bromenshenk et al, PLoS ONE 5(10):e13181, October 6, 2010.) As noted, the protein analysis part of the work is almost incomprehensible.

More on CCD... A parasitic fly that causes hive abandonment in bees: Is this relevant to CCD? (January 27, 2012).

More mass spectrometry... Close-up view of an unwashed human (July 29, 2015).

* * * * *

After writing the above, I discovered that an ethical issue has arisen about this work. Here is the news item that raises the concern: now archived at What a scientist didn't tell the New York Times about his study on bee deaths. (CNN Money, October 8, 2010.) Caution... This story itself is something of a tirade. As you read it, try to sort out the factual points that are made.

What is this about? Let's assume that the basic facts stated in the CNN story are correct. The authors of a scientific paper are supposed to disclose possible conflicts of interest. In fact, there is a section on the first page of the paper called "Competing Interests", in which they do make disclosures. However, they did not disclose one connection -- one which the authors do not consider important, but which others might reasonably think is important. Regardless of details, I do think that the intent of a disclosure section is clear enough. Conflicts of interest are about perceptions. Our emerging standards in science, with more and more communication with the general public (surely that is good), says that we disclose anything that might reasonably be perceived as relevant. If in doubt, disclose.

The journal's page on reporting conflicts is: PLoS Policy on Declaration and Evaluation of Competing Interests. It's not exactly fun reading. If you do read it, I suggest you read it more for general background than to try to judge this case. Our information on this case is incomplete. Anyway, no purpose is served by making such a judgment.

What effect does disclosure (or lack thereof) have on the science story? Well, it certainly distracts. In fact, that is perhaps the big concern. Science proceeds in steps. In the long run, the importance of this paper will be judged by how well the ideas stand up upon further testing, including by others. I already noted above that I consider the main contribution of the paper to be putting a new virus on the table for consideration. I do not conclude that they have proven the cause of CCD -- and they do not conclude that in the paper. However, the news story does make a stronger claim -- especially in the headline. That is unfortunate. Will be scientific community be affected by whether or not the authors disclosed the possible conflict? I doubt it. Would the reporter have written the story with the same tone had he known of the possible conflict? I wonder.

The CNN article raises a second ethical concern, which is of some general interest. The main testing of a new product for safety is done by the manufacturer (of a pesticide in this case; a similar procedure holds for drugs). This is obviously a conflict of interest built into the system. It is inevitable that we will question the integrity of safety results from the manufacturer. Why do we continue with such a system?

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Ethical and social issues.

The original Watson-Crick paper on the structure of DNA

October 25, 2010

Diagram of DNA double helix, from the original Watson & Crick paper. A truly historic paper. As the web page below headlines, this is a "document that started a revolution". Hype? Of course; no single paper stands alone. But this paper symbolizes the revolution -- and it is quite an unusual scientific paper. It is only a page long, and has no original data in it. It is accompanied by related papers in the same issue, but this is the paper that gets the recognition: it symbolizes the revolution. It presents the model -- a model that has become iconic, to scientist and non-scientist alike. It presents "the solution" to the molecular basis of hereditary. Part of the mystique of the paper is that one of their concluding statements is often quoted (or paraphrased) from memory -- a statement one writer called the most coy statement in the scientific literature: "It has not escaped our notice... ".

A Structure for Deoxyribose Nucleic Acid. (J D Watson & F H C Crick, Nature 171:737, April 25, 1953.) An annotated copy of the paper, from the Exploratorium and Cold Spring Harbor Laboratory. You can read the paper itself, and if you click on any of the underlined parts you will get some discussion of it along the side. It's worth a read, even if you stumble over some of the technical details along the way.
The figure from the paper.

There is controversy about the role of Watson & Crick, which is noted at the above site. For those who would like a serious discussion of this issue, I recommend Brenda Maddox's book, listed on my page of Book suggestions: Maddox, Rosalind Franklin - The dark lady of DNA (2002). Regardless of the controversy, the finding they reported stands.

Another post on molecular biology history -- also involving Francis Crick: Central Dogma of Molecular Biology (August 16, 2011).

More molecular biology history, this one pre-dating Watson & Crick Salvador Luria, on his 100th birthday: the Luria Delbrück experiment (August 13, 2012).

This post notes more DNA history... Uptake of small pieces of ancient mammoth DNA by bacteria: What are the implications? (May 13, 2014).

Many posts deal with some aspect of DNA work. Examples...
* Who is #1: the most DNA? (March 7, 2011). Genome size -- the amount of DNA an organism has.
* DNA: Watching the hopping supercoils (November 24, 2012). The dynamic aspect of DNA structure.

Therapy based on embryonic stem cells: the first clinical trial

October 23, 2010

This was a big news story, so let's note it for its historical significance -- and also make an important clarification.

The simple story is that Geron Corporation has begun a clinical trial in humans of a therapy based on embryonic stem cells (ESC, or hESC to specify that they are human cells). This is the first such trial, thus this is a milestone. hESC were first isolated only in 1998.

The clarification that is needed is to emphasize that the patients are being given cells derived from hESC; they are not being given hESC. Many news stories, including the one I list below, fail to make this distinction. ESC have the potential to become any kind of cell. "Guiding" them to become the kind of cell that is needed for a particular use is a complex issue. It is done in the lab.

The clinical trial is "phase 1". This means that there is "pre-clinical" evidence, based largely on tests with other animals, that seem to justify moving forward to human tests. The initial tests are aimed at seeing if the drug is safe; there is no particular attempt to gain information on its usefulness at this stage.

A couple of general comments...
* There are varies classes of stem cells being explored. The ones used here are ESC -- derived, as the name implies, from embryos. These cells are pluripotent: able to become any type of cell, just as they do in the body. A new type of stem cell is induced pluripotent stem cells (iPSC). These are derived from regular body cells, such as skin cells, by treating them in the lab so that they revert to the pluripotent state. iPSC are similar to ESC -- but not identical in practice; people are actively studying the differences, and whether they are important, one way or the other. Adult stem cells are natural cells from the body that have some but limited ability to fill certain roles. (Adult stem cells are said to be multipotent.) Bone marrow transplantation is an established procedure which we now understand as involving adult stem cells.
* Much of the emphasis, especially in the popular press, is on the use of stem cells -- or cells derived from them -- for therapy. In this context, each of the classes of stem cells has pro and con features -- and none are well understood at this point. Further, we should emphasize that studying stem cells is also an important part of modern biology. That is, stem cells are research tools.

News story: First trial of embryonic stem cells in humans. (BBC, October 11, 2010.)

An informational page from Geron, intended for the general public, but with a more detailed description of the therapy and the trial: hESC-Derived Oligodendrocytes - GRNOPC1. See below for a new source of this page. (Geron is a local company here; they are in Menlo Park, very near Stanford University, south of San Francisco.)

Among other posts related to stem cells:
* A test of a stem cell therapy based on iPSC, in monkeys (August 29, 2014).
* Restoring sight by use of stem cells to regenerate a new cornea (July 13, 2010);
* Do you need some new brain cells? (March 22, 2010).

There is more on stem cells on my page Biotechnology in the News (BITN) - Cloning and stem cells. It includes an extensive list of Musings posts in the fields of stem cells and regeneration -- and, more broadly, replacement body parts, including prosthetics.

Another approach to treating spinal cord injury: Recovery of breathing following spinal cord injury (July 29, 2011).

* * * * *

Geron announces it is leaving the stem cell field, and stopping further work on this trial. Therapy based on embryonic stem cells: the first clinical trial -- follow-up (December 5, 2011).

Geron has removed their web pages on the subject. The informational page noted above, originally at "", is archived at: hESC-Derived Oligodendrocytes - GRNOPC1. (Geron, 2010; now archived)

And then... Geron sells its stem cell business (January 23, 2013).

Berkeley Bionics: From HULC to eLEGS

October 22, 2010

Thien sends: Berkeley Bionics reveals eLEGS exoskeleton, aims to help paraplegics walk in 2011. (engadget, October 7, 2010.)

This is an interesting -- and perhaps important -- development following on a big news story from 2008. At that time, Berkeley Bionics announced the HULC -- the Human Universal Load Carrier. The HULC is basically an "exoskeleton" -- a device strapped on to the body to make it stronger. A person wearing a HULC is stronger: they can carry more weight, with reduced metabolic cost. The HULC is now a commercial product, through Lockheed Martin, with the military as the prime customer.

But what about those whose skeleton (and neuromuscular system) precludes walking? Now, the same company has just announced a "medical exoskeleton" to assist the disabled. It is called eLEGS -- the Exoskeleton Lower Extremity Gait System -- shown at the right. It uses the same general approach as the device for the military, but now customized for those whose skeleton is inadequate for basic walking. In this case, the "walker" (crutches) is part of the package, along with the exoskeleton per se that the person wears; signals from the "walker" are used to help coordinate the motions, thus achieving something close to a normal walking gait.

eLEGS is not yet a commercial product, but they expect to have it in rehab centers next year for real-world testing.

The web site Thien sent, above, includes pictures and videos.

Here are a couple more news stories; both have more complete information about how the device works.
* Robotics: Berkeley Bionics' newest exoskeleton lets wheelchair users walk. (Gizmag, October 7, 2010.) More good pictures.
* Local company's technology mimics human gait. (Daily Cal, October 11, 2010.) Good explanation. And this is where I found what eLEGS stands for. (This article is from the school paper here. But I really did learn about the announcement from Thien.)

For more... Berkeley Robotics & Human Engineering Laboratory. The UC Berkeley lab that is behind the work. The site has information about the two products noted here, and more (including CALibot, "the most naturally swimming robotic fish in the world"). The picture above is from their home page. Click on Publications, and you will find some scientific papers from the lab; some are available there as pdf. Dr. Homayoon Kazerooni, Professor of Mechanical Engineering, is head of the lab and founder of the company.

FDA approval of such a device (from another company): Another FDA approval: exoskeleton (August 11, 2014).

Another approach to making an exoskeleton for human use: An exoskeleton that assists with walking but does not require an external energy source (September 8, 2015).

Also see:
* Prosthetic arms (September 16, 2009)
* Reading the brain waves from speech (October 17, 2010)

For more on walking...
* "Moonwalkers" -- flies that walk backwards (May 28, 2014).
* What is it? (March 8, 2011).

More about exoskeletons: How do you breathe while changing your skeleton? (October 31, 2014).

Also see my Biotechnology in the News (BITN) page for Cloning and stem cells. It includes an extensive list of Musings posts in the fields of stem cells and regeneration -- and, more broadly, replacement body parts, including prosthetics.

* * * * *

Here are two news stories from the UC Berkeley student newspaper, mid 2011, on aspects of this. The two stories refer to different devices, a point that is made clear in the June story.
* Campus graduate takes new first steps. (Daily Cal, May 18, 2011)
* Locally created walking aid to sell next year. (Daily Cal, June 8, 2011)

* * * * *

Berkeley Bionics: From HULC to eLEGS -- Follow-up (July 26, 2011). Talk by Homayoon Kazerooni, at the Science@Cal series. Kazerooni is the man behind the work discussed here; he is head of the Berkeley Robotics and Human Engineering Laboratory at UCB, and founder of Berkeley Bionics.

* * * * *

November 7, 2011: Berkeley Bionics is now Ekso Bionics.

October 20, 2010

Device intended for medical diagnostics moves into the world of entertainment

October 20, 2010

The CellScope was designed to allow microscope images to be transmitted by cell phone. For example, a blood smear from a patient at a remote site could be transmitted to a distant expert. The CellScope was introduced in the post Connecting a cell phone and a microscope (September 2, 2009).

For the new application of the CellScope, see Video: UK Animators Use Cellphone and Microscope To Film Smallest Stop-Motion Animation Ever. (PopSci, September 20, 2010.) This page includes the two-minute video, which is also available at YouTube: The video of Dot.

For more about the CellScope, see a page from Professor Dan Fletcher, in the Bioengineering Department at UC Berkeley: CellScope -- Mobile Microscopy. At the bottom is a link to a separate page focusing on the CellScope.

Also see a section of my page Internet resources: Biology - Miscellaneous on Microscopy.

Bird theater

October 19, 2010

Bowerbirds are noted for the complex displays ("bowers") used during mate selection. An example is shown at the right. The female, at the back, is entering the "avenue". (Ignore the black motion sensor at top right.)

The figure is from the news story listed below, and is also Figure 1A of the paper.

Now, scientists have examined the distribution of objects (in the front, as shown here). The scene may look rather "random" to you (or perhaps uniform), but the objects actually are ordered by size.

Here is an example...
A Bower
Bower birds will rearrange bower objects to proper size distribution. Figure 3. The key measurement here is the "slope". This is a measure of how the objects are arranged. It is the relationship between the size of the objects and their position. A positive slope means that the size of the objects increases with distance -- from the opening where the female appears. Note then that a positive slope, which is what they find, opposes the normal effect of perspective, which makes more distant objects look smaller.

The graph shows this slope (object size vs distance) for several bowers at various times. The slope is on the x-axis; the y-axis shows the number of bowers with that slope. Just look at the open bars on the graph; the dark bars are for controls. What is important is the main pattern, so don't worry if you don't follow the details.

Frame A shows the slope for several bowers at the start; this is how the birds made them. Frame B shows the bowers after the experimenters have intervened, and "messed up" the bowers; you can see that the set of open bars is very different. Three days later (frame C), the measurements are now very similar to the original measurements; the birds have restored the bowers. (Frame D is just another time point.)

In reading this story, be sure to distinguish the actual evidence from the interpretations by the authors. What the birds do is fascinating. Some of what the authors do seems excessive.

News story: In Attracting Mates, Male Bowerbirds Appear to Rely on Special Optical Effect. (Science Daily, September 10, 2010.)

The article, via abstract at PubMed: Great Bowerbirds Create Theaters with Forced Perspective When Seen by Their Audience. (J A Endler et al, Current Biology 20:1679-1684, September 28, 2010.)

A Musings post on bird behavior: Complex tool use by birds (May 28, 2010).

More birds: Of birds and butts (February 2, 2013).

* * * * *

Bower building is an example of Darwinian sexual selection. For a previous example: Spiders (December 21, 2009).

* * * * *

More, October 26, 2010...

Darsh notes three videos on bowerbirds. I encourage you to check at least the first one. Note that there are different kinds of bowerbirds, so you will see similarities and differences.

Bowerbird videos:
(Each is 3-6 minutes. The first two include narration; the third has sound, but not narration.)
* David Attenborough - Animal behaviour of the Australian bowerbird - BBC wildlife.
* Life - The Vogelkop Bowerbird - Nature's Great Seducer - BBC One. (Also narrated by David Attenborough.)
* Vogelkop Bowerbird - Amblyornis inornata.

Using genetically engineered mosquitoes in the real world

October 18, 2010

Mosquitoes carry disease agents, including dengue and West Nile viruses and the malaria parasite. We have noted attempts to control these diseases by controlling the mosquito populations. Among the approaches are those that involve genetic modification of the mosquitoes.

Most of what we discuss is lab science, as presented in scientific papers. However, I noticed a news story about an upcoming real world test of such genetically engineered mosquitoes. There is little to go on, so let's just leave it at this for now.

The news story originally provided here is no longer available. Here are two new links. One is an equivalent story; one is newer, and has some new information.
* Dengue Fever To Be Fought With Genetically Modified Mosquitoes In Malaysia. (Huffington Post, October 11, 2010; now archived.)
* Malaysia releases 6,000 GM mosquitoes in attempt to combat dengue fever -- Malaysia has released thousands of genetically modified mosquitoes into a forest in an attempt to curb dengue fever. (Telegraph, January 26, 2011.)

Related posts include...
* Checking mosquito saliva (November 19, 2010). A surveillance system, to see if local mosquitoes carry disease.
* An anti-freeze story: Why a tick carries a human pathogen (October 29, 2010).
* Mosquitoes are delectable things to eat (August 21, 2010). A serious discussion of the good and bad of mosquitoes. Good perspective. Links to posts on specific approaches for modifying the mosquitoes.
* Dengue fever -- Two strikes and you're out (August 10, 2010).

More on disease-causing mosquitoes (and malaria) is on my page Biotechnology in the News (BITN) -- Other topics under Malaria.

Reading the brain waves from speech

October 17, 2010

Is it possible to tell what word a person is trying to say just by reading their brain waves? If this could be worked out, it could bring new possibilities of communication to those who are physically unable to speak. "Locked-in syndrome" is the extreme case, where a person is fully aware, but completely lacking any way to communicate -- whether speech or blinking or finger movements.

A new paper discusses some work along this line. Of course, it makes use of recent developments in microelectronics. The results show some limited success.

The general plan was to use miniature electrodes to monitor the brain. The electrodes are under the skull, but seated on top of the brain; that is, they do not invade the brain per se. (They were placed there in this experimental work during other surgery that the patient needed.)

The figure at the right is a photo of the surface of the brain, with electrodes attached. The electrodes of interest here are the two 4x4 arrays. (The spacing of the individual electrodes in that array is 1 millimeter.)

The figure is reduced from one in the Science Daily news story. (The same picture is part of Figure 1 of the paper, but the view in the news story is better -- and so is the discussion of it.)
Electrodes on surface of brain.

The patient was then asked to say specific words, and the brain waves detected by the electrodes were recorded. Afterwards, they analyzed the recorded brain waves to see if they could figure out patterns that would allow them to identify words based on these brain waves. They found that they could distinguish pairs of words with accuracy around 80% (chance would give 50%). Identifying words from a list of 10 could be done at around 30% accuracy -- well above chance (10%), but not very good.

The conclusion? This first work showed that the method has some promise, but needs work. They intend to continue the work. Directions for improvement include smaller electrodes, as well as improved signal processing.

News story: The Brain Speaks: Scientists Decode Words from Brain Signals. (Science Daily, September 7, 2010.) Good overview of what they did, and the results.

The article: Decoding spoken words using local field potentials recorded from the cortical surface. (S Kellis et al, Journal of Neural Engineering 7:056007, October 2010.)

Also see:
* Prosthetic arms (September 16, 2009)
* Berkeley Bionics: From HULC to eLEGS (October 22, 2010)

Another use of mind-controlled devices: Music-making technology -- for the physically disabled (April 23, 2011).

In vitro fertilization: an improvement and a Nobel prize

October 15, 2010

In vitro fertilization (IVF) is, as the name implies, the process of carrying out the joining of egg and sperm "in the test tube", i.e., under laboratory conditions. The fertilized egg, after some period of observation in the lab, is implanted into the uterus for further normal development. IVF may be done with various mammals, but IVF for humans is of particular interest. IVF allows couples for whom there is some barrier to normal fertilization to have children. Since the fertilization process is done in the laboratory, there is also the possibility of doing testing or other work on the embryo before implantation into the uterus. Of course, IVF also allows research to be done on a stage of development not normally accessible.

Human reproduction is a rather sloppy process. Only a small fraction of fertilized eggs end up developing normally. The high percentage of miscarriages is one reflection of this. With IVF, a fairly expensive procedure, it is common to implant multiple fertilized eggs -- simply to increase the chances of one developing. Unfortunately, this also leads to a high frequency of multiple births.

What if we could look at the multiple fertilized eggs in the lab, and tell which ones are going to make it? Maybe we can.

What we have here is a paper which is remarkable in many ways. First, what they did is -- logically -- very simple. Technically it was extremely demanding, but it is easy to explain the general idea of what they did -- and what they found. They simply watched fertilized eggs develop -- taking pictures every five minutes for several days. They found that about 40% of their eggs successfully developed to the blastocyst stage (a ball of cells). (It is "common knowledge" that embryos that make it to the blastocyst stage are likely to continue normal development.) They then went back to their pictures, and asked how early they could see clues that a particular embryo was going to succeed or fail. Turns out they found simple clues very early. For example, the timing of even the very first cell division, when the fertilized egg divides to progress to the two-cell stage, differed between successful and unsuccessful embryos. Using three such criteria, they were able to predict whether a fertilized egg would succeed with over 90% accuracy.

Pictures of embryo, Day 1 & 2. Photographs of a particular human embryo, days 1 and 2. You can see that the embryo has gone from having one cell to four cells. The scale bar is 50 µm.

Does your album of baby pictures start like this?

Graph showing key parameters that reflect whether or not the embryo is developing properly.
A 3D graph showing their main findings. The graph shows the data for 100 embryos that were observed for several days. Of these, 36 developed into blastocysts, and 64 did not. Each embryo is plotted as a single symbol, based on the three key measurements they made (the details of which don't matter for the moment). Results for embryos that developed successfully are shown as circles; x is used for embryos that did not develop.

The graph makes a nice visual impression, even before you look at any details. Almost all of the circle symbols, indicating "success", fall into a small region of the graph. Most of the x symbols, for "failures", are outside that region. Thus simple microscopic observation of the developing embryos over the first couple of days yields information that is highly predictive of whether the embryo will successfully develop.

This is a research finding for now. What they did here was to develop the automated imaging and automated image analysis that made the work practical. Further work can follow up, try to confirm the conclusions, and explore the reasons why some fertilized eggs develop but others do not. If the basic pattern is confirmed, it could lead to a huge increase in the efficiency of IVF. That would allow IVF to be done with implantation of only a single egg, thus reducing the high frequency of multiple births that is now a problem. (Some observation and choosing is done now, but with limited success.)

News story: Which Fertilized Eggs Will Become Healthy Human Fetuses? Researchers Predict With 93% Accuracy. (Science Daily, October 4, 2010.)

The article: Non-invasive imaging of human embryos before embryonic genome activation predicts development to the blastocyst stage. (C C Wong et al, Nature Biotechnology 28:1115, October 2010.) The figures above are from parts a and d of Figure 2 of the paper. In addition to the figures, the web site includes several movies of the embryonic development; just choose Supplementary Information. To give a sense of the timing... Movie 1 shows nearly five days of embryo growth in 1 1/2 minutes of video. With that time compression, a long human life (85-90 years) would take about a week.

The day following formal (online) publication of that paper, the Nobel Prize was awarded to Robert Edwards, co-developer of IVF for humans. (His key collaborator, Patrick Steptoe, died some years ago.) The Nobel announcement: The Nobel Prize in Physiology or Medicine 2010: Robert G. Edwards. (October 4, 2010.)

Here is a Musings post that discusses ethical issues in the testing of IVF embryos before implantation: Let parents decide (May 14, 2010).

More about embryo screening: In vitro fertilization: Will it suffice to transfer only one embryo? (May 19, 2013)

Also see:
* A gene that reduces the chance of successful pregnancy: is it advantageous? (May 18, 2015).
* Children with two fathers (January 3, 2011).

* Previous post that featured a Nobel in the title: Nobel Peace Prize (October 25, 2009).
* Next: Nobel notes (October 13, 2015).

October 13, 2010

Spider silk: Can you teach an old silkworm new tricks?

October 13, 2010

Borislav sends this news story: Mutant Worms Produce Piles of Spider Silk. (Wired, October 4, 2010.)

It's a simple story, in some ways. Common silk is made by silkworms, a domesticated animal specialized for making silk. Spiders also make silks, and some spider silks have properties of interest, such as strength. However, making spider silk in large quantities has proved challenging. Spiders are not well suited for mass cultivation; it is a common observation that if you put a bunch of spiders together in a "production vessel", you will soon have only one spider. Simply moving the silk genes to another organism, and making the silk there -- as often done with drugs -- is not a good solution. Making silk is not just about properly making the silk protein, but about properly "spinning" the threads.

The solution is obvious enough: move the spider silk genes to the silkworm, so the silkworm now makes spider silk. That is precisely what the current work reports. It just took a while to work out the methodology for doing the genetic engineering of the silkworm.

We don't have much information at this point. The news stories are based on a press release made in conjunction with a presentation at a meeting. There is no paper yet, so let's be cautious. They have obviously made a technical advance of interest. How practical their system is remains to be seen.

Here is the original press release that the above story is based on: Notre Dame and University of Wyoming scientists genetically engineer silkworms to produce artificial spider silk. (Notre Dame, September 29, 2010.) This page includes a video, which is largely a statement by the lead scientist. It includes some nice pictures, but little substantive information. The video is also available at YouTube: Video from Notre Dame press release, at YouTube.

More on this... Spider silk: Can you teach an old silkworm new tricks? -- Update (February 11, 2012).

More about spider silk: What else are feet good for? (August 8, 2011).

The first truly habitable exoplanet?

October 12, 2010

Planets, planets, everywhere. When I was in school, only nine planets were known -- in the entire universe. That number is now near 500 (even if one of the original nine has been demoted). We are so overwhelmed with planets that we now want to focus on a special type of planet. Earth-like planets, or habitable planets. Planets that would seem capable of having life "as we know it". (As for life beyond what we know, that would be entirely speculation, and I will leave it.) The problem is that the detection systems used to find extrasolar planets have not really been capable of finding Earth-size planets. This background was introduced in an earlier post on the search for extrasolar planets (or "exoplanets"): Extrasolar planets (December 8, 2009).

Now we have it: a report of a planet which seems to have the right characteristics to be a candidate for having life. It's about Earth-size, and rocky. They estimate that its gravity would be a bit more than ours: enough to hold an atmosphere, and an Earthling would be able to walk on its surface. Its temperature would allow there to be liquid water -- a key requirement for life "as we know it". Note that this characteristic, the temperature on the planet, depends on its location in its solar system, as well as on the nature of the planet itself. That's about it. It is a huge technical accomplishment to find it. And they did find it.

How excited should we get? Well, we should celebrate the technical accomplishment of finding it. It extends the emerging story that there are lots of planets out there -- diverse planets. There are planets more or less everywhere scientists look -- planets of diverse characteristics. We now know there is at least one planet similar enough to Earth that we can imagine it having life -- Earth-like life. Only a tiny sample of the universe has even been examined for planets. We can now predict, with good comfort and even some experimental support, that there are many many Earth-like planets out there.

Are we any closer to knowing if there is life anywhere else in the universe? I fear not. Finding Earth-like planets is no surprise. However, we still know nothing about the probability of life arising under any conditions. We do not know under what conditions life arose on Earth, so cannot even ask whether this new planet shares (shared?) those conditions. This new candidate for life is 20 light years away. Does anyone really think we are going to visit? Can we develop remote measurements, such as spectroscopy, that will reveal life processes at that distance? I wonder.

Anyway, this story is getting much attention, as the first extrasolar planet considered habitable. Good, let's enjoy the story. But let's not get too excited about the prospect of finding life; finding such a planet is the easy part.

News release: Newly Discovered Planet May Be First Truly Habitable Exoplanet. (National Science Foundation, September 29, 2010.) A good overview of the work, and the ideas behind it.

The article: The Lick-Carnegie Exoplanet Survey: A 3.1ME Planet in the Habitable Zone of the Nearby M3V Star Gliese 58. (where ME means mass of the earth). (S S Vogt et al, Astrophysical Journal 723:954, November 1, 2010.) Rather technical! (If you can't access the article... A pre-print of the accepted manuscript is freely available at the Arxiv: pre-print.)

Science magazine included the broad topic of exoplanets as one of its Insights of the Decade. Science: highlights of the decade (January 25, 2011).

Planet discovery -- in olden times: The first report of a new planet (March 13, 2011).

A post about the Kepler mission -- a large-scale search for extrasolar planets... The Kepler Orrery (June 3, 2011).

Also see...
* Added June 19, 2016. Habitable planets very close to a star (June 19, 2016).
* Atmosphere suggests planet might harbor life (August 30, 2010).

* * * * *

More, October 26, 2010...

Apparently the basic finding of that work has been called into question. We don't have much to go on. The critique of the initial finding was done at a meeting, and we have a newspaper account. I'm sure the two groups will be working together in analyzing the existing data. Perhaps it will take more data to reach a better conclusion. For now, it must remain an open question. Such uncertainties about new planets are common; the detection methods are pushing the limits of the technologies.

News story: Gliese 581g: 'Goldilocks' planet might not exist after all -- Gliese 581g, a newly discovered, first-of-its-kind planet thought to exist in its star's habitable zone, might just be 'noise,' astronomers say. (Christian Science Monitor, October 13, 2010.) A good overview both of the original report and of the doubts that have been raised. It seems to be by someone quite knowledgeable in the field.

* * * * *

More, July 27, 2012...

A new article provides support for the existence of Gliese 581g. Further, Gliese 581g now ranks as #1 in the Habitable Exoplanets Catalog. See: Habitable Exoplanets Catalog (July 27, 2012).

* * * * *

How probiotics work: a clue?

October 11, 2010

It has long been recognized that our "gut" (our gastrointestinal -- or GI -- tract) contains huge numbers of diverse microbes. In recent years, we have come to learn not only that some of them are good whereas others may cause disease, but we have begun to recognize specific roles for some of them. It is increasingly appreciated that our gut microbiota is an intrinsic part of who we are.

One aspect of gut bugs is the possible intentional digestion of "good" bacteria. In particular, the use of Lactobacillus bacteria as "probiotics" has considerable appeal among some. Unfortunately, rigorous scientific testing of probiotics has yielded little objective information to support their use. But what is it one should test?

We now have a paper that suggests at least an approach, and I think it is worth noting. What they do is logically simple enough -- though technically quite demanding. They feed people various probiotic strains of Lactobacillus; a few hours after the "dose" they get some cells from each person's gut, and test to see which genes are functioning. They see specific gene responses to the various probiotic bacterial strains; intriguingly, those gene responses are similar in some ways to those obtained for "specific bioactive molecules and drugs".

I think the most important aspect of this work is the approach: the development of a system that begins to measure what probiotic bacteria do, at the underlying molecular level. One can imagine that subsequent work with this approach could yield much useful information. I caution that it would be premature to reach conclusions about the effectiveness of probiotics from this work alone.

News story: Probiotics shown to influence gene activity and metabolism in the gut. (Environmental Illness Resource, September 17, 2010.) (I am not familiar with this news source. In judging the individual page, I look for something that is a reasonable overview of the work: what they did, why they did it, what they found -- without too much hype. This page seems fine; that is not an endorsement of the site, about which I really know nothing, good or bad. Remember, the story here is about one scientific paper. It is interesting, but its importance will become clear only after people reproduce and extend the core findings.

The article: Human mucosal in vivo transcriptome responses to three lactobacilli indicate how probiotics may modulate human cellular pathways. (P van Baarlen et al, PNAS 108(suppl. 1):4562, March 15, 2011.) You might try reading the abstract or even the introduction.

This is part of a big story of the interaction of micro-organisms with macro-organisms. The post immediately below is another example, and includes links to others. I would also note the following posts as related:
* Added May 16, 2016. How to administer Bt toxin to people? (May 16, 2016).
* A clinical trial of ice cream (June 2, 2015).
* Could we treat obesity with probiotic bacteria? (August 5, 2014).
* Designing a probiotic that fights cholera (December 13, 2010).
* Can the Staph solve the Staph problem? (July 12, 2010). Probiotics for the nose?
* Is Arthromitus a key bug in your gut? (January 16, 2010). This post is about a role for our gut bacteria in the proper functioning of the immune system.

Thanks to a couple of readers for stimulating interest in probiotics.

Plants need bacteria, too

October 9, 2010

We have noted how microbes, such as those in our gut, are important functional parts of the human body. [Example: Sushi, seaweed, and the bacteria in the gut of the Japanese (4/20/10).] A human without its microbes is not a complete functional unit. Of course, this makes good sense as we more broadly understand biology; organisms do not live alone in nature. (At times, we must wonder what we mean by "organism"!)

Here is an example of the importance of resident bacteria to a higher plant. The plant is the poplar tree, which is of interest as a possible source of renewable energy. Poplar trees grow rapidly, and can grow on "poor" land (where they may not compete with food production). Recent work showed that poplar trees carry a type of bacterium, known as Enterobacter -- and that the bacteria, growing inside the plant tissues, stimulate growth of the trees by as much as 40%. In the new work, they report a genome sequence for the Enterobacter, and discuss some of what they learn from the bacterial genome about the role of the bacteria in tree growth. The interaction of plant and bug is complex! For example, the bacteria help make certain plant growth hormones, and promote tolerance to drought and to some metals. Once again, if we want to understand growth of the tree, we need to understand its resident microflora. If we are to develop poplar as an energy crop, we need to look not only at the poplar per se, but also its associated bacteria, which contribute to its desirable characteristics.

News story: Bacterial Genes That Improve Plant Growth by 40% Identified. (Science Daily, May 17, 2010.)

The article, which is freely available online: Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638. (S Taghavi et al, PLoS Genetics 6:e1000943, May 13, 2010.) As typical of genome papers, the article contains an overwhelming amount of information. If you browse the introductory material, including the Author Summary (p 2 of the pdf), you will get a sense of the big picture of the complexity of the plant-microbe interaction.

Another example of plant-microbe cooperation that you might know is for legumes: plants such as clover, alfalfa and soybean. An important characteristic of these plants is that they can use ("fix") atmospheric nitrogen, N2. In fact, they do this by use of nitrogen-fixing bacteria, which are intimately associated with the plant. A recent post described an intimate and mutually beneficial association between a fern and a cyanobacterium; nitrogen fixation is clearly one aspect of this association: A new organelle "in progress"? (September 13, 2010).

For another way plants get their nitrogen... Why would a plant have leaves underground? (January 21, 2012).

Also see...
* An anti-freeze story: Why a tick carries a human pathogen (October 29, 2010).
* Renewable energy for the school bus: let the kids pedal (April 24, 2012).
* Getting along: animals and bacteria (August 6, 2012).
* Sharing microbes within the family: kids and dogs (May 14, 2013).
* DEEPER ROOTING leads to deeper rooting -- and to drought tolerance (August 16, 2013).
* Added May 20, 2016. Using light energy to power the reduction of atmospheric nitrogen to ammonia (May 20, 2016).

There is more about genome sequencing on my page Biotechnology in the News (BITN) - DNA and the genome. It includes a list of Musings posts on sequencing and genomes.

What happened to the Neandertals?

October 8, 2010

Neandertal man lived in Europe for around 400,000 years. Then, perhaps rather abruptly about 40,000 years ago, they were gone. Why? Did Homo sapiens (that's us -- modern humans, or MH) displace them, winning some sort of competition? Or did the Neandertals suffer some calamity and die out -- much as we now think the dinosaurs did 65 million years ago after an asteroid impact? Those are perhaps the two general classes of models invoked to explain the disappearance of the Neandertals.

A new paper suggests that the Neandertals were decimated by a series of major volcanic eruptions. These eruptions may well have also decimated any MH in Europe. But "we" survived, as a species, because of a wider geographic distribution; that is, MH were present elsewhere, such as in Africa, and the wider distribution allowed our species to survive.

It's a fun story. It's also not very well supported by the data at hand. That is, it is a bold hypothesis, stimulated by some new data. Even the authors recognize that it is a bold hypothesis; others in the field have a wide range of views, including claiming it is impossible. So why include this here? Because it is fun -- and it represents how science proceeds. The paper presents an idea; the idea is controversial, but it will serve to guide further work in the field. That is good, regardless of the outcome. Whether the hypothesis presented here ends up being accepted depends on future work. Thus we present this as a window into a field, not as a conclusion.

What's the problem with this new hypothesis? Much of the argument depends on dating ancient events, using C-14 dating. Although such methods are well established, there are problems in actual use. The hypothesis depends on determining the order of certain events, and this ends up relying on very small differences in measured ages -- differences that end up being controversial.

News story: Volcanoes Killed Off Neanderthals, Study Suggests -- Modern humans escaped extinction due to their farther-flung populations?. (National Geographic, September 22, 2010.) A nice overview of the problem, the hypothesis, and its controversy. Recommended.

The article: Significance of Ecological Factors in the Middle to Upper Paleolithic Transition. (L V Golovanova et al, Current Anthropology 51:655, October 2010.) A long -- and difficult -- paper. An interesting aspect of the paper is that it includes comments from five other scientists (p 25 of the pdf), and a reply by the authors (p 31). Those who are willing to tackle the paper itself may find it interesting to skip down and browse this dialog. Inevitably, the dialog highlights key issues, including the disagreements; thus it gives a real sense of where the paper stands.

A previous post on the various types of humans, including: The Siberian finger: a new human species? (April 27, 2010).

More about Neandertals...
* Did Neandertals use cosmetics? (January 24, 2010).
* Analysis of teeth confirms that Regourdou was right-handed (September 7, 2012).

More about C-14 dating... Tree rings, carbon-14, cosmic rays, and a red crucifix (July 16, 2012).

More about dust... Dust (February 19, 2011).

More about volcanoes...
* What caused the dinosaur extinction? Did volcanoes in India play a role? (April 13, 2015).
* VPOW (July 14, 2010). Pictures!

October 6, 2010

Book review: Galileo

October 6, 2010

Another new review of an old book. In this case, the book is Sidereus nuncius (The Celestial Message, or Messenger) by Galileo, 1610. The short review provides insight into not only the book but also the author and the times. Galileo's little book is the first survey of the skies based on telescopic observations. It includes numerous drawings by the author. As an indication of the state of the art... Galileo discovered four moons around Jupiter -- thus increasing the number of known moons (around planets) five-fold.

In retrospect: The celestial message. (J Heilbron, Nature 467:398, September 23, 2010.) The review's author -- retired UC Berkeley historian John Heilbron -- has a way with words, and is always fun to read.

The book itself is available online, in the original Latin and in English and other translations. Google on the title (Sidereus nuncius may work best, since the translated title varies), plus the language you want, and look around.

From the same Nature series about books of yesteryear... Book review: Kepler (February 3, 2010). Kepler's Astronomia Nova (New Astronomy), from 1609.

More from Space: European journal open to authors around the world -- and beyond (January 2, 2012).

This post is also noted on my page Book suggestions: Galileo, Sidereus nuncius (The Celestial Message).

CO2 emissions: What if we just stopped making new CO2-emitters?

October 5, 2010

It's easy to get bogged down in the global warming story. A recent article in Science intrigued me in part because it made a very simple assumption: What if we stopped making new devices that emit CO2? How much CO2 emission are we committed to by the CO2-emitting devices we already have? We assume that these existing devices, such as power plants and cars that run on fossil fuels, continue through their normal lifetime, but that all new devices are C-neutral. Of course, we can quickly think of why this is not a realistic model. However, it seems a baseline case that we can at least understand, so perhaps it is worth looking at a bit. Further, the article has an interesting set of maps, which I will include below.

Summary of key results, showing CO2 levels and temperature change. Figure 1 Parts C and D. The graphs summarize their main findings. Frame C shows the atmospheric CO2 level that would result from their model. Frame D shows the temperature change -- that is the global mean temperature change, compared to the "pre-industrial" value. (These are parts of Figure 1 of the paper.)

The various curves reflect the uncertainty in even a simple model. We won't make much of this here. You can choose to look at the "Middle" curve, for their "average" prediction, at the "Upper" curve for their "worst case", or at the set of curves together, as a region, to get an overall sense of the range of their predictions. The big picture: If we just stop making new CO2-emitters, atmospheric CO2 and global temperature will continue to increase -- but not by much.

The paper includes a series of maps showing CO2 emissions around the world. Figure 2: World maps of CO2 emissions. The maps are almost self-explanatory. On each map, CO2 emissions are color-coded, as described; red is high CO2 emissions, blue is low. The top map is simply the amount of CO2 emissions in the country, the second is CO2 emissions per person, and the third is CO2 emissions per dollar of GDP. (In each case, there is a large map showing the world, plus a smaller map at the right with a magnified view of Europe.) As an example... China is very red in the top map: high emissions, as one might expect for a large country. In the middle it is green, showing medium emissions per person. At the bottom, it is red -- apparently the most emitting country relative to its economy. Does this last point mean it is being wasteful, or does CO2 emissions precede economic development? Australia and Canada are examples of countries with low emissions -- because they have low population; both have high emissions per person.

News story: Main Climate Threat from Carbon Dioxide Sources Yet to Be Built. (Science Daily, September 10, 2010.) Good overview of what they did and what they found.

* News story accompanying the article: Climate change: Farewell to Fossil Fuels?. (M I Hoffert, Science 329:1292, September 10, 2010.)
* The article: Future CO2 Emissions and Climate Change from Existing Energy Infrastructure. (S J Davis et al, Science 329:1330, September 10, 2010.)

Other posts on climate change include:
* Where is the control knob for global warming? (November 16, 2010).
* Climategate: a book and a cartoon (September 27, 2010).
* CO2 emissions threaten clowns (September 20, 2010).

A virus associated with obesity?

October 4, 2010

Is it possible that a virus could play a role in promoting obesity? Some would argue that a particular virus, a cold virus called adenovirus-36, may in fact do just that. Here is a new paper with some evidence for an association between this virus and obesity.

Here is some of their key data. This is summarized and simplified from Table 1 of the paper, which includes more details and statistics. AD-36 refers to adenovirus-36; negative and positive refer to whether the people do not or do (respectively) have antibodies to the virus.

Characteristic AD-36 negative AD-36 positive
Number 105 19
Weight (kg) 69 93
Height (cm) 159 165
BMI (kg/m2) 27 34

A simple summary is that people who are AD-36 positive, indicating that they have been exposed to this virus, have greater weight and body mass index (BMI) than the people without evidence of the virus.

As so often, the results show an association, but not causality. However, animal work has suggested causality, and even offered some clues of mechanism. On the other hand, a comment (eLetter) posted at the paper's web site offers an alternative explanation: that obese people tend to be deficient in vitamin D, and that vitamin D deficiency leads to susceptibility to the virus. Under this explanation, the obesity is "causing" virus infection, rather than the other way around. I would note that this explanation does not offer any simple explanation for why this specific virus is found. However, the more general and more important point is that it will take further work to sort out what the finding means.

I would also emphasize that even if there is a causal relationship, it may be complex. That is, it may be that, in some cases, the virus is one contributing cause.

Work on developing a diagnostic test and a vaccine is noted.

In some ways, this story should remind us of the story of the possible association of a virus with chronic fatigue syndrome. [A virus that is or is not associated with chronic fatigue syndrome (February 12, 2010).]

News story: Childhood Viral Infection May Be a Cause of Obesity. (ScienceDaily, September 20, 2010.)

The article, via abstract at PubMed: Adenovirus 36 and Obesity in Children and Adolescents. (C Gabbert et al, Pediatrics 126:721, October 2010.) A readable paper, with discussion of other evidence relating to this virus.

Other posts related to obesity include...
* A gene for obesity (May 7, 2011).

More about vitamin D... Vitamin D: How much is too much? (July 9, 2013).

Also see the section of my page Organic/Biochemistry Internet resources on Lipids. The list of Musings posts there includes more on obesity.

Dog psychiatry: Implications for humans

October 3, 2010

It is common in biology to work on model systems to study human biology. Studying humans is slow and difficult -- and there are ethical restrictions on experimenting with humans. So we study other organisms, including other animals. The general unity of biology allows this to be meaningful. However, each organism is different. So it is hard to know for sure how well a model organism predicts human biology. What study of model organisms does is to generate "clues" that can then be followed up in humans. Model organisms are chosen because they seem to have certain specific advantages.

The dog is being recognized as an important model system. A key point is that modern dog breeds were made by intensive inbreeding, in recent centuries. If two dog breeds differ in some trait, we have at hand rather large populations known to differ in that trait. This helps the geneticist find underlying genes for the trait. Of course, this was first applied to typical dog traits, such as size and hair. [Example: Bichon frise (November 17, 2009).] But it can also be applied to other traits. The new development is studying the genetics of neurological or psychological traits in dog breeds, and this work is bearing fruit. For example, study of Doberman pinschers, which show a high frequency of narcolepsy, led people to the correct pathway that is affected in humans with this condition. (With narcolepsy, the animal suddenly falls asleep, for no apparent reason. The work points to a key hormone involved in this condition.)

Dog work has double merit. The dog is being used as a model system to study humans, but dog psychiatry is itself an area of interest.

Here is a recent "News feature" overview of the field of dog psychiatry, and its implication for humans. Pet project. (D Cyranoski, Nature 466:1036, August 26, 2010.) For a quick view, look at the featured boxes about various dog breeds, each one noting specific psychiatric features characteristic of that breed.

Here is a specific current example. Analysis of the genetic basis of a breed-specific neurodegenerative disease in a dog offers insight into a human disease. I'll just give the links without further comment. The news story is a good overview of the case.

News story: Researchers find gene responsible for neurodegenerative disease in dogs, possibly in humans. (PhysOrg, August 23, 2010.)

The article: A canine Arylsulfatase G (ARSG) mutation leading to a sulfatase deficiency is associated with neuronal ceroid lipofuscinosis. (M Abitbol, PNAS 107:14775, August 17, 2010.)

* * * * *

More about narcolepsy: What's the connection: Narcolepsy and the flu vaccine (or getting the flu)? (October 3, 2015).

More about dogs: Do dogs respond to their owner's yawns? (May 29, 2012).

Why a tree cultivates ants

October 3, 2010

Ants love certain acacia trees. Why? Because the trees provide food and shelter for the ants. The trees make a special nectar, just for the ants; tree thorns have expanded into bulbous swellings -- spacious quarters for a queen and her entourage.

And why do the trees take such care of their ants? Because the ants protect the trees from elephants. Apparently, a swarm of ants attacking an elephant's nose is very irritating -- enough so that the elephants quickly learn to avoid trees with swarming ants.

Response of elephants to number of ants on tree branches. Here is an example of the new data on ants vs elephants...

In this experiment, they measured the amount of elephant damage to the tree as a function of how many ants there were. The y-axis is the number of branches browsed by elephants, from direct observation of the trees at intervals. The x-axis is a simple measurement they make of the number of ants; it is presumed to correlate with the actual level of ants. The graph shows that elephant damage is greatly reduced by even a low level of ants.

This is Figure 4 of the paper, with the results of the in situ ant removal experiment.
At right: Branch of an acacia tree, with its elephant-defense system crawling around.

You can see the swollen thorn at the bottom; this serves as "housing" for the ants.

This is from the BBC news story listed below.
Branch of an acacia tree, with its elephant-defense system crawling around.

News story: Ants work with acacia trees to prevent elephant damage. (BBC, September 2, 2010.) Excellent overview.

The article: Defensive Plant-Ants Stabilize Megaherbivore-Driven Landscape Change in an African Savanna. (J R Goheen & T M Palmer, Current Biology 20:1768, October 12, 2010.) Includes some interesting discussion of the competition in nature between trees and tree-eaters, including the role that the ants play in this balance.

Do these ants and their plants seem familiar? See The vegetarian spider (October 21, 2009).

More about ants:
* How the spider avoids being attacked by the ants (January 10, 2012).
* Death-grip scars from zombie ants, 48 million years ago (November 9, 2010).

More about elephants: If the elephant can't find its dinner, should you help by pointing to it? (October 18, 2013).

GSAP -- a clue to treating Alzheimer Disease?

October 2, 2010

A recent report has uncovered a new clue as to how Alzheimer disease (AD) works. Whether it will lead to useful treatment remains to be seen, but the story is interesting biology -- and has caught media attention because of the 84-year old scientist who led the work.

AD is a disease involving degeneration of the brain. One key player in the development of AD is a small peptide called amyloid-β. That amyloid-β is a fragment of a larger protein, called amyloid precursor protein (APP). How amyloid-β is made from APP was uncovered a few years ago. In part... there is an enzyme that cuts the APP and produces amyloid-β; that enzyme is known as γ-secretase (γ = gamma). As soon as that was understood, people were intrigued by the idea of inhibiting γ-secretase; that should reduce production of amyloid-β. Good idea. It even works -- but it has a fatal flaw. γ-secretase cuts various things -- and turns out to be an essential enzyme for normal body function. Simply inhibiting this enzyme is not acceptable.

Terms. Here are some related terms that may come up...
Presenilin. For our purposes, γ-secretase and presenilin are approximately synonymous. Beyond that, presenilin is a part of the γ-secretase complex. (I'm not sure the terms are used entirely consistently.)
Amyloid-β may be abbreviated as Aβ or AB. It may also be followed by a number, such as 40 or 42, indicating the number of amino acids in the chain.

So, what's new? A few years ago they found that the cancer drug Gleevec reduced production of amyloid-β. However, the drug did not inhibit the γ-secretase enzyme. How, then, did it work? Follow-up of this finding has revealed an additional protein that helps γ-secretase decide where to cut. This protein is called gamma-secretase activating protein (GSAP). Gleevec binds to GSAP, and prevents it from activating γ-secretase for cutting APP -- yet allowing its other functions. GSAP immediately becomes an attractive target for a drug against AD. (Gleevec itself will not work, because it does not cross the blood-brain barrier.) Will this work? Who knows. γ-secretase seemed a good target, but it turned out not to be when we learned more about the complexity of the system. People will now try to study GSAP, and see whether inhibiting it -- with a drug that can get to the brain -- is useful. Whatever the outcome of that search, finding GSAP adds to our understanding. More such additions are inevitable.

News story: Finding Suggests New Aim for Alzheimer's Drugs. (New York Times, September 1, 2010.) It tells the story of GSAP, but also emphasizes the story of the scientist who led the work, 84-year-old Paul Greengard -- who has already won a Nobel prize for earlier work on brain function.

* News story accompanying the article: Alzheimer's Disease: selectively tuning γ-secretase. (P St George-Hyslop & G Schmitt-Ulms, Nature 467:36, September 2, 2010.)
* The article: Gamma-secretase activating protein is a therapeutic target for Alzheimer's disease. (G He et al, Nature 467:95, September 2, 2010.)

Other posts on Alzheimer's Disease include...
* Reversing Alzheimer's Disease (March 4, 2011). A different treatment approach.
* The Alzheimer's Disease peptide: Why does it accumulate? (January 22, 2011).
* Do cell phones prevent Alzheimer's Disease? (January 13, 2010).
* My page for Biotechnology in the News (BITN) -- Other topics includes a section on Alzheimer's disease. It includes a list of related Musings posts.

September 29, 2010

A phosphorus shortage?

September 29, 2010

Something else to worry about. Phosphorus (P) is an element essential for life; it is a component of nucleic acids (DNA, RNA) and typical membrane lipids. P is one of the "big three" elements of fertilizers used for agriculture (along with N and K). But we may be running out.

Here is a brief readable introduction to the P problem: Does peak phosphorus loom? (American Scientist 98:291, July 2010.)

That is based, in part, on a serious report in a scientific journal last year. The article is actually quite delightful, with perspectives on the history as well as current issues, including geopolitics. It's a good example of a resource analysis. The story of phosphorus: Global food security and food for thought. (D Cordell et al, Global Environmental Change 19:292-305, May 2009.)

A great city is the most mighty of dung-makers. Victor Hugo, Les Miserables, 1862. Quoted in the above article.

Other posts on phosphorus include...

The post, How do you make phospholipid membranes if you are short of phosphorus? (November 1, 2009), discussed how some microbes in the ocean respond to a local P shortage by making novel P-free lipids. This illustrates the issue of P shortage, but the solution -- an evolutionary adaptation of certain groups of organisms, is not likely to be general.

Phosphorus long long ago... The origin of reactive phosphorus on Earth? (July 5, 2013).

How to seat a spider in front of the computer

September 28, 2010

Spider on ball. Here is one way: give the spider a ball to sit on. Seems to work fine.
Why are we trying to seat a spider in front of the computer? In this case, it is because the scientists want to give the spider an eye exam -- want to test the spider's vision.

Giving an eye exam to these spiders is quite a deal: they have lots of eyes. The close-up picture at the right shows half of the eyes (and half of the legs) for this type of spider, a jumping spider called Servaea vestita. (Relax. The spider is no threat to you unless you are a fly -- or a computer screen.)
Jumping spider

Of course, they don't want the spider to use all its eyes at once. So they cover most of the eyes, with dental silicone -- a process they say is fully reversible.

The point? Scientists do not understand well the role of the multiple sets of eyes in these spiders. The goal of the tests here is to see how well the spiders can track prey (flies). One test is to have the spiders track moving dots on the computer screen. They also test the spiders with real flies. In both cases, the spiders seem to do just fine with one pair of "secondary" eyes -- a result that came as something of a surprise. They also find that that the spiders prefer real food to the video version. (Hm, I wonder if this test has been done with human teenagers.)

A couple of good news stories:
* Backup eyes track targets. (Science Alert, July 12, 2010.) The figure above showing spider on ball is from this story.
* Jumping spider vision not so clear cut. (ABC News (Australia), July 12, 2010.) The figure above with a full view of the spider is from this story.

The article: The role of the anterior lateral eyes in the vision-based behaviour of jumping spiders. (D B Zurek et al, Journal of Experimental Biology 213:2372, July 15, 2010.)

More about spider vision: Why the spider needs green light to find its food (March 3, 2012).

More about spiders: What else are feet good for? (August 8, 2011).

More about arthropod vision: What can we learn by giving a praying mantis 3D glasses while it watches a movie? (March 12, 2016).

Climategate: a book and a cartoon

September 27, 2010

Climategate refers to the incident where emails of a climate researcher were stolen. Aside from the theft issue, the content of the emails raised concern about the behavior of the scientists. Subsequent analysis has revealed no problems with the science, though it has served to emphasize the need for transparency.

Nature has a review of a book on the Climategate affair. The review is perhaps of some interest -- and it includes a nice cartoon. Posting the cartoon is not allowed, but I can provide a web site where you can see it, regardless of access to the Nature article.

The book review: Lessons from Climategate. (D S Reay, Nature 467:157, September 9, 2010.) The review is of the book "The Climate Files: The Battle for the Truth About Global Warming", by Fred Pearce, 2010.

The cartoon: Climategate cartoon. (Nick Anderson. Originally published in the Houston Chronicle, December 8, 2009.)

* * * * *

This item has already stimulated some discussion. Good. The whole topic is a complex mix of politics and science, and people sometimes tend to see what they want to see in stories. I note the cartoon here because I think it is both funny and insightful. But that does not mean it tells the whole story. The scientists are not without "blame". Although their science has withstood scrutiny, their behavior served to undermine public confidence, and caused a distraction from the big story.

If someone reads the book, I would welcome a short review of it. I can post it here or on my page of Book suggestions.

Other posts on climate change include:
* CO2 emissions: What if we just stopped making new CO2-emitters? (October 5, 2010).
* CO2 emissions threaten clowns (September 20, 2010).

A cancer drug with a switch: it acts only in a cancer cell

September 26, 2010

Cancer treatment is still one of medicine's great challenges. One reason is the heterogeneity of the disease. What is it, exactly, that we want to treat? In fact, many cancer treatments have serious side effects, because they are not specific. For example, common treatments simply kill rapidly growing cells. That includes the cancer cells, but also includes cells in hair follicles and the gut lining -- thus leading to common side effects.

A new approach is to try to target a treatment to the cancer. For example, the drug Herceptin attacks only cells carrying a certain marker -- one found on the cancer cells. This only works for a particular class of cancers, but it does reduce side effects.

New work offers a different way of providing specificity to a cancer drug. The drug is based on an RNA molecule that is targeted to a specific mutation in the cancer. The RNA molecule is something of a switch. If it gets into a cell with the mutation, it binds -- and changes its shape, thus activating its drug function. The authors make an analogy to the drug being something like an IF statement in a computer program: it executes conditionally -- if it finds its target. Of course, that analogy holds, in some way, for any targeted drug.

Scheme for making RNAs that will act conditionally against a cancer cell.

The figure shows the idea... Start with the second box, labeled "Small conditional RNAs". To start, it is not important to worry about the details of what the molecules look like; on the first pass, we simply try to establish the idea. That second box shows the drug (actually a mixture of two types of RNA molecules), which is designed to act against cancer cells carrying a certain mutation. Now look at the left box, labeled "Normal cell"; this cell does not contain the cancer marker (the mutation), and nothing happens.

But now look to the right, the box labeled "Cancer cell". It has the cancer marker, shown as a specific piece of messenger RNA labeled M. M binds to the drug, and the drug changes shape. You can see this in the next frame, labeled "Diagnosis": the M on the mRNA (blue) binds to drug RNA molecule A (light green). This causes the RNA hairpin of the drug molecule to unfold, and sets in motion a series of events, leading to the death of the cell. We don't need the details for now, but briefly... the events -- all programmed by the drug RNA -- make a large double-stranded RNA, thus mimicking a virus infection. The cell responds to the apparent infection by carrying out apoptosis, a natural process by which bad cells kill themselves.

The work is impressive, but also limited at this time. They have established an idea. It now remains to be seen whether it can be made to work in the real world: real cancer patients. That is a long road.

Press release: These Cells Will Self-Destruct in Five ... Four ... -- New treatment activates death program in cancer cells. (NSF, September 6, 2010.)

The article, which is freely available: Selective cell death mediated by small conditional RNAs. (S Venkataraman et al, PNAS 107:16777, September 28, 2010.)

Other posts about cancer include:
* Why do elephants have a low incidence of cancer? (March 20, 2016).
* Targeting cancers (January 15, 2011).
* Cancer in the ancient world (November 1, 2010).

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Cancer.

Also see... How HIV destroys the immune system (March 3, 2014). This post deals with various types of cell death processes.

Restricting excessive use of antibiotics on the farm

September 25, 2010

A recent post raised the issue of antibiotic resistant bacteria: Antibiotic resistance: A new concern from New Delhi (August 24, 2010). The problem is not simply that certain bacteria become resistant to commonly used antibiotics, but that the antibiotic resistance can be transferred from one microbe to another (in some cases).

Antibiotic usage promotes the development of resistance in a population, by providing an advantage for the resistant mutants. Over-usage of antibiotics promotes "excessive" development of resistance. The editorial by Abdul Ghafur, listed in the post noted above, was an eloquent plea to moderate antibiotic usage.

However, there is a big concern beyond how humans use -- or abuse -- antibiotics: the use of antibiotics to treat farm animals. It's not just that farm animals are treated when sick. They are given antibiotics routinely prophylactically -- to keep them from getting sick. Further, they are treated with antibiotics to promote growth (and reduce feed consumption); the mechanism of this growth-promoting effect is not well understood. Use of antibiotics in farm animals promotes development of resistance, and sometimes that gets transferred to microbes that affect humans. Thus antibiotic usage in farm animals impacts human health. The question is whether it is worth it. This is controversial, though microbiologists and medical people would predominantly argue that it is not.

The European Union has already moved to reduce antibiotic usage on the farm. Now, the US Food and Drug Administration (FDA) is considering a small step in that direction.

Here are two news stories to introduce the issue:
* U.S. Meat Farmers Brace for Limits on Antibiotics. (New York Times, September 14, 2010.) A good overview of the controversy.
* FDA Issues Draft Guidance on the Judicious Use of Medically Important Antimicrobials in Food-Producing Animals. (FDA, June 28, 2010.)

* Restricting excessive use of antibiotics on the farm -- follow-up (January 30, 2012)
* Restricting excessive use of antibiotics on the farm -- follow-up #2 (April 16, 2012)

Here is a Musings post that may make one wonder about the problem of antibiotic resistance in ancient times: Antibiotics in ancient times (January 10, 2011).

More about antibiotic resistance... A rapid test for antibiotic sensitivity? (July 19, 2013).

More about antibiotics... Killing persisters -- a new type of antibiotic (January 3, 2014).

Another story about FDA regulation... FDA to fast-track prosthetic arm (February 14, 2011)

Also see... Silent Spring -- on its 50th anniversary (October 5, 2012).

More on antibiotics is on my page Biotechnology in the News (BITN) -- Other topics under Antibiotics. It includes a list of related Musings posts.

Ice nucleation -- by airplanes

September 24, 2010

A recent post discussed how water can remain liquid even below the freezing point. [Developing improved degradation of organophosphate pesticides (September 7, 2010).] The context there was that some bacteria can cause such "super-cooled" water to freeze, by their ice nucleation protein (INP). While that post was "in progress", we came across a new article about a rather larger object that induces ice nucleation: the airplane. (Does INP now mean ice-nucleating plane?) I'm not sure I would have noted the paper at all if Gunjan had not brought up the topic of ice nucleation. So here it is, briefly noted...

Canal clouds - example An example of canal clouds, also known as hole punch clouds. This is a satellite image -- a "top view".

The figure is reduced from part of Figure 1 of the paper.

The key idea they develop relates to the large pressure drop that occurs at the propeller or wing. The rapid expansion of the air at those sites leads to cooling by several degrees; if the super-cooled water is cold enough, the further cooling caused by the plane may be enough to induce ice formation. As always, once ice formation starts in a super-cooled region, it continues. Thus they see channels (canals) or holes in clouds, with snow below, where the plane passed. What is new in the current work is that they are able to make a connection between specific events: a specific plane flight, a specific cloud hole, and a specific snow event directly underneath.

The following stories provide good overviews of the work:
* News release: Mysterious Clouds Produced When Aircraft Inadvertently Cause Rain or Snow -- Jets, turboprops leave behind odd-shaped holes or channels in the clouds. (National Science Foundation, June 14, 2010.)
* News story: Planes Create Weird Clouds - And Snow, Rain Fall Out. (National Geographic, June 16, 2010.)

The article, which is freely available: Aircraft-Induced Hole Punch and Canal Clouds: Inadvertent Cloud Seeding. (A J Heymsfield et al, Bulletin of the American Meteorological Society 91:753, June 2010.) I found much of the article difficult, but there are some neat pictures of the phenomenon. The article also includes discussion of various ways planes may interact with clouds.

Related: Might it be good if airplanes emitted more CO2? (September 5, 2014).

More about airplanes... How to board an airplane (September 16, 2011).

More on wings: Introducing Supersonus -- it stridulates at 150,000 Hz (June 16, 2014).

September 22, 2010

Genome from Mars

September 22, 2010

A scientist from Mars and his subject matter The figure shows a scientist from Mars and his subject matter.

News story: Rival Candy Projects Both Parse Cocoa's DNA. (New York Times, September 15, 2010.)

Not much to say about it at this point.

   The figure is reduced from the one in the news story listed above.

More from Mars...
* Added August 23, 2016. A better way to make chocolate, inspired by brake fluid (August 23, 2016).
* Water at the Martian surface? (August 27, 2011).

Added May 3, 2016. More chocolate... Better chocolate? Use better yeast? (May 3, 2016).

There is more about genome sequencing on my page Biotechnology in the News (BITN) - DNA and the genome. It includes a list of Musings posts on sequencing and genomes.

Engineering cyanobacteria to make high-value chemicals

September 21, 2010

Our main source of energy is the sun; the more efficiently we use solar energy, the better. Among the most efficient ways to use it is photosynthesis by cyanobacteria. (Cyanobacteria are bacteria that carry out oxygen-evolving photosynthesis. Cyanobacteria are thought to be the ancestors of chloroplasts.) The bacteria are about 10-fold more efficient in their use of solar energy than the more complex higher plants. So why don't we use them? Because they don't make things of interest to us.

Scientists have been exploring how to engineer cyanobacteria to make useful things, such as fuels that could substitute for oil. There is progress, but it is questionable that such processes would be economical, at least without major development work.

Would it be possible to make chemicals of higher value than fuels? (Whatever you may think of gasoline prices, as chemicals go, fuels are cheap. That is because most of the production cost was incurred ages ago -- by the geochemical processes that made the fuels. We don't pay for that.) The new work explores that, and makes some significant progress. The key problem they address is that cyanobacteria do not normally use or make polar molecules (hydrophilic molecules; loosely, water-soluble molecules). So, one thing they did here was to genetically engineer the bacteria to make them transport certain common and useful water-soluble chemicals across the cell membrane. The chemicals they study include some simple sugars (glucose and fructose) and lactic acid.


Scheme for lactic acid production The scheme for making lactic acid. The bacteria normally use CO2; a major normal product is pyruvate. They add two genes to the bacteria. One, labeled ldhA, codes for the enzyme that converts pyruvate to lactate. The second, labeled lldP, codes for a lactate transport protein, to allow the lactate to leave the cell.
Results for lactic acid production Some results. The left hand graph shows lactic acid production, over time, for four strains. The "red" strain is the one engineered to have both genes noted above. The other three curves are for strains with only one of the two genes or the parent with neither. It is clear that the strain with both added genes is the best at making lactate and secreting it into the medium. The right hand graph shows the growth of the four strains; they are all similar.

News release: Researchers at Harvard's Wyss Institute Develop Technology to Produce Sugar from Photosynthetic Bacteria. (Harvard, June 28, 2010.)

The article: Engineering Cyanobacteria To Synthesize and Export Hydrophilic Products. (H Niederholtmeyer et al, Applied and Environmental Microbiology 76:3462, June 2010.) The figures shown above are parts of Figures 1 and 2 of this paper.

* * * * *

Late news... Borislav just sent the following item: Biotech Company to Patent Fuel-Secreting Bacterium. (New York Times, September 13, 2010.) The gist of it is that a company, called Joule Unlimited, has been issued a patent for a process using cyanobacteria to make fuel. Further, they are doing development work on the process. (I do not see a paper at this point, but the page has a link to the patent.) The article notes other work in the field.

This is the type of process I argued above is less likely to be economical. So, let's clarify... Learning to use cyanobacteria for large scale production of chemicals is new -- and good. No one has any such process at the moment, and it will take a while to develop and optimize a new process. The people whose work is above, making lactic acid, would argue that -- all else equal -- it is better to start by making a higher value product (and perhaps one with a more stable market). Joule Unlimited would, it seems, argue otherwise. Have they worked this out, or are they naive? None of the work discussed here presents even basic economic analysis. So we have lots of good science, taking various approaches. It is early-stage work, in a complex field with economic barriers. Who will win? Who knows. Maybe no one.

Other posts on energy development include:
* Making electricity in your windows: sharing the solar spectrum (July 5, 2011).
* A Christmas present: Using concentrated sunlight to split water and CO2 (February 18, 2011).

More about cyanobacteria: A whiff of oxygen three billion years ago? (April 6, 2015).

CO2 emissions threaten clowns

September 20, 2010

At the right is the reason for posting this item.

For those who want a bit more of the science...

Musings has already noted some effects of increased levels of CO2 on the oceans. Some of these effects are due to increased acidity (lower pH). Most studies so far have looked at the effect of the increased CO2, which increases acidity, on organisms that make calcium carbonate (CaCO3) skeletons. [Example: Increased CO2: effect on animals that make carbonate skeletons (January 11, 2010).]

The new work explores the effect of increased CO2 on non-calcifying animals in the oceans. They tested two types of fish: the clownfish, shown above, and the damselfish. The basic finding was that increased CO2 affected the behavior of the fish, and led to them being more susceptible to predation. The effect seems to be due to interference with their olfactory system, so that they do not sense cues of a threat. The effect, in this work, becomes important only at rather high levels of CO2, more than double current levels. Further, the work does not address how the fish populations would adapt to new conditions. Overall, the work reports some interesting effects, but be careful to avoid generalizing from them.

A brief note about this work in Science -- and the source of the picture above: Ecology: Down with the Clowns. (Science 329:610, August 6, 2010.)

News story: Carbon emissions threaten fish populations. (e! Science News, July 7, 2010.) Good overview of the work.

The article: Replenishment of fish populations is threatened by ocean acidification. (P L Munday et al, PNAS 107:12930, July 20, 2010.)

Other posts on climate change include:
* CO2 emissions: What if we just stopped making new CO2-emitters? (October 5, 2010).
* Climategate: a book and a cartoon (September 27, 2010).

Also see:
* Pregnancy in males: It's similar to pregnancy in females (February 22, 2016).
* The opah: a big comical fish with a warm heart (July 13, 2015).

Finding cancer genes

September 19, 2010

Cancer cells have altered regulation of cell growth; they grow beyond what they should. Typically, cancer cells carry multiple mutations, which together lead to the less-regulated growth. Mutations in many different genes can result in cancerous growth; thus cancers, even of the same general type, are quite varied. Genes that can lead to cancer are broadly grouped into two classes: those that promote cancer when mutated, and those that serve to suppress it, until they are mutated. The former are called oncogenes, and the latter are called tumor suppressors.

Recent advances in DNA sequencing have opened up a new era in finding cancer genes. It is becoming practical to "blindly" screen cancer cells for mutations. The hard part, then, is sorting out which of the information that is obtained is significant, and which is just "noise". The current paper is a good example of this approach.

In the first part of this paper, they did massive DNA sequencing of both normal and tumor tissues from eight patients with a particular type of ovarian cancer. They did not sequence the entire genomes, but only the parts thought to code for proteins, the so-called exome. This is about 2% of the genome -- a small amount, but still far more than anyone would have done before the new sequencing technologies. This part turned up 268 mutations in 253 genes -- comparing a person's cancer cell genome with the same person's normal genome. The rest of the work was to confirm these results, and then to focus on those few genes that showed up more than once. The simple idea is that genes that show mutations in the most tumor samples are most likely to be relevant -- somehow -- to the tumor. One gene they focus on -- that with the most mutations -- is called ARID1A; it is involved with chromatin remodeling -- moving proteins around on the chromosomes.

Sequencing result; cancer gene ARID1A An example...

The Figure shows a result from the step where they confirm a mutation, by careful resequencing. The upper panel shows the sequencing result for the normal DNA. Each base is shown as a different color; for example, the base A is green. Note that the result at each position is "clean"; there is only one colored peak for each position. The lower panel shows the result for the corresponding region from a particular tumor. At one position there is a clear difference: there are two peaks, one for the original base (C) and also one for T.

The simple interpretation is that the tumor sample contains a mutation. In the tumor cells, one copy of the gene is normal at this position, and the other copy is mutated. The mutation is C-to-T, and is at position 553 (of the mRNA); thus the mutation is labeled, below the sequencing results, as 553C→T. Position 553 of the mRNA corresponds to the first base of the codon (coding triplet) for the 185th amino acid in the protein. The codon is changed from CAG, which codes for the amino acid glutamine (symbol Q), to UAG, a codon which causes chain termination (symbol X). Thus the change is also shown as Q185X, in terms of the protein. It is very likely that this mutation, which severely truncates the protein, eliminates its normal function.

Further analysis of this particular tumor shows that the other copy of this gene also carries a mutation. That is, both copies carry mutations that will lead to loss of function. If this gene is relevant to the cancer, then it seems that losing its normal function is what is bad. Thus we infer that this gene may be a tumor suppressor; its loss can contribute to tumor development. Since this gene had not previously been associated much with cancer, this is a new finding of some interest. But we should also note... It is interesting that 57% of the cancers checked carried a mutation in this gene. That seems to attest to the importance of this gene for the cancer process. However, that result also means that 43% of that type of cancer did not have mutations in this gene, thus mutating this gene is not essential for the cancer pathway. It's complicated.

News release: Scientists Discover Gene Mutation Common in a Class of Ovarian Cancers. (Howard Hughes Medical Institute (HHMI), September 8, 2010.)

The article: Frequent Mutations of Chromatin Remodeling Gene ARID1A in Ovarian Clear Cell Carcinoma. (S Jones et al, Science 330:228, October 8, 2010.)

Thanks to Jitesh Dundas for recommending this new paper.

* * * * *

There is another new paper covering the same ground, with similar conclusions. The two papers do not refer to each other, so the work was probably independent. ARID1A Mutations in Endometriosis-Associated Ovarian Carcinomas. (K C Wiegand et al, New England Journal of Medicine 363:1532, October 14, 2010.)

The above article was accompanied by an editorial: The Origin of Ovarian Cancer -- Is It Getting Clearer?. (M J Birrer, New England Journal of Medicine 363:1574, October 14, 2010.)

* * * * *

Related post: More on cancer genome sequencing... Studying cancer development by analyzing the genomes of individual cancer cells (May 16, 2011).

The bisphenol A (BPA) controversy

September 19, 2010

The chemical bisphenol A (BPA) is a component of some plastics; we ingest tiny amounts of it by using such plastic containers for food. Depending on whom you believe, BPA is either harmless or a serious insidious poison. People on each side are adamant about their position, and think the other side's data is irrelevant.

BPA Bisphenol A

more formal name:

I've been thinking about posting something on BPA, but frankly could not figure out what to say. I still don't know what to say, but now have a couple of nice articles, at different levels. I encourage you to read over at least one of them, with an open mind. If you have an opinion, or form one, fine. But do remember that it is tentative, because there really is no agreement -- not even much agreement on what the right tests would be. I hope these two items will give you a sense of what the issues are; for now, that is more important than the answers.

In Feast of Data on BPA Plastic, No Final Answer. (New York Times, September 6, 2010.) A good place to start

Assessing risks from Bisphenol A. (H Patisaul, American Scientist 98:30, January 2010.) Article is freely available here, but only as a web page. The article is something of a review, but written for the general audience. More technical than the New York Times article above, but intended as useful for those not in the field.

More on BPA... BPA: Effect on thyroid hormones in pregnant women and babies (December 8, 2012).

Not only is BPA of interest, but the BPA controversy typifies a type of debate that society is now having, over many chemicals that do not quite fit in our usual thinking.

Also see: The sperm count problem (June 18, 2011). This post deals with some new evidence on the issue of whether sperm counts are declining (for humans). Evidence for declining sperm counts is part of what is behind the concern about BPA and other possible "endocrine disrupters". Be cautious in interpreting this!

Another plastics issue... Degradable polyethylene isn't (October 17, 2011).

How about a dry cleaning solvent... Does dry cleaning cause cancer? (November 30, 2011).

Also see... How to dispose of unused medicines (September 10, 2012).

September 15, 2010

Turning sewage into profit -- via rocket fuel

September 15, 2010

Sewage treatment is a big deal. Simply releasing sewage into the environment is no longer acceptable. Treating sewage to make it "benign" is expensive. Or is it?

Scientists are now suggesting a new process, with the goal of making it less expensive -- or even profitable. The problem is getting rid of the nitrogen in the sewage, which is mostly in the form of ammonia (NH3) or the equivalent ammonium ion (NH4+). In the common sewage treatment process, the NH3 is eventually released to the atmosphere as nitrogen gas (N2). That's good, but the process is complex and energy intensive. The new proposal is for a more direct process, using bacteria that can oxidize NH3 to N2 anaerobically. These anaerobic ammonia oxidizers (anammox bacteria) were discovered only a couple decades ago. The proposed process is less expensive (or perhaps even profitable) for two reasons: first, it requires less oxygen, and second, it produces more "biogas" (methane) as a useful by-product. Making a practical energy-yielding process using anammox bacteria still has hurdles, but is at least now a serious goal.

An interesting aspect of anammox bacteria is that one of the intermediates is hydrazine, N2H4 -- a substance better known as a rocket fuel. This is so toxic to the bacteria themselves that they make a special compartment, bounded by a novel type of membrane never before seen in biology. It contains fused four-membered rings (cyclobutane); these unusual membrane lipids (fats) have been nicknamed ladderanes. The wonders of the microbial world!

Here are two news stories:
* Bugs will give us free power while cleaning our sewage. (New Scientist, May 7, 2010.) A brief overview, which points to the following article for more...
* Engineering: Sewage Treatment with Anammox. (B Kartal et al, Science 328:702, May 7, 2010.) A brief but serious discussion of the issues in sewage treatment research.

More about sewage: Reducing corrosion of sewage pipes (September 27, 2014).

More about lipids is in the section of my page Organic/Biochemistry Internet resources on Lipids. That section contains a list of related Musings posts.

More about cyclobutane rings... 2 + 2 = 4: Chemists finally figure it out (October 9, 2015).

Open access publication: a status report

September 14, 2010

There has been considerable movement in recent years towards open access (OA) publication, where scientific papers are available for free on the Internet. This requires a new economic model for publishing, and raises new questions.

Science magazine has just done a short overview of the status of OA publishing. Much attention is given to two major OA families: PLoS (Public Library of Science) and BMC (BioMed Central). Both are at or near economic sustainability.

Those interested in this developing story of how scientific work is published may enjoy browsing this news story.

Free Journals Grow Amid Ongoing Debate. (J Kaiser, Science 329:896, August 20, 2010.)

Also see: Growth of open access publishing (July 17, 2011).

A new organelle "in progress"?

September 13, 2010

We know about mitochondria and chloroplasts. We see them now as specialized organelles within the cells of "higher" organisms (eukaryotes). From their characteristics, we infer that they are derived from bacteria. Of course, we do not know the details of how all that occurred.

Over time, other relationships between organisms show up. In the case reported here, we see a close association of a bacterium with a fern. At least it used to be a bacterium. It is still extracellular, but is so degenerated that it cannot survive on its own. The new work is a study of its genome, which shows the degeneration. Few genes have actually been lost, but an amazingly high percentage have become inactivated -- have become pseudogenes. Yet, this bacterial symbiont is providing an essential function to the "host" fern: nitrogen fixation, in this case.

So we can observe this association, and describe it at various levels of detail. It is a symbiotic relationship. Roles of both host and symbiont are clear. The microbe provides a function for the host and the host must be providing essential functions for the symbiont, which cannot grow on its own. We can infer how the association developed -- and that story has parallels with what we infer for the development of chloroplasts. A key difference is that the current microbial symbiont is an extracellular agent. Now, where is this going? Is this a snapshot along the pathway for forming an intracellular symbiont? There is no way to know. Perhaps this is a different type of symbiosis, or perhaps it is a step toward being like what we see now as a chloroplast. We'll post more information as it becomes available. Check back in a few million years, and we can see how this has progressed.

News story: Azolla & endosymbiosis. (Sciblogs, Science Media Centre, Aug 1, 2010.)

The article, which is freely available: Genome Erosion in a Nitrogen-Fixing Vertically Transmitted Endosymbiotic Multicellular Cyanobacterium. (L Ran et al, PLoS One 5(7):e11486, July 8, 2010.)

Terminology... An endosymbiont is a symbiont that lives within the host organism. An endosymbiont may be within the cells (intracellular) or not (extracellular). People sometimes use the term endosymbiont when they really mean an intracellular symbiont.

Related posts include:
* Tarsier; eukaryotic cells (August 31, 2009)
* Can you die from an infection without being infected? (March 19, 2010).
* Plants need bacteria, too (October 9, 2010). A very different kind of plant-bacteria association.
* Getting along: animals and bacteria (August 6, 2012).
* Chromosomes -- 180 million years old? (April 18, 2014).
* How does worm "fur" divide? (January 4, 2015).
* Origin of eukaryotic cells: a new hypothesis (February 24, 2015).
* The aphid-bacterium symbiosis: a step toward manipulating it (May 15, 2015).
* Is the warnowiid ocelloid really an eye? (October 12, 2015).
* Added May 20, 2016. Using light energy to power the reduction of atmospheric nitrogen to ammonia (May 20, 2016).
* Added July 27, 2016. Venus flytrap: converting defense into offense (July 27, 2016).

Happyness, a House, and a Mouse

September 12, 2010

Friends Darsh sends three short items. Try reading them aloud. They are shown on the supplementary page: Happyness, a House, and a Mouse.

The figure is from Darsh's web site, listed on the supplementary page.

The great Tonga earthquake: how many quakes were there?

September 12, 2010

Can you imagine being near the epicenter of a "great" earthquake (magnitude 8 or higher) -- and not knowing it? It happened.

On September 29, 2009, a great quake struck in the South Pacific; the quake is known as the Tonga quake. Not only a major quake, but a major tsunami. Fortunately, this is an area of low population, but some of the islands suffered substantial damage.

As geologists tried to sort out the details, they found problems. The seismic records did not seem to consistently point to a clear center. The type of tsunami was inconsistent with the type of quake they thought had happened. Further, the island of Tonga moved the wrong way! These anomalies in the data forced them to examine the records more carefully. The conclusion: the great Tonga quake was actually two quakes, each of magnitude about 8. The two quakes occurred within a minute or so of each other. (In fact, there may even have been three quakes, but we will ignore that additional complexity here.)

Two major quakes, very close in both time and space. It is quite likely that the first one triggered the second. And now we have another amusing story, as described in a pair of papers published together in the August 19 issue of Nature. Both papers announce that the great Tonga quake was really two (or three) quakes, but...

Let's call the two quakes the "red" quake and the "blue" quake.

The top panel of the figure at the right shows the events as one of the papers describes them. Briefly, the blue quake followed by the red quake.

Skip the second panel for now. The third panel, labeled Lay et al, shows the events as described by the other paper: the red quake followed by the blue quake.

That is where it stands. Two groups have analyzed the available data. They agree that the quake was more complex than originally described, but they quite disagree about the sequence of events. (Both papers note the uncertainties in their analyses.) Does this disagreement matter? It does to them. Understanding how one earthquake triggers another is a relatively new area for the seismologists; in this case they can't even agree on who triggered whom.

Above, I skipped the second frame. It shows a simplified view of the seismic record. Superficially, it seems to agree with Lay. But there are enough other issues that the point seems to remain open.
The Tonga quake.

Part b of the figure is a map of the area, with the two quakes shown as red and blue bars. As you can see there, the blue quake is a near-horizontal slippage, with one plate sliding under another. This is the type of quake we most often talk about, especially around the Pacific Ocean. The red quake is a more vertical slippage within a plate. You will see the term "normal" used for this quake. That is normal in the sense of perpendicular, a second meaning of normal you may have learned in a geometry class. You can also see that the two quakes should move Tonga in opposite directions.

News story: Noticing a Magnitude-8.0 Earthquake Months Later. (New York Times, August 23, 2010.)

* News story accompanying the article: Earthquakes: Double trouble at Tonga. (K Satake, Nature 466:931, August 19, 2010.) A quite readable story; give it a try. The figure above is from this story.
* First article: Near-simultaneous great earthquakes at Tongan megathrust and outer rise in September 2009. (J Beavan, Nature 466:959, August 19, 2010.)
* Second article: The 2009 Samoa-Tonga great earthquake triggered doublet. (T Lay et al, Nature 466:964, August 19, 2010.)

This post was noted in the post Nature's "Top 50" institutions for scientific research (May 9, 2011).

Other posts on earthquakes include:
* Could we block seismic waves from earthquakes? (June 23, 2014).
* Are large earthquakes occurring non-randomly? (February 10, 2012).
* The Quake-Catcher Network: Using your computer to detect earthquakes (October 14, 2011).

More on the geology of the Pacific islands: Hawaii's hot spot(s) (October 9, 2011).

More from Tonga: File dates and human settlement in Polynesia (November 16, 2012).

Dolphins, bulls, and gyroscopes

September 10, 2010

Dolphin, carrying device to measure head motions. The figure at the left is the reason for including this item.

Unfortunately, I was unable to find the other figure that obviously should be included. There must have been something about the other guy's contract that precluded publishing a photo.

Is there some science here, or is this just a cute picture? Well, the underlying issue is how we keep our balance. A key organ for balance is a part of our ears called the semi-circular canals (SCC). The SCC contain fluid, which of course "sloshes" around as we move our head. Our brain interprets what goes on in our SCC as balance.

Bigger animals have bigger SCC -- as one might expect. Except for the dolphins, and their relatives, the other marine mammals. These cetaceans have tiny SCC. The SCC of the dolphin pictured here is about the size of that of a mouse. (The dolphin is about the size of a human.) Why do dolphins have such tiny SCC? No one knows. The work here is a test of one hypothesis.

The hypothesis is that the dolphins have smaller SCC because they move their heads more. That is, the smaller SCC protects them from getting excessive stimulation due to greater natural motions. The test is to compare the head movements of the dolphin with the head movements of a another mammal of similar size. The bull was chosen because it is a fairly close relative of the dolphin. And a rodeo bull was neat -- because it does a lot of head movement in its "work". Head motion was measured with a motion sensor, essentially a set of gyroscopes. The dolphin cooperated by holding the device, as shown in the figure above. Attaching the sensor to the bull was an interesting challenge.

The results were rather straightforward. Dolphins and bulls move their heads about the same. Thus they reject the hypothesis that the small size of the dolphin SCC is to reduce its sensitivity to greater head movements. Why the dolphin has a smaller SCC remains a mystery.

News story: Rodeo Bull Goes Head-to-Head With Zoo Dolphins in a Study of Balance. (Science Daily, March 28, 2010.)

* News story accompanying the article and freely available: Why are cetaceans' vestibular systems so small?. (K Knight, Journal of Experimental Biology 213(7):i, April 1, 2010.)
* The article: The relationship of head movements to semicircular canal size in cetaceans. (B M Kandel & T E Hullar, Journal of Experimental Biology 213(7):1175, April 1, 2010.)

Next post on gyroscopes: A simpler bicycle (May 23, 2011).

More on dolphins:
* Cultural transmission of fishing techniques among dolphins (September 13, 2011).
* On a similarity of bats and dolphins (September 15, 2013).

September 8, 2010

Killer eggs: The American egg problem

September 8, 2010

The US is currently dealing with a massive recall of contaminated eggs. Briefly, after a burst of cases of food poisoning by Salmonella bacteria, the source was traced to eggs -- in particular to eggs from two major producers. Subsequent investigation has found Salmonella-contaminated feed at those producers, as well as a range of other problems.

A recent headline from the New York Times caught my eye. It pointed to the lack of vaccination of chickens against Salmonella despite there being an inexpensive effective vaccine. The story is interesting -- and not as simple as it might seem. But it certainly raises questions about the oversight of the food supply. So I encourage you to read this newspaper article, not necessarily to reach any particular conclusion, but to see the complexity of the issues. In particular, note the tension between two broad approaches to regulation: one is to establish standards, and one is to specify procedures.

U.S. Rejected Hen Vaccine Despite British Success. (New York Times, August 24, 2010.)

Musings has presented various aspects of the problem of food poisoning from chickens, under the general heading of "Killer chickens". One post was specifically on the proposed new USDA rules: Killer chickens -- follow-up: some progress (June 7, 2010).

I think it is broadly understood that the US food safety "system" is not doing a good job of keeping up with modern demands. Reasons include industry pressure, the desire to keep food cheap, politics, and inertia. The article above just hints of the concerns. Among the critics is Dr. Marion Nestle; one of her eloquent books on the topic is listed on my page of Book suggestions: Nestle, Safe Food (2003).

Developing improved degradation of organophosphate pesticides

September 7, 2010

Gunjan shares the powerpoint set made for a Microbiology class presentation, based on a literature review. I think you will find the topic interesting.

The work combines a couple of interesting issues.

The first issue is detoxifying organophosphate pesticides, such as parathion, methyl parathion, fenitrothion, and others. There are microbes with enzymes that will degrade these pesticides, but these enzymes are intracellular thus cannot interact with the pesticides present in the environment (outside the cells).

The second issue is even more fascinating: how bacteria make ice. You might not have thought about that before. Seems that cooling some water to its freezing point (FP; 0° C) should give ice. But it may not. If the water is clean, it may cool to well below the FP without freezing. The hard step in freezing is getting started: forming the first bit of ice. Pseudomonas syringae bacteria can initiate crystallization at temperatures as high as -3° C. High? Yes, -3° C is warm for ice formation considering that pure water may crystallize at temperatures as low as -40° C! How does P. syringae do it? Well, in its membrane is lodged a protein -- known as the ice nucleation protein (INP) -- which is at the heart of ice nucleation. Precisely. The protein's structure is such that it could well act as a template for the ice nucleation process by mimicking the pattern of an ice crystal lattice. These bacteria can cause frost injury to the plants by promoting ice formation when it would not have occurred otherwise. (In addition to P. syringae, some Xanthomonas and Erwinia species also show this phenomenon.)

So, the connection? Bacteria that make INP display it on the bacterial surface. Scientists have hijacked that system for degrading the pesticides, by making hybrid genes carrying the pesticide-degrading enzyme and the surface-localization signal of INP. This results in bacteria that make the pesticide-degrading enzyme on the cell surface, where it can act. (Hijacking the surface-display system can also be used in making vaccine bacteria, carrying antigens of interest.)

Slide 12: Degradation of pesticide in soil. An example, from slide 12...

The graph shows the degradation of a pesticide (chlorpyriphos) in soil. For the lower two curves, the soil was inoculated with an engineered strain of Pseudomonas putida, carrying the degrading enzyme on its surface. For the upper two curves, the soil was not inoculated with bacteria. You can see that the pesticide is much more rapidly degraded when the engineered bacteria are added.

What is the difference between the two upper curves? The curve with circles is for soil that had been fumigated. The curve with triangles is for soil that had not been fumigated, and thus has its "natural" microbes. You can see that the natural microbes stimulated degradation a bit -- but not nearly as much as adding the engineered bacteria.

Detoxification of organophosphates by INP-surface display systems [link opens in new window]. (Powerpoint presentation; 3 MB file.)

Thanks to Gunjan for sharing the presentation, and for writing parts of this post.

* * * * *

A side note: a bit of history about the Pseudomonas syringae ice nucleation protein... It was involved in one of the very first examples of genetically engineered organisms. From what Gunjan wrote above, one might predict that a mutant P. syringae unable to make the INP -- a so-called "ice-minus" mutant -- would not cause ice formation. Further, it might even protect plants from frost damage, if it displaced the wild type, ice-promoting bacteria. In fact, ice-minus P. syringae were made; these bacteria did help protect plants from frost damage. However, this was one of the first applications of the new recombinant DNA technologies, in the early 1980s, and it got mired in the controversy of this new field. For a brief introduction to this story, see Wikipedia: Ice-minus bacteria. In particular, look over the "Historical perspective" section.

* * * * *

For more on ice nucleation: Ice nucleation -- by airplanes (September 24, 2010).

Some organisms promote ice nucleation, but some do the opposite: An anti-freeze story: Why a tick carries a human pathogen (October 29, 2010).

More on the degradation of organophosphates: Self-powered micromotors for speeding up chemical reactions, such as destruction of chemical weapons (March 14, 2014).

Other degradation issues...
* Drug degradation: A drug that reappears after being degraded (November 2, 2013).
* Degradable polyethylene isn't (October 17, 2011).

What kind of a prison guard would you be?

September 7, 2010

Borislav sends a recommendation of a movie -- one that is based on a famous and important social science experiment. He writes...

In 1971 Prof. Philip Zimbardo conducted a revolutionary psychological experiment at Stanford University. The experiment, known as the Stanford prison experiment, was abruptly cut off after getting out of hand after only six days.

The experiment was designed to simulate prison environment. Psychologically stable students were selected to take part in experiment, and were randomly assigned to either prison guard or prisoner role.

Some of the guards showed increasingly sadistic behavior toward the prisoners, and Zimbardo started losing control over the situation. A prison riot was broken up, the tenants were relocated to another "prison," they were punished and humiliated, etc. The experiment had to be terminated prematurely.

For background on the Stanford prison experiment: Wikipedia: Stanford prison experiment.

The German movie called Das Experiment is based on the Stanford prison experiment.

The film might be an exaggeration of the specific laboratory conditions, but in reality this does happen. A known example is what happened in Abu Ghraib prison in Iraq, where people were tortured and killed in manner similar to the one in Das Experiment.

For the Abu Ghraib story... Wikipedia: Abu Ghraib torture and prisoner abuse.

While the movie is nothing short of fantastic, mind that Das Experiment is about the experiment, and is an experiment itself. If you decide to watch it, prepare yourself for a profound effect at first, and later to be shaken really hard.

On the plus side, the film is built around a nice love story.

For information on the movie... International movie database: Das Experiment.

Thirty years after the experiment, Zimbardo wrote a book about what happened at his "prison." It is called The Lucifer Effect. Here is a quote from the preface:

"... first part of this book was actually begun thirty years ago under contract from a different publisher. However, I quit shortly after beginning to write, as I was not ready to relive the experience while I was still so close to it."

Berkeley wildlife

September 3, 2010

Berkeley cat For a better view: Larger image.

For info: The story. (Berkeleyside, August 31, 2010.) The picture here is from this page.

(I doubt that the picture is of the particular animal involved in this incident.)

Man takes land from the wildlife and restricts their resources. Sometimes, wildlife near developed areas come "into town", perhaps looking for food, perhaps just exploring. The deer wandering the streets of Berkeley may be considered cute, but they also damage our gardens. Mountain lions are potentially dangerous. It is an interesting problem.

More Berkeley wildlife...
* He hi - ha - he (April 10, 2010).
* The Berkeley hyenas (March 20, 2012).

How acupuncture works: another clue

September 2, 2010

Acupuncture may reduce pain. How? One mechanism, for which there is evidence, is that the treatment causes the release of endorphins -- the body's internal opioids. New work suggests another mechanism, involving the small molecule adenosine, which is known to be a pain-killer. In this work, they give acupuncture treatments to mice. They showed not only that adenosine levels increased and that the mice showed less discomfort, but they connected adenosine and the lessened discomfort by multiple approaches. For example, if they used mutant mice that lacked a key receptor for adenosine, the adenosine level still increased, but there was no change in the discomfort. Evidence such as that begins to make a causal connection between the adenosine increase and the reduced discomfort.

What does this lead to? One thing they did was to use a drug that serves to keep adenosine levels high (by inhibiting its breakdown). This enhanced the response of the mice to the acupuncture. This feature should be testable in humans.

It's hard to avoid some technical terms here. Here are some key ones...
* The prefix noci- refers to harm -- or more specifically in context, to pain. A nociceptor is a pain receptor.
* Ipsilateral means "same side" -- as probably becomes clearer when you see it juxtaposed with contralateral. For example... If you hold an ice cube in your right hand, the ipsilateral hand (right -- same side as the ice cube "treatment") will feel colder than the contralateral hand (left).

Adenosine is the A of the nucleic acids DNA and RNA -- sort of. The problem is that there are multiple forms of A: the free base adenine, and various larger molecules containing adenine. It is the base adenine that has the informational properties that are key in the nucleic acids. Adenosine is the combination of adenine with the sugar ribose. Adenosine can have phosphate groups attached; the form with three phosphates is called adenosine triphosphate, or ATP. ATP is used in making RNA, and it is also a major energy carrier molecule for cells. Further, ATP itself can cause pain. That is, two members of the A family have opposite effects: ATP is painful, and adenosine is a pain killer. Here are structures of some of these key "A" chemicals: Adenosine and related compounds [link opens in new window].

News story: Acupuncture's Molecular Effects Pinned Down: New Insights Spur Effort to Boost Treatment's Impact Significantly. (Science Daily, May 31, 2010.)

* News story accompanying the article: Needling adenosine receptors for pain relief. (M J Zylka, Nature Neuroscience 13:783, July 2010.) This article includes a couple of nice figures outlining some of the key ideas from the work. (Note that caffeine, a chemical similar to A, may inhibit the pain relief; that was not tested in this work.)
* The article: Adenosine A1 receptors mediate local anti-nociceptive effects of acupuncture. (N Goldman et al, Nature Neuroscience 13:883, July 2010.)

For an interesting follow-up... PAPupuncture -- an improved acupuncture (June 10, 2012).

For more about caffeine... Your desire for caffeine: It may be in your genes (May 31, 2011).

More about adenosine and such: Blood thinning: a new approach (February 2, 2015).

September 1, 2010

The Most Remarkable Funeral Treasures

September 1, 2010

Borislav sends a bit of history, and writes...

Pharaoh Tutankhamen ruled for ten years, around 1300 BC, and died aged 19. His mummified body was laid down in one of the most magnificent tombs ever made. The tomb was opened in 1922; treasure and inscriptions found there helped scientists shape our understanding of the ancient Egyptian civilization.

National Geographic published an article on the then-recent find in 1923; they now feature this historic article from their archive. At the Tomb of Tutankhamen -- An Account of the Opening of the Royal Egyptian Sepulcher Which Contained the Most Remarkable Funeral Treasures Unearthed in Historic Times. (National Geographic, May 1923.)

The figure here is reduced from the lead figure at that web page. It is probably the lead figure of the article as originally published in 1923.
King Tut - tomb

More on mummies... Diagnosis of prostate cancer in a 2100 year old man (November 8, 2011).

More on monarchs: Genetically modified crops and the fate of the monarch butterfly (April 1, 2012).

Some other Musings items of historic interest...
* SETI (October 20, 2009). An article that was the inspiration for SETI.
* Goethe, Huxley, and Nature (November 22, 2009). An article from 1869.
* Book review: Kepler (February 3, 2010). A review of a book originally published in 1609.
* There's plenty of room at the bottom (March 1, 2010). Feynman's seminal paper on nanotechnology.

Lighting the heart

August 31, 2010

Scientists have shown that they can control the beating of a heart by shining pulsed light on it. The heart beats follow the pulse rate of the light.

Figure 2c. Heart beat vs laser pulse frequency An example, from Figure 2c of the paper...

The figure shows the heart beat, in red, and the laser pulses, in blue. You can see that the heat beat adjusts to conform to the laser pulse rate, and quickly returns to near normal when the laser is stopped.

This work is with the heart of a two day old quail embryo. How it works is not entirely clear. However, since they use quite low energy infrared light, they suggest that local temperature effects are the key. Whatever the mechanism, the effect seems to be rapidly reversible, and with little if any damage.

The method may be useful as a research tool to explore heart action. Possible use of the method for a new type of heart pacemaker is intriguing, but speculative at this point.

News stories. Both of these are good. Either will give you a good idea of the work; reading both is a bonus.
* Embryonic Heart Paced With Laser. (Science Daily, Aug 16 2010.)
* Controlling heart beats with lasers. (Physics World, Aug 18, 2010.)

* News story accompanying the article: Biophotonics: A light to move the heart. (N I Smith, Nature Photonics 4:587, September 2010.)
* The article: Optical pacing of the embryonic heart. (M W Jenkins et al, Nature Photonics 4:623, September 2010.) Also at the site is a movie; choose "Supplementary info". You can watch the heart beat in synchrony with the light pulses.

For more on heart beats: Using stem cells to study a heart condition (April 19, 2011).

Atmosphere suggests planet might harbor life

August 30, 2010

As starlight passes by a planet, the light spectrum may be modified. Some of the light may be absorbed by the planet's atmosphere -- depending on what gases are in that atmosphere. If analysis of starlight passing a planet suggests that the atmosphere contains gases we think are typical of a living system, such as oxygen, that would be a hint that the planet might support life; further study of that planet would be warranted.

Astronomers have actually analyzed planetary atmospheres by such methods. A few years ago, they analyzed the atmosphere of a large extrasolar planet. Now, they report analyzing the atmosphere of an earth-size planet -- and finding the "gasses of life".

Before you get too excited at their result, we should note that it was not entirely unexpected. The astronomers live on the planet whose atmosphere they studied. The paper is thus an interesting technical achievement, not a scientific finding of note. Further, the assumption that other planets of life will have the same atmospheric gasses as Earth is just that -- a working assumption, which may well hold some surprises. What's important is that they have made progress in analyzing planets, and over time this will be applied to extrasolar planets. Interpreting the results will be another story.

What is the technical achievement? After all, surely people have studied the Earth's atmosphere before? Indeed. What they did here was to analyze the light reflected off the moon during an eclipse. That light includes light that has passed through the Earth's atmosphere. This serves to mimic more closely what the astronomers will face when analyzing an extrasolar planet transiting its star. Much of the paper is highly technical, sorting out what a complex spectrum means.

News story: Earth as an Extrasolar Planet. (Science Now, July 23, 2010.)

The article: The Earth as an extrasolar transiting planet: Earth's atmospheric composition and thickness revealed by Lunar eclipse observations. (A Vidal-Madjar et al, Astronomy & Astrophysics 523:A57, November 2010.) I encourage you to read the abstract, for a useful overview. (There is also a freely available copy of the accepted paper, at the Arxiv: accepted paper.)

Other posts on extrasolar planets include:
* Added June 19, 2016. Habitable planets very close to a star (June 19, 2016).
* GJ 1132b: "the most important planet ever found..." (December 18, 2015).
* The first truly habitable exoplanet? (October 12, 2010).
* Extrasolar planets (December 8, 2009).

Swarming locusts have bigger brains

August 29, 2010

Bigger than what, you ask? Bigger than solitary locusts.

Locusts have an unusual life history. They commonly live as solitary individuals. However, under some circumstances, they come together as swarms. It is this swarming phase that we perhaps think about, as a swarm of locusts is a dramatic -- and sometimes devastating -- phenomenon.

Terminology. The paper uses the unusual word solitarious, apparently as a synonym for solitary. We'll use both the words swarming and gregarious to refer to the more social locust phase.

Locust brain: one half each from solitary and gregarious phases. Locust brain. The figure shows two half-brains, one from a locust in the solitary phase and one from a locust in the gregarious phase. The locusts were approximately the same size.

The key observation is that the half-brain on the right, from a gregarious locust, is bigger. This is perhaps most obvious by eye for the mid-brain (MBr). This observation is supported by extensive data in the paper.

The figure here is part of Figure 1 of the paper. The full figure includes a scale bar, which shows that the entire brain, above, is about 4 millimeters wide.

Why is this interesting? The inference is that swarming locusts need a more complex brain to carry out the more complex -- and more social -- life in a swarm. Differences in the proportions between brain parts for various functions also seem consistent with this. These ideas will surely be debated -- and tested with other systems. For now, it is simply neat to have such information for two distinct forms of the same organism.

News story: Swarming Locusts Need Larger Brains. (Science Daily, May 26, 2010.) Includes some good background information about locusts.

The article: Gregarious desert locusts have substantially larger brains with altered proportions compared with the solitarious phase. (S R Ott & S M Rogers, Proc. R. Soc. B 277:3087, October 22, 2010.)

Added March 25, 2017. Among other posts on brain size... A possible genetic cause for the large human brain (March 25, 2017).

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Brain (autism, schizophrenia). It includes a list of brain-related posts.

Personalized medicine -- and the entering students at UC Berkeley: follow-up

August 27, 2010

Original post: Personalized medicine -- and the entering students at UC Berkeley (May 25, 1010). That links to other posts about personalized medicine.

Briefly, entering students at UC Berkeley were asked to submit a sample of their DNA, to be tested for three simple traits. This is part of a program to talk about personalized medicine with the entering class; the DNA testing is a voluntary but small practical activity. The program stirred controversy -- as does everything in the emerging field of personalized medicine (and as does everything in Berkeley).

In fact, aspects of the program have been curtailed, as a result of a legal ruling that the students had not been adequately protected. The main difference is that the students will not obtain their personal results; the voluntary testing and the discussions, including discussion of the collective results, will continue.

As you read about this, try to emphasize seeing what the arguments are by each side. As noted in numerous Musings posts, personalized medicine (DNA testing) holds promise, but is also of concern. The current story represents people trying to work out a reasonable way to proceed. Many in the molecular biology community do not agree with the outcome. However, I would note that the outcome "errs" on the side of being cautious -- and that is probably good.

Here are two news stories about this development.
* University news release: UC Berkeley alters DNA testing program. (UC Berkeley, August 12, 2010.)
* School paper: Program will not provide individual DNA results. (Daily Cal, August 16, 2010.)

Killer chickens -- A clue to the underlying problem?

August 27, 2010

Our food can be a source of disease. One reason we generally cook meat is to kill infectious agents it may carry. In modern society, the most deadly food is almost certainly chicken. It is one of the most common foods, and also one most likely to carry disease. Chicken-caused disease is largely due to two types of bacteria: Salmonella and Campylobacter. We should note that cooking chicken is not a sufficient solution to the problem, since the pathogenic bacteria may spread in the kitchen through "juices" from the meat during handling prior to cooking.

We have noted the problem, and also some improved US regulations: Killer chickens (December 2, 2009), and links there. What we have now is some work suggesting a reason for the high level of Campylobacter in chicken -- a reason that might lead to a simple solution.

Many chickens are treated with a marinade before marketing. The marinade is thought to improve the quality and market appeal of the chicken. Among other things, the polyphosphate in the marinade is thought to inhibit microbial growth.

The new work challenges that point. The key finding is that the marinade -- from so-called "enhanced" processing -- actually promotes growth and survival of Campylobacter.

The basic procedure is based on collecting the fluid "exudate" from enhanced (marinated; with polyphosphates) and non-enhanced (non-marinated; without polyphosphates) chickens. (The exudate -- also called weepings or drippings -- is the fluid you would commonly find around a meat. It has nothing to do with excrement.) They sterilize the exudates, and then try to grow Campylobacter in the sterilized samples. The bacteria grow better in the exudates from enhanced chickens. Further, they show directly that adding increasing levels of polyphosphate to exudates from non-enhanced chickens leads to improved growth of the Campylobacter.

An example of the results...

Each pair of adjacent bars (labeled B and A) is for one type (strain) of Campylobacter.

The pair of bars represents two different growth conditions: exudate from chickens without the "enhancement" (light bar, on left, "B") and exudates from chickens with the "enhancement" (polyphosphates) (dark bar, on right, "A").

The height of each bar shows the number of bacteria after 24 hours of growth -- on a log scale. That is, "4" means 104, and "8" means 108. (CFU means "colony-forming units". CFU is a more precise way to say "bacteria"; we only count the bacteria that actually form colonies. No big deal.)

The results are clear. For each strain shown here, the right bar is higher than the left bar. That is, the bacteria grew better in the exudate from chickens with polyphosphate enhancement. (It was also true for 11 other strains tested, though the magnitude of the effect varied widely. See the full Figure 1 of the paper.)
Growth of Campylobacter in exudates from chickens with non-enhanced vs enhanced processing.

In following up this basic observation, they made an additional important observation. The results are different with exudates from chickens from different processing companies. In one case, the enhanced processing does not lead to increased growth of Campylobacter. Importantly, that is because both enhanced and non-enhanced chicken exudates support the bacteria quite well in this case. They also look at the pH (acidity) of the exudates. The simple pattern is that high pH exudates support bacterial growth, and low pH exudates do not. That is, in the original experiments, the unenhanced chickens were too acidic to allow growth of the Campylobacter; the polyphosphate enhancement raised the pH of the chicken enough to allow the bacteria to thrive. However, in another case, chickens were less acidic, and allowed growth anyway, with or without the enhancement.

Overall, the paper shows that the type of processing of the chickens affects the ability to support Campylobacter. The full story of why remains to be worked out, but it is an intriguing possibility that something as simple as the pH (acidity) of the processed chicken is key; certainly that would be easy to measure during processing as a quality control measure.

A brief note about the article from the government lab where the work was done: The Effects of Polyphosphate Additives on Campylobacter Survival in Processed Chicken Exudates. (ARS, USDA; 2010.)

The article: Effects of Polyphosphate Additives on Campylobacter Survival in Processed Chicken Exudates. (N W Gunther IV, Applied and Environmental Microbiology 76:2419, April 2010.)

As noted above, chicken is a problem because it carries Salmonella and Campylobacter. The work here deals with the latter. There is no information in the paper on Salmonella. From my general knowledge of Salmonella, I suspect they will thrive over the entire pH range at issue here. I do not know whether they are stimulated by the "enhanced" processing.

Thanks to a reader for contributing the article.

More about Campylobacter: Campylobacter -- how do the chickens feel? (September 6, 2014).

August 25, 2010

Antibiotic resistance: A new concern from New Delhi

August 24, 2010

A news story a couple weeks ago seemed to portend a new "superbug". The media reports I heard were quite confusing -- so typical of the primary news media that most people depend on. Over time, I have managed to track this down, find the actual work, and see some range of commentary. Here is an attempt to briefly but fairly introduce the topic.

As general background... Antibiotic resistance is a serious problem, which is making current antibiotics less effective. Many practices promote antibiotic resistance, including excessive use -- by both people and farm animals. Further, some types of resistance are transmissible from one microbe to another, thus speeding up the spread when a resistance does develop. What about new antibiotics, to replace those we "lose"? Antibiotics are no longer considered a good target by much of the pharmaceutical industry; the pipeline of new antibiotics is sparse.

The current "scare"... A new antibiotic resistance gene was uncovered last year, and traced back to a hospital in New Delhi. Hence the name NDM-1, where NDM stands for New Delhi metallo-beta-lactamase; a beta lactamase is the type of enzyme that degrades penicillin and other drugs with a beta-lactam chemical structure. A new paper presents some data on the prevalence of this new resistance gene in India (and some neighboring countries) and the UK. The short message is that prevalence is increasing, almost certainly enhanced by travel, and possibly enhanced by "medical tourism". It is a concern; this new resistance needs to be monitored, and any procedural improvements to reduce the pressure for the development of resistance are encouraged. In many ways, this is "routine". This is not the first emergence of a new antibiotic resistance gene -- and will not be the last. The measures called for here are called for regularly -- everywhere. And progress is spotty. We cannot predict precisely how a particular antibiotic resistance gene will spread; we can only predict that it is not good. Any action that comes from any such scare to improve practices for antibiotic usage is good.

Some government officials in India have objected to some of the coverage, suggesting that India was being attacked. It is nice to see that government officials there can say things as stupid as ours do. But let's leave the politics, perhaps understandable, aside. Appropriate public health officials in India are using this as an opportunity to re-examine antibiotic practices.

Because of the complexity and importance of the issue, I'm including several items below. Except for the article itself, all are short, and should be at least partially understandable by the general audience. The two items marked with ** are perhaps the ones to emphasize if you want a brief serious view of the science.

News stories:
* Antibiotic-Resistant Bacteria Moving From South Asia to U.S.. (New York Times, August 11, 2010.)
* Drug-resistant bacteria reach UK. (UK NHS, August 11, 2010.) From the UK government health service, a page for the general public.
* Experts offer perspective on NDM-1 resistance threat. (CIDRAP, August 20, 2010.) CIDRAP (Center for Infectious Disease Research & Policy, University of Minnesota) is generally recognized as a high quality source of information on infectious diseases. Thanks to Judy for sending this item.

Indian perspective:
* Intra-hospital committee to look into NDM-1 bug issue, says Apollo chief. (The Hindu, August 14, 2010.) This item gives a taste of the Indian criticism, but also of their action. (I don't have a good feel for what is fair coverage in India. Comments, alternative views, or additional links are welcomed.)
** An editorial, freely available: An obituary- On the Death of antibiotics!. (A K Ghafur, Journal of Association of Physicians of India 58:143, March 2010.) This came out based on earlier work on the NDM gene. It is both delightful and strongly worded. It starts with a wise overview of the relative importance of microbes and man in the world. Remember, it was written by an Indian doctor for the Indian public health community. It is intended as a call-to-arms for his locals, but much of the general message is widely applicable. (This is reference 26 of the article below.)

The article and commentary are in a Lancet journal. At least the article itself is freely available at the Lancet site, with registration. Those who have subscription access may find it simpler to access both via the Science Direct site.
* Commentary accompanying the article, via abstract at PubMed: The latest threat in the war on antimicrobial resistance. (J D D Pitout, Lancet Infectious Diseases 10:578, September 2010.)
* The article, via abstract at PubMed: Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study. (K K Kumarasamy et al, Lancet Infectious Diseases 10:597, September 2010.)

More on the problem of antibiotic resistance: Restricting excessive use of antibiotics on the farm (September 25, 2010).

More on antibiotics is on my page Biotechnology in the News (BITN) -- Other topics under Antibiotics.

A photosynthetic salamander?

August 24, 2010

Plants photosynthesize; animals do not. It seems a rather basic distinction. But, like most distinctions in biology, it turns out to be imperfect. We know that corals are photosynthetic. Musings has noted other examples of photosynthetic animals; see Croatian Tethya beam light to their partners (December 16, 2008), and links there. All of these examples involve invertebrate animals, with some type of association with a photosynthetic microbe.

But what about higher animals? Vertebrates? Surely they are "pure" animals, and do not photosynthesize? If you insist on maintaining that view, then do not read further.

The story of the photosynthetic salamander is a bit murky at this point; it was presented at a recent meeting, and is not yet published. So we have only some news stories, lacking detail. An interesting part of the story is that it is not entirely new. The basic finding of algae associated with salamander eggs goes back to the 19th century. There has been evidence that the developing salamander embryos benefit from the photosynthesis in the eggs. However, the notion that the algae are within cells of the salamander body is new -- and tentative. We eagerly await more on this.

News stories:
* Salamanders and Algae. (California Academy of Sciences, August 2, 2010.)
* Salamander's egg surprise. (Nature 466:675, August 5, 2010.) Left side of the pdf page. Includes pictures of developing salamander embryos, in green eggs.

* * * * *

More, April 27, 2011... An article on this work has now appeared: Intracellular invasion of green algae in a salamander host. (R Kerney et al, PNAS 108:6497, April 19, 2011.)

Also see:
* Getting along: animals and bacteria (August 6, 2012).

Mosquitoes are delectable things to eat

August 21, 2010

We have posted some work on trying to reduce disease transmission by mosquitoes. Much of such work involves eliminating the mosquitoes. [An example: Mosquitoes that can't fly (May 3, 2010).] A reader responded, raising the question of what the role of mosquitoes is in nature -- beyond disease transmission. The concern was whether eliminating mosquitoes might cause harm. I must admit that I was rather dismissive of the concern, based not so much on any great understanding of mosquitoes as on the intuitive sense that mosquitoes are "bad" and reducing disease is "good".

Nature has just put together a "news feature" in which they address the question of the role of mosquitoes. The article presents the views of numerous biologists with diverse views on what mosquitoes are good for out there in nature. (The title of this post is taken from a quote in the article.) It's a good read; I suspect that most will find out much more about mosquitoes than they knew. A world without mosquitoes. (J Fang, Nature 466:432, July 22, 2010.)

So, what about it? Should we eliminate mosquitoes to reduce disease transmission? It's a serious question, worthy of serious discussion of the pros and cons. That's better than my earlier position, and I appreciate the reader challenging that position. But let's be careful. To my knowledge, no one is proposing "eliminating mosquitoes". The proposals are to eliminate certain species in certain places, where there is a major problem. Indeed, let's be careful to examine what the possible downside of such an action might be, but in the context of a specific proposal.

Also see...
* An easier way to get infected with malaria (January 18, 2013). Can we infect people with malaria without using a mosquito?
* What does "Anopheles" mean? (August 27, 2012). The name of the mosquito may actually relate to the topic of the current post.
* Using genetically engineered mosquitoes in the real world (October 18, 2010). An announcement of a test to be done.

The oldest known multicellular organisms?

August 21, 2010

Beautiful pictures -- on the cover of Nature (July 1).

What are they? Computer reconstructions of a fossil. Each picture is a "slice", at a different depth into the sample.

The "headline" is "joining forces". That refers to the idea that a structure of this size and complexity must have been produced by a collection of cells, somehow interacting. What makes this exciting is that the fossil is about 2.1 billion years old. It is the most complex biological structure ever found for that era. It is possible that this represents the oldest known multicellular organism. More about this below.
Cover, Nature 7/1/10.

This post is as much about some spectacular pictures as anything. So, before discussing more about what they might be, let's include some more pictures.
* Two reconstructions, hi resolution [link opens in new window]. This figure shows two slices from one particular fossil. The figure is from the BBC story listed below; it is commonly seen at various news sources for this story.
* The original fossils [link opens in new window]. It is Figure 2 of the paper -- a hi-res version. In each part, the scale bar (white bar near bottom edge) is 1 cm.

What do they mean?

The simple story is that they found some spectacular fossils, and then did high tech imaging of them -- more or less like a CAT scan -- to generate even more spectacular reconstructions of what they looked like. Among the issues they dealt with... They had to date the samples, and they had to make the case that the fossils were of biological origin. Both of these involve very technical arguments, so we will just take their conclusions: the fossils are about 2.1 billion years old, and "definitely" biological. If these conclusions deserve challenge, we will hear about it in subsequent work.

So, what are they? The main clue is how organized they are. This is a sign that the cells were interacting with other; otherwise, they would have produced simply a "glob" of cells. That is, the fossils indicate there was intercellular (between-cells) signaling. This is important here, because it is the oldest known evidence for such signaling. I think there is general agreement on this part of the interpretation.

Beyond that? What kinds of cells are they? They might be bacteria (prokaryotic cells), forming complex colonies. They might be more complex eukaryotic cells, forming complex colonies. Or the fossils might even represent multicellular organisms. The problem is that they have absolutely no evidence to distinguish any of these possibilities. Interpreting fossils is always a matter of making educated guesses, with much guidance from the context. Interpretation changes as more information becomes available over the years. For now, these are unique fossils. There is nothing like them known of this age. So, enjoy the pictures, and admire the work that went into producing them. As to what they are, relax. Take the comments of the authors and various commentators as speculations, and don't worry much about them -- for now.

News story: 'Cookie-shaped' fossils point to multicellular life. (BBC, July 1, 2010.)

* News story accompanying the article: Early life: Origins of multicellularity. (P C J Donoghue & J B Antcliffe, Nature 466:41, July 1, 2010.)
* The article: Large colonial organisms with coordinated growth in oxygenated environments 2.1 Gyr ago. (A El Albani et al, Nature 466:100, July 1, 2010.)

More on multicellularity: Bacteria induce simple "pre-animal" to become colonial (September 8, 2012).

Also see: A whiff of oxygen three billion years ago? (April 6, 2015).

More old things...
* Added June 13, 2016. A 1.6 billion-year-old macroscopic multicellular eukaryote? (June 13, 2016).
* Claim of oldest fossilized cells refuted (May 3, 2015).

Octopus will only pay attention to television if it is "high definition"

August 20, 2010

A recent paper, which I came across accidentally while looking for something else in the same journal issue, reports that octopi will try to eat a crab that appears on their TV screen -- if the TV is of high enough quality. In fact, at this point, the work is as much as anything a study of the octopus visual system: setting up a TV system that the octopi will respond to. The potential for a range of behavioral studies is clear enough; the paper hints of them.

TV-viewing arrangements for the octopus. TV-viewing arrangements for the octopus.

The octopus starts at the right side ("Start arena"), and a video is shown at the left side ("Monitor").

The octopus is being watched ("Overhead video camera").

This is Figure 1 from the paper.

Two movie files are available at the web site for the article (see below). Choose "Supplementary material". Each movie shows a top view of the action -- what the octopus does, in response to the video shown. The video -- what the octopus sees -- is shown for you as a small inset at the lower left. The simple interpretation of the two movies is that the octopus attacks the crab but avoids the other octopus; both of these are normal behavior, showing that the octopus is responding properly to what is shown in the video.

News story: Octopuses React to Predators and Prey on TV. (Live Science, March 22, 2010.)

* News story accompanying the article and freely available: Octopuses react correctly to HDTV. (K Knight, Journal of Experimental Biology 213(7):i, April 1, 2010.)
* The article: Video playback demonstrates episodic personality in the gloomy octopus. (R Pronk et al, Journal of Experimental Biology 213(7):1035, April 1, 2010.)

Other octopus posts include:
* How an octopus adapts to the cold -- by RNA editing (March 5, 2012).
* The octopus and the coconut (December 28, 2009).

More about video for non-human animals:
* What can we learn by giving a praying mantis 3D glasses while it watches a movie? (March 12, 2016).
* Use of instructional videos -- in the wild (November 3, 2014).

I now wonder if we should reconsider what Paul did. Perhaps we should consider the possibility that Paul watches ESPN regularly, and fully knew what he was doing. (If anyone doesn't know what this is about... google on Paul octopus.)

A book, listed on my page of Books: Suggestions for general science reading. Sy Montgomery, The Soul of an Octopus -- A surprising exploration into the wonder of consciousness (2015).

August 18, 2010

Why African-Americans have a high rate of kidney disease: another gene that is both good and bad.

August 17, 2010

There is a high incidence of certain kidney diseases in African-Americans. There have been indications of a genetic effect; the current work follows that, and shows that African-Americans have a high incidence of certain specific mutations in a gene called APOL1, and that those mutations correlate well with the kidney diseases. So, the first important finding here is that they have uncovered an underlying genetic cause of these diseases.

Why does a group of people have a high incidence of a mutation that is obviously harmful? One would suggest that there must be some benefit of the mutation, which is helping to maintain it. And again, they have a clue, which they follow up: they show that blood plasma from people with the mutations lyses (breaks open) certain trypanosome parasites that are normally resistant to such lysis. Thus it seems that the mutations may protect against trypanosome diseases. That part needs further testing, though they certainly make a strong case for it.

The overall conclusion, then, is that certain mutations in the APOL1 gene are beneficial in protecting against certain diseases, and harmful in causing other diseases.

As a bonus, they suggest that the mutant trypanosome-lysing APOL1 protein may be useful in treating people with such infections. This has not yet been directly tested, I think. One would also expect that the information discovered here could be useful in genetic counseling.

News story: Genes May Explain High Rate of Kidney Disease in Blacks. (MedPage Today, July 19, 2010.) The final two paragraphs of this story present some limitations of the new work, and suggest how it may be pursued.

* A news story previewing the article upon posting online (prior to print): Genetics: Kidney Disease Is Parasite-Slaying Protein's Downside. (M Leslie, Science 329:263, July 16, 2010.)
* The article: Association of Trypanolytic ApoL1 Variants with Kidney Disease in African-Americans. (G Genovese et al, Science 329:841, August 13, 2010.)

A reminder that the general point here is one that is well understood... Sickle cell is the best known case: the sickle cell gene protects against malaria, but also leads to anemia. In areas of high malaria incidence, it is "good" on balance, but in areas where there is little or no malaria, it is "bad" on balance. We can talk about its good and bad aspects, but the gene itself can be either, depending on context. (Thalassemia genes behave similarly.) (When we say sickle cell gene, more precisely we mean the sickle cell allele -- the sickle cell form of the hemoglobin gene.) See
* Genes that protect against malaria (January 19, 2010).
* Sickle cell disease: a step toward treatment by activation of fetal hemoglobin (October 29, 2011).

Another mutation associated with a particular group of people: Alcohol consumption, an "ethnic" mutation, and a possible new drug (October 28, 2014).

Also see:
* Added July 1, 2016. WAK: Early clinical trial is encouraging (July 1, 2016).
* In humans, rare mutations are common (July 24, 2012).
* The good and bad of the immune system -- a sheep story (January 21, 2011).

More about trypanosomes: Chagas: the guinea pig connection (September 15, 2015).

Frequency-notched music: a treatment for tinnitus?

August 17, 2010

Tinnitus, commonly referred to as "ringing in the ears", is the perception of non-existent sounds, typically extended single tones. It is likely due to a mis-wiring in the auditory region of the brain, so that the brain reports sounds due to stimulation of an incorrect input.

New work reports a simple and pleasant treatment for tinnitus. Patients choose music, and it is modified to remove the frequency of their tinnitus. That is, the music is frequency-notched (or more simply, "notched"). Listening to such music, with the offending frequencies removed, leads to a reduced perception of tinnitus, and to correspondingly reduced activity in the offending auditory cortex.

How music was notched for treatment of tinnitus. Fig 1. The diagram shows how music was "notched" for the treatment of tinnitus. The x-axis is frequency of the sound; the arrow marks the offending frequency for the individual -- the tinnitus frequency. Briefly, an octave surrounding the main frequency of the tinnitus was removed from the music, by digital processing.

"Placebo" music was made by notching at "incorrect" frequencies.
Treatment results. Fig 3.
Results, showing perceived loudness of the tinnitus after treatment.

Results are shown for three groups of patients. The "Target" group listened to the notched music, as shown in the figure above. The "Placebo" group listened to incorrectly notched music. The "Monitoring" group received no treatment.

Let's look at one set of data... The left-most data is for the Target group after six months of treatment. Each x shows the result for one patient. Most values are negative, indicating a reduced loudness (which is good). The gray bar shows the average, which is almost -15%. The black line shows the confidence limits, which seem to be about 0 to -30%.

The best results were obtained with the Target group. At 12 months, all patients in that group showed some benefit. Note that the Placebo group, with incorrectly notched music, got worse.

News story: Notched Music Therapy May Diminish Tinnitus. (MedPage Today, 12/28/09.)

The article: Listening to tailor-made notched music reduces tinnitus loudness and tinnitus-related auditory cortex activity. (H Okamoto et al, PNAS 107:1207, 1/19/10.) The two figures above are Fig 1 and Fig 3 from this paper.

A recent Musings post about music: Why are musical instruments featured on the cover of EID? (June 7, 2010).

Joint Center for Artificial Photosynthesis (JCAP)

August 16, 2010

The Department of Energy (DOE) has announced a formal program to move artificial photosynthesis from lab chemistry towards commercial development. We have discussed some aspects of this work from time to time; the establishment of JCAP would seem to reflect a feeling that the current status of lab chemistry is good enough to make it worthwhile to begin to put together the pieces, and design an overall practical process. Time will tell; there will be hurdles, but it is good to see a start.

* The DOE announcement: California Team to Receive up to $122 Million for Energy Innovation Hub to Develop Method to Produce Fuels from Sunlight. (DOE, July 22, 2010.)
* An external news story: Fuel from the Sun -- The DOE funds a research center aimed at making artificial photosynthesis practical. (MIT Technology Review, July 27, 2010.)

The main purpose here is to simply note the announcement of this project. But let's briefly remind ourselves of what is involved. The sun is our primary energy source. One major way to capture the energy of the sun is by photosynthesis. The heart of modern photosynthesis is splitting water, which yields electrons, in the form of hydrogen atoms. Plants take the electrons (hydrogen atoms) and make reduced cofactors such as NADH; these are then used to fix carbon dioxide from the atmosphere. The initial reaction of splitting water is complex, but chemists have made progress toward making it work in the lab. How we should use the resulting flow of electrons is open for development.

If you'd like a bit more of the science at this point, check out the web page for project leader Nate Lewis.

Some previous posts on solar energy issues:
* Alternative energy for a sustainable future (May 7, 2009).
* Materials for solar cells (March 10, 2009).

Another project from Lewis was presented earlier: An electronic nose to monitor air quality on spacecraft (March 2, 2010).

More about artificial photosynthesis: An artificial forest with artificial trees (June 7, 2013).

There is more about energy on my page Internet Resources for Organic and Biochemistry under Energy resources. It includes a list of some related Musings posts.

Restoring sight by use of stem cells to regenerate a new cornea -- follow-up

August 16, 2010

Original post: Restoring sight by use of stem cells to regenerate a new cornea (July 13, 2010).

Nature has published a News and Views story on this work. (Most of their N&V are on articles in their own journal, but a few are on outside articles -- of special interest.) The work is an exciting development, and the quality of this story is really superb, so I thought it worth adding. I really encourage you to add this short item to your reading. In addition to listing it here, I have added it to the original post.
* Regenerative medicine: An eye to treating blindness. (E Ezhkova & E Fuchs, Nature 466:567, July 29, 2010.)

Rendezvous with Lutetia

August 14, 2010

Borislav writes (starting with a quotation) ...

"Space is big. You just won't believe how vastly, hugely, mind-bogglingly big it is. I mean, you may think it's a long way down the road to the chemist's, but that's just peanuts to space."
      - The quote is by Douglas Adams, best known by his Hitchhikers Guide to the Galaxy.

The introduction nicely puts in perspective that anything flying through the space would be doing it through a rather large, well, space. Last month, a probe that was designed and built by the European Space Agency (ESA) and named "Rosetta," returned some stunning images of a largish asteroid called Lutetia. Apart from the fact that getting a close-up image of anything so far in space is stunning, Rosetta returned an even more fascinating image of both Lutetia and "neighbouring" Saturn in the background.

Asteroid Lutetia, with Saturn in the background

Lutetia isn't that big, but is a decent asteroid! Dimensions of our space lady are 132 x 101 x 76 km. (That is, Lutetia is about the size of the state of Connecticut, or about half the size of Belgium.) Lutetia is in the main asteroid belt between Mars and Jupiter; its orbit is 2-3 times Earth's orbit. The craft was about 36,000 km away for this picture.

For comparison: Saturn is 100X more massive than our Earth and has about 10X larger diameter. The distance from the craft to Saturn is not stated, but it must be at least a billion (109) km -- the approximate distance between the orbits of Lutetia and Saturn (see below).

There is more. This was a planned encounter, and many pictures were taken. Rosetta space probe traveled at speed about 15 kilometers per second (34,000 miles per hour), so the time to photograph the asteroid was very short. Everything had to be carefully planned way ahead, so the rendezvous will be a success. When the probe was at its closest point to Lutetia, it was still over 3000 kilometers away. For more pictures and information, see the ESA site: Rosetta triumphs at asteroid Lutetia (ESA, July 10, 2010).

* * * * *

The picture has stimulated us to play with some numbers...

One of the striking features of the picture is how tiny yet distinctive Saturn is. We can estimate how big Saturn should appear...
* Saturn is about 1000 times larger than Lutetia (in diameter).
* We want to know how much further away Saturn is. As noted above, the craft was about 36,000 km from Lutetia for this picture. Unfortunately, we don't -- offhand -- know the distance to Saturn, though it is surely well known to ESA. As an estimate, the orbits are about a billion kilometers apart. The distance between the two bodies could be much more than that, depending on where they are in their orbits. But if we use a billion (109) km for our illustration, then Saturn is 109/36,000 = 28,000 times further away.
* If Saturn is 1000 times bigger and 28,000 times further away, then we would expect that its size in the image should be 1000/28000 = 1/28 as big.
* We estimate, using a ruler on the computer screen, that Saturn is about 1/20 the size of Lutetia in this figure. This is in reasonable agreement with the 1/28 prediction above. As noted, the prediction and measurement are both rough, but perhaps it is useful to show this calculation, for the idea.

A second calculation of some interest deals with the relative sizes of Saturn and Earth. The statement above that "Saturn is 100X more massive than our Earth and has about 10X larger diameter" reminds us of an interesting point. The volume of a sphere increases with the cube of the diameter. Thus a sphere with 10X larger diameter has 103X = 1000X larger volume. But only 100x larger mass? That implies that it has a low density: that Saturn has about 1/10 the density of Earth. Now, you know that Saturn is a gas giant, whereas Earth is a rocky planet, so perhaps this seems reasonable. In fact, Saturn has the lowest density of any of our planets: about 0.7 g/cm3; Saturn would float in water! (Uranus has the next lowest density, at 1.0 g/cm3. The density of Earth is a bit over 5 g/cm3.)

More about this Rosetta encounter with Lutetia: Lutetia: a primordial planetesimal? (February 13, 2012).

Rosetta's next adventure: Twins? A ducky? Spacecraft may soon be able to tell (August 4, 2014).

Previous asteroid posts include: Jupiter injured again! (June 11, 2010).

Uranus: The first report of a new planet (March 13, 2011).

More about peanuts... Can eating peanut protein reduce the incidence of peanut allergy? (March 3, 2015).

The kangaroo family tree: the American ancestry of kangaroos

August 13, 2010

Marsupials are a branch of mammals in which the developing fetus is born at an extremely immature stage, and then develops further within the protected environment of a maternal pouch. The best known marsupials are the kangaroos and opossums. The former are common in Australia, the latter in the Americas.

The family tree of the marsupials has been unclear. How are American marsupials and Australian marsupials related? Now, we must note that getting from South America to Australia was not as hard back in the days of the development of marsupials as it is now; these two modern continents were then both part of the supercontinent Gondwana.

A new paper claims progress in sorting this out. Their methods are interesting, and in some ways typical of how one tries to sort out family trees.

The basic approach is to find differences between the organisms being studied, and then work out the simplest relationship that accounts for the differences. To illustrate... Consider two traits, A and B. If we find that primitive animals had neither and modern animals have both A and B, then the question is which came first. If we examine many organisms, and find that many have A alone (without B), but that none have B alone (without A), then it follows that the simplest pathway to explain the data is that A was acquired first, then B. The logic is fine, but in the real world there are many possible complications -- and often a shortage of data. So, we take the pathway that is simplest (most parsimonious) as a tentative hypothesis for what happened.

In the new work, they use the presence of transposons as the traits. Transposons, sometimes referred to as jumping genes, are somewhat similar to a type of virus that can insert into the genome. An important feature of these transposons is that the insertion event is essentially irreversible. Thus the trait is more stable than most traits commonly studied. So, much of their analysis is based on looking at transposons in marsupial genomes. A special trick is to look for a case where one transposon is within another one. Obviously, the outer one must have come first, with the inner one being inserted into it.

Their results are summarized in the following figure, which is Figure 2 of the paper: Phylogenetic tree of marsupials derived from retroposon data [link opens in new window]. You can see that the upper three groups (orders) of marsupials -- the oldest groups -- are South American (shown in gray), while the lower four -- the youngest groups -- are Australian (shown in black). Thus it seems, from this data set, that all Australian marsupials are derived from the American marsupials. (The figure also shows a feature that makes the paper itself hard to follow: the animals are referred to mainly by their formal Latin names, which are not familiar to most of us.)

News story: Australia's marsupials 'have American roots'. (BBC, July 27, 2010.)

* News story accompanying the article, freely available: Jumping Genes Reveal Kangaroos' Origins. (M Inman, PLoS Biology 8(7):e1000437, July 27, 2010.)
* The article, freely available: Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions. (M A Nilsson et al, PLoS Biology 8(7):e1000436, July 27, 2010.)

More about kangaroos: An animal that walks on five legs (February 3, 2015).

For another post on marsupials: The devil has cancer -- and it is contagious (June 6, 2011).

Added May 2, 2016. More about maternal care: The earliest known example of maternal care? (May 2, 2016).

August 11, 2010

Dengue fever -- Two strikes and you're out

August 10, 2010

Dengue fever (DF) is a viral disease with an unusual feature: it tends to kill people the second time they get it.

Think about the implications for a vaccine. A traditional vaccine gives you something like a mild first case, to protect you from a full-blown case. That's how our immune system is supposed to work: the first exposure primes the immune system to respond better the second time. But if what we said above for DF is really true, the mild first case sets you up for a worse second case. We might worry, then, that a DF vaccine would set us up to all die from any subsequent DF case. That's not what a vaccine is supposed to do.

So, what do we have now? A new report examines the response of our immune system to the DF virus in some detail. They think they have found specific antibodies that are causing the problem. DF induces these antibodies, but they are not good at inhibiting (neutralizing) the virus; in fact they seem to help the virus! If this holds up, it would provide some guidance on designing a vaccine. The vaccine must be designed so that it induces only good antibodies, not bad ones.

News story: New Understanding of Dengue Fever Could Help With Vaccine. (Science Daily, May 10, 2010.)

The article: Cross-Reacting Antibodies Enhance Dengue Virus Infection in Humans. (W Dejnirattisai et al, Science 328:745, May 7, 2010.)

Breaking news... As I was finishing up this item, I got a press release from the US National Institutes of Health (NIH) that they are starting a clinical trial of a dengue vaccine. Human clinical trial of NIH-developed dengue vaccine begins. (NIH, August 9, 2010.) Some points to note...
* The issue of second infection; the approach here is to make the vaccine broad enough to cover all major strains.
* Relevance to the US. (DF is not well known in the US, but it is a major disease on the world scene, and its range is expanding.)
* The current status: They are starting a Phase 1 trial -- the most preliminary testing. There is little point of trying to anticipate the chances of success.

Some related posts...
* Added May 7, 2016. A Zika-dengue connection: Might prior infection with dengue make a Zika infection worse? (May 7, 2016).
* Dengue vaccine follow-up: Phase 3 trial (September 15, 2014).
* A new type of dengue virus (October 27, 2013).
* A dengue vaccine trial (December 1, 2012).
* Dengue fever: an overview (February 28, 2011). Good readable overview of dengue fever.
* The good and bad of the immune system -- a sheep story (January 21, 2011). A study of a natural isolated population of sheep.
* Why are HIV-infected people more susceptible to Salmonella infection? (May 21, 2010). Another example of the immune system causing a problem.
* Using genetically engineered mosquitoes in the real world (October 18, 2010). An announcement of a test to be done.
* Science: Love songs (March 26, 2009).

A shoe

August 9, 2010

Size 7. (Women's; US system.)


5500 years old.

News story: This Shoe Had Prada Beat by 5,500 Years. (New York Times, June 9, 2010.)

The article, which is freely available: First Direct Evidence of Chalcolithic Footwear from the Near Eastern Highlands. (R Pinhasi et al, PLoS ONE 5(6):e10984, June 9, 2010.) (Chalcolithic? Refers to the "Copper Age", or early Bronze Age.)

An old shoe

The picture is from the New York Times story listed above. A similar picture, with other views, is in the article (Figure 1).

This is something of a fun item. But I do encourage you to look over the article. Much is quite readable. You'll learn some things about shoes -- and feet -- as well as a bit about archeology.

The paper discusses some foot pathologies with and without shoes; therefore, the following prior post seems relevant: Should you run barefoot? (Feb 22, 2010).

More about feet: What else are feet good for? (August 8, 2011).

Global warming, boric acid, and a noisier ocean

August 9, 2010

Are those really connected? Maybe. It's really the carbon dioxide, CO2, that starts the story. Increased CO2 in the atmosphere warms the planet, but also leads to more CO2 dissolving in the ocean, which lowers the pH (makes the ocean more acidic). That changes the form of the boric acid, H3BO3, in the ocean -- to a form that absorbs sounds less, thus leading to a noisier ocean. Magnesium sulfate, MgSO4, is another chemical that is important in this effect.

The work reported here is entirely modeling of what might be expected. It is based on what is known about the properties of the various chemicals. It remains to be seen whether the effects they predict can be measured. What is important for now is that they put the topic of possible effects of CO2 increases on sound transmission "on the radar screen". Ocean sound has already been the subject of controversy, due to the testing of underwater sonar by the US Navy.

News stories:
* Rise in Human-Made Carbon Dioxide Affects Ocean Acoustics. (Science Daily, Dec 23, 2009.)
* Amplifying with acid -- More carbon dioxide in the atmosphere means a noisier ocean. (American Scientist 98:121, March 2010.)

* Future ocean increasingly transparent to low-frequency sound owing to carbon dioxide emissions. (T Ilyina et al, Nature Geoscience 3:18, Jan 2010.) A pdf of full article. This is the current article that is the basis of the news stories.
* Unanticipated consequences of ocean acidification: A noisier ocean at lower pH. (K C Hester et al, Geophysical Research Letters 35:L19601, Oct 1, 2008.) A recent related article (partly) from the same people. Check Google Scholar for a copy from the authors.

Previous posts on global warming and the oceans:
* The effect of defecation by whales on global warming (Aug 2, 2010).
* Increased CO2: effect on animals that make carbonate skeletons (Jan 11, 2010).

More about ocean noise: Effect of simulated sonar on whale behavior (March 16, 2014).

Nanorobots: Getting DNA to walk and to carry cargo

August 7, 2010

Ah, once again, the fascination of robots. Now, combine that with the fascination of DNA. A key property of DNA is that the two strands are complementary; thus a single DNA strand will find a specific other DNA strand: its complement. It's easy enough to make DNA in the lab. By a wise choice of DNA strands, one can make complex structures based simply on each strand finding its complement.

Here we have two new papers that advance the field of DNA technologies. They present DNA-based structures that can move in defined ways, by an extension of the same ideas. Further, these DNA-based robots can pick up cargo -- tagged with appropriate complementary DNA strands.

Gu, Fig 1, part vi Here is a brief description of what they did in article #1 (listed below), from their Figure 1.

It's complicated -- and I'm only showing less than 1/3 of the full figure. So let's go slowly.
Gu, Fig 1, part vi

The two frames at the left are diagrams, showing the plan; the two at the right are "photographs" showing what actually happened.

The two frames at the top are for the initial state (i); the two at the bottom are for the final state (vi). As you might guess, the full figure shows four intermediates along the way (actually more!).

So, let's start with the upper left frame: a diagram of the initial state (i)...
* The border outlines a "workbench".
* The red thing, at the left front, is a DNA molecule -- a DNA "walker". Among other properties, it can bind to three sets of "pegs" on the workbench. In this frame, it is bound to the left-hand set of pegs, but you can also see the two other sets of pegs.
* Above the red DNA and its pegs are three colored blocks, each labeled JX2.
* Attached to each of those JX2 blocks is a "cargo", shown as a greenish dot and labeled C1, C2, C3. The cargoes, each consisting of specific types of gold nanoparticles, are distinct.

Now, the upper right frame: a "photograph" of the initial state. It was taken by atomic force microscopy (AFM). What is detected is the workbench and the three cargoes. You can see that the three cargoes are at distinct positions, and are at the top of the workbench -- all as expected from the diagram to the left. (The scale bar is 50 nanometers. Remember that individual atoms are considerably smaller than 1 nm; a DNA double helix is about 2 nm across.)

Lower left: a diagram of the final state (vi). The DNA walker is now on the right-hand set of pegs. And all three cargoes are attached to the DNA walker.

Lower right: a photo of that same final state. Remember, the AFM is detecting only the workbench and the three cargoes. The cargoes are all together, at the front right -- just as in the diagram to the left.

So, what happened? Well, the DNA walker walked across the workbench, from the left set of pegs to the right set of pegs. And along the way, it picked up three cargoes. It did all this on its own, simply due to the properties of the DNA molecules -- which strands were complementary to which other strands. Thus the DNA has acted as a machine -- a nano (or molecular) machine.

Well, this item is already longer than my "limit", so I won't try to explain more. As usual, the point is to introduce one aspect of the work. In this case, that is making a DNA machine. It's complicated, as the discussion above shows -- but it does work. The news stories listed below will give you a broader picture of the work in these two papers, at two different levels. Most people will probably not want to tackle the paper themselves, which are rather difficult reading. That's fine. I provide papers so you know there is full documentation of what we present.

News story: Molecular robots on nano-assembly lines. (Chemistry World, Royal Society of Chemistry, May 12, 2010.)

* News story accompanying the articles: Nanotechnology: Molecular robots on the move. (L M Smith, Nature 465:167, May 13, 2010.)
* Article #1: A proximity-based programmable DNA nanoscale assembly line. (H Gu et al, Nature 465:202, May 13, 2010.)
* Article #2: Molecular robots guided by prescriptive landscapes. (K Lund et al, Nature 465:206, May 13, 2010.)

#1 is from Nadrian Seeman's group, at NYU. Seeman was co-winner of the 2010 Kavli prize for Nanoscience, along with Don Eigler. The award was introduced in the post The 35 most famous Xenon atoms (June 29, 2010), which discussed some work of Eigler's. That post also links to other information on atomic force microscopy.

Previous Musings item on robots: Folding towels (April 10, 2010).

Other posts on "DNA technologies":
* Making big "molecules" from big "atoms" (December 7, 2012).
* The nano-alphabet (June 29, 2012).
* What is it? (May 25, 2011).

More about Seeman: Profile: Nadrian Seeman (September 25, 2011).

Another post with an application of AFM: Graphene bubbles: tiny adjustable lenses? (January 15, 2012).

For more on AFM, see a section of my page of Internet Resources for Introductory Chemistry: Atomic force microscopy and electron microscopy (AFM, EM). Some of the links are to galleries of AFM images. It also includes a list of other Musings posts on AFM.

Added August 26, 2016. More molecular robots: Why air may inhibit the performance of small cars (August 26, 2016).

Graphene by the roll -- and soon in your living room: Update

August 6, 2010

Original post: Graphene by the roll -- and soon in your living room (July 31, 2010).

I have replaced the pre-publication version of the article with the official published version. More importantly, perhaps, I have added the "News and Views" story that accompanied the article in the journal. It is excellent! If graphene or touchscreens is of interest, have a look at this news story.

Can giraffes swim?

August 6, 2010


Surprise. Apparently it is "well-known" that they don't swim. But it was also "well-known" that camels and pigs don't swim -- and they really do.

The giraffe used in this study is shown at the right. Top, side, and front views. This is from Figure 1 of the paper. A horse was used as a control -- an animal known to be able to swim. If you want to see the horse, check out the paper; the horse is also shown in that Figure 1 (part a). They seem not to have used any negative control.
The giraffe

News story: Portsmouth expert proves giraffes can swim -- A Portsmouth academic has used mathematics and computer modelling to prove that giraffes can swim. (BBC, June 3, 2010.) A nice overview of what they did and what they learned; it even notes why the issue came up. It has some nice pictures of giraffes. Real giraffes. But no water.

The article, via abstract at PubMed: Predicting the buoyancy, equilibrium and potential swimming ability of giraffes by computational analysis. (D M Henderson & D Naish, Journal of Theoretical Biology 265:151, July 21, 2010.)

If anyone has any hard facts on the matter, please let me know. Have you ever seen a giraffe swim? If you have a facility (a swimming pool?) you would allow to be used for a proper test, let me know.

Added May 27, 2016. More about giraffes: Genetics of the giraffe neck (May 27, 2016).

More about camels: Cloning: camel -- update (June 11, 2012).

More about horses: Leopard horses (December 2, 2011).

More about swimming:
Why don't penguins fly? (August 24, 2013).
How bacteria swim and why -- a physics view (October 2, 2009).

August 4, 2010

Cometnapping in the stellar nursery

August 4, 2010

The Sun has been accused of stealing comets. From its siblings.

The Oort cloud is an outer region of our solar system, containing comets. It has generally been presumed that these comets were formed in the same basic condensation process that produced the rest of the solar system. However, the accumulating data is making this seem unlikely.

So we now have a new model being presented: that our Sun captured these comets from other stars, under the relatively crowded conditions of the stellar nursery, where many star systems were being formed. To test their suggestion, they do computer modeling -- and they present a few movies along with their article.

I encourage you to at least look at Movies 2 and 3. They are available from the link for the article, below. Choose Supporting Online Material. This leads to a page that lists the movies, and gives some information about them. Briefly...
* Movie 2. Watch the relationship between the (big) red star and the many (small) blue comets. Note that seven million years of action is compressed into 14 seconds of video.
* Movie 3. I suggest you start by focusing on the right hand frame of this. The two frames show the same action, but the view is different. The left hand view is the ordinary view: you are looking at a region of space. But in the right hand view, the position of the big red star is fixed, so you can see all the action -- the same action -- as it relates to that star.

Distances are given in astronomical units (AU). One AU is the average distance between Earth and Sun; it is about 1.5x108 km.

News story: Most comets may have extrasolar origin. (BBC, June 11, 2010.)

The article: Capture of the Sun's Oort Cloud from Stars in Its Birth Cluster. (H F Levison et al, Science 329:187, July 9, 2010.) For the movies, click on Supporting Online Material; access to this is open, regardless of your access to the article.

Remember, they are presenting an idea, and are presenting only computer modeling to support it. What you see in the movies is a simulation of what they think might have happened. They have no evidence for it. But it is now "on the table", and can be evaluated by the scientific community, along with alternative models.

Another possible consequence of complex gravitational interactions is that, in some cases, a planet might be ejected from its solar system, and be left to wander through space unbound to any star. Is it possible that life could exist on such an unbound planet? See... Steppenwolf: Life on a planet that does not have a sun? (July 2, 2011).

Added October 3, 2016. More about orbit complexities: Who is perturbing the orbit of Halley's comet? (October 3, 2016).

More about comets. What has six tails -- and is beyond Mars? (November 20, 2013).

Also see: Observing the birth of quadruplets (March 29, 2015).

Language: What do we learn from other animals?

August 3, 2010

Language is a trait that at first seems distinctly human. Yet we increasingly recognize that other animals show some aspects of communication, though certainly not full-blown "language". What does human language build on? What is really uniquely human? What is the role of gestural language -- in humans and in other animals? None of this is clear, but it is the subject of much work -- and debate. The article here is based on a recent meeting (April 2010), and gives a nice overview of some of the ideas, including some of the controversies.

Evolution of language: Animal Communication Helps Reveal Roots of Language. (M Balter, Science 328:969, May 21, 2010.) The picture at the start is cute!

Also see...
* Mountains and human language? (June 28, 2013).
* Can French baboons learn to read English? (May 13, 2012).
* Are some languages spoken faster than others? (November 21, 2011).

The effect of defecation by whales on global warming

August 2, 2010

You see the connection? Well, let's focus a bit... We are talking about deep-diving whales, such as sperm whales, which feed at considerable depth. And we are talking about the Southern ocean.

The story is really about the effect of the whales on the level of CO2 in the atmosphere; increased CO2 leads to global warming. The simple story is that photosynthetic organisms, such as plants and some microbes (algae and some bacteria), remove CO2 from the atmosphere; some of the removed CO2 ends up sinking (to the ocean bottom), thus leading to a long-term loss of CO2 from the atmosphere. In contrast, animals respire, and thus add CO2 to the atmosphere. Whales are animals. They respire. And therefore they add CO2 to the atmosphere. Yes, but ...

What is shown in the new work is that whales can also stimulate photosynthesis -- at least under certain circumstances. There are two key points, both noted above when I added some "focus" in the introductory statement for this item.
* First, this is about the ocean in the southern hemisphere. In much of this region, primary productivity (i.e., photosynthesis) is limited by low levels of iron in the ocean. It has been directly demonstrated that adding soluble iron in that region stimulates primary productivity.
* Second, whales -- deep-diving whales -- manage to add iron to the ocean. More precisely, that add iron to the region of the ocean where photosynthesis occurs. They feed at considerable depth, below where there is enough light for photosynthesis, and they feed on iron-rich prey. The whales then defecate near the surface (in the "photic" zone) -- and discharge most of that iron, in a useful form. That is, the whales serve to fertilize the upper levels of the ocean, by cycling a nutrient that is limiting for photosynthesis.

They estimate that the amount of photosynthesis a whale stimulates by bringing iron to the surface is twice what it respires; thus, on balance, it seems that the whales actually serve to remove CO2 from the atmosphere. The logic seems good, and it is an interesting story. It's not so clear how good their numbers are; some seem just rough estimates based on other types of work. So, enjoy the story, and take their message as an interesting hypothesis. It does serve to illustrate how complex the real world is.

News story: Pooping for the Planet -- Sperm whale feces triggers carbon removal from atmosphere. (Conservation Magazine, 6/10.)

The article: Iron defecation by sperm whales stimulates carbon export in the Southern Ocean. (T J Lavery et al, Proc. R. Soc. B 277:3527, November 22, 2010.)

The story of the iron limitation in the Southern ocean has been around for a while. As noted above, some testing has shown that adding iron to the ocean stimulates photosynthesis. There have been commercial proposals to do this on a large scale to combat global warming. However, scientists have been very reluctant to endorse such ventures, without much more consideration of the overall and long term consequences.

* * * * *

Other posts on global warming, oceans, and whales...
* Fertilizing the ocean may lead to reducing atmospheric CO2 (August 24, 2012).
* Tracking new songs as they cross the Pacific (June 21, 2011).
* Global warming, boric acid, and a noisier ocean (August 9, 2010).
* Increased CO2: effect on animals that make carbonate skeletons (January 11, 2010).

More feces: What can we learn by looking at the DNA in vampire bat feces? (May 27, 2015).

Playing music can make you sick

July 31, 2010

It's really quite funny -- but also a serious story. (The victim seems to have survived fine in this case.)

Just go look at the article, which is freely available: Gastrointestinal Anthrax after an Animal-Hide Drumming Event --- New Hampshire and Massachusetts, 2009. (L Mayo et al, Morbidity and Mortality Weekly Report 59:872, July 23, 2010.)
The drums

The link is to a web page containing the complete article, plus an "Editorial Note" that discusses the report. Casual readers may just want to read the first paragraph. But those who enjoy microbiology may find it worthwhile to read through. If the main report gets too detailed, skip down to the Editorial Note, which is very readable, putting the incident in perspective.

The figure above is reduced from the figure in the article, near the bottom of the page. There seems to be no pdf form of the article per se, but you can download a pdf of the entire issue.

Added September 13, 2016. Also see: Death by bagpipe (September 13, 2016).

Other posts on drumming... Drumming affects caste development (March 21, 2011).

There is more about anthrax on my page for Biotechnology in the News (BITN), under Anthrax.

More about animal skins: What can we learn from reading (the DNA from) old parchments? (January 30, 2015).

There is more about music on my page Internet resources: Miscellaneous in the section Art & Music. It includes a list of related Musings posts.

Graphene by the roll -- and soon in your living room

July 31, 2010

Graphene is a chemical that has fascinated scientists and engineers ever since it was first made, at least in the modern context, in 2004. It fascinates scientists simply by its structure -- sheets, as large as you can imagine, but only one atom thick. (A piece of graphene the size of a football field would weigh about 2 grams -- about the weight of a dime, the smallest US coin.) It fascinates engineers with its remarkable electrical, optical, and mechanical properties.

Information on graphene has accumulated rapidly, in large part because of another of its fascinating properties: it is easy to make -- almost child's play. Just take a chunk of common graphite, and some ordinary household adhesive tape (what we often call Scotch tape). Press the tape onto the surface of the graphite; gently peel it off. Graphite consists of layer upon layer of carbon-ring structures. A single such layer comes off onto the tape; that single layer of graphite, one atom thick, is what we call graphene.

So simple to make. But that is the catch. It is simple to make small amounts of graphene -- say, the size of your thumbnail. Enough for lab work. But making large amounts of graphene, for real industrial use, has been a barrier. Here is one approach.

Making graphene by the roll: a flow chart A flow chart showing the process for making graphene by the roll.

The graphene is deposited onto a copper foil; this is standard technology. What is new here is the subsequent series of transfer steps, which are practical even with large sheets of graphene.

This figure is from the news story listed below. It is similar to Figure 1 of the paper.

There is a movie showing use of the material as a touchscreen -- on a Samsung notebook computer. Samsung is one of the affiliated institutions for the paper -- so we know that this work is in the hands of an appropriate industrial partner. Thus the suggestion that this product will be on the market, as an improved touchscreen material, within a couple years is credible. We'll see. The movie is available from the news story, and is also available as "Supplementary information" at the article web site.

News story: Large sheets of graphene film produced for transparent electrodes (w/ Video). (PhysOrg, June 21, 2010.)

* News story accompanying the article: Nanomaterials: Graphene rolls off the press. (Y P Chen & Q Yu, Nature Nanotechnology 5:559, August 2010.) Excellent.
* The article: Roll-to-roll production of 30-inch graphene films for transparent electrodes. (S Bae et al, Nature Nanotechnology 5:574, August 2010.)

Here is a background article, from last Fall. It may serve as a useful introduction to graphene. Selling graphene by the ton. (M Segal, Nature Nanotechnology 4:612, 10/09.) A news feature, on the current status of graphene. It's not very technical, though it does introduce key properties, some methods for making it, and some of the applications being developed. (One of you sent me this -- I think. Whoever it was, thanks!)

A previous post on a lab use of graphene illustrates some of its properties: Image of a carbon atom that isn't there (August 17, 2008).

More on graphene: Graphene bubbles: tiny adjustable lenses? (January 15, 2012).

Another example of using the dime as a reference point for weight... A microscope small enough that a mouse can wear it on its head (November 12, 2011).

Your gut bacteria: where do you get them?

July 30, 2010

We have noted the importance of bacteria, especially the gut bacteria, for the human body. So, where do they come from? In particular, does it matter whether birth occurs vaginally or by Cesarean section (C-section)?

The emerging answer is that baby's first bacteria come from some combination of mother and the environment, and that the mode of birth does matter. The work noted here makes a useful contribution to this story.

The basic idea here is that they analyze the types of bacteria found at various body locations in the mother, then do the same for the babies. The set of babies includes some that were born vaginally and some that were born by C-section.

A general point of some interest... It is well known that we have different bacterial communities in different parts of our body (e.g., gut vs skin). In this work they find that is not true for the newborns; they seem to have about the same bacterial communities at all locations sampled. This is reasonable if the babies have just acquired their microbes during birth, and there has been no time for local colonization to occur.

The key finding is that the bacteria from the newborn do depend on the mode of birth. For vaginal-birth babies, their bacteria are similar to those of the mother's vagina. For C-section babies, their bacteria are similar to those of the mother's skin.

Figure 1A: patterns of bacterial communities from mothers and babies Here is a visual representation to show that pattern. I caution that it is not easy to explain how the plot was made.

Each point is a statistical summary of one particular bacterial community -- from a mother or a baby. The color coding is shown at the upper right.

An example... Dark blue points represent bacterial communities from mothers' skin. Light blue points represent bacterial communities from babies born by C-section. You can see that that these two groups of points tend to cluster together -- and are different from the other clusters of points.

This is from Figure 1A of the paper.

That analysis can be refined, by comparing the bacteria from specific individuals. For vaginal-birth babies, their bacteria are similar to those from their own mother's vagina -- not just to the general collection of vaginal bacteria. But for C-section babies, they find the opposite: their bacteria are not specifically similar to those on their own mother's skin. It is, therefore, possible that C-section babies are getting their initial inoculation of bacteria from the general environment, not simply mother's skin. This has implications for the importance of the C-section environment, and also perhaps for the possibility of artificial inoculation.

News story: Baby's Beneficial Bacteria Depend on Birth. (Peaceful Parenting, June 23, 2010; reprinted from Science News.)

The article: Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. (M G Dominguez-Bello et al, PNAS 107:11971, 6/29/10.)

More on gut bacteria:
* Antibiotics and obesity: Is there a causal connection? (October 15, 2012).
* Obesity, gut bacteria, and the immune system (May 24, 2010).

For a broader perspective on sharing our microbiota: Sharing microbes within the family: kids and dogs (May 14, 2013).

Book. The following book is listed on my page of Books: Suggestions for general science reading. Blaser, Missing Microbes -- How the overuse of antibiotics is fueling our modern plagues (2014). The author of the book is the husband of the lead author of the article featured here. The book is more broadly about the implications of our changing microbiota. Recommended!

July 28, 2010

Africa is falling apart

July 27, 2010

A spectacular story -- both in terms of what actually happened, and in what they predict will happen.

Although the story is spectacular, it is now mainstream. But it is only within the last half century or so that we have had much understanding of how continents and oceans form.

What happened? In 2005, a 20-foot wide rift opened up, over a 35 mile long stretch, largely in Ethiopia, in the Horn of Africa. It happened rather suddenly -- over a few days.

Rift, 2005 event, Horn of Africa

Analysis of the event makes it fairly clear that it happened because of underground volcanic activity, and that the event is very similar to what we understand goes on routinely at mid-ocean rifts.

The future? With that background, it is easy enough to predict... The process will continue. The rift region is below sea level; there is a fairly small strip of land that prevents water flowing in. At some point, that natural wall will itself be broken by the spreading -- and Africa will split in two. A new "continent" will form -- and "float" away. (It will be fairly small -- Somalia and much of Ethiopia -- so they call it an island rather than continent.) In between will be a new body of water -- a new ocean.

I first heard about this story on the BBC radio news: Africa 'witnessing birth of a new ocean'. (BBC, 6/25/10.) The immediate stimulus for the news coverage was a presentation of the work in London. I was able to trace the work back, and find the paper and accompanying story, from late last year and listed below. (The picture above is from this site.)

A news story from the time of the paper: African Desert Rift Confirmed As New Ocean In The Making. (Science Daily, 11/3/09.)

The paper: September 2005 mega-dike emplacement in the Manda-Harraro nascent oceanic rift (Afar depression). (A Ayele et al, Geophysical Research Letters, 36:L20306, 10/20/09.)

More about rifting: How were the Gamburtsevs formed? (December 7, 2011).

More cracks: Using bacteria to promote self-healing (December 28, 2012).

A virus that is or is not associated with chronic fatigue syndrome -- an update

July 26, 2010

Original post: A virus that is or is not associated with chronic fatigue syndrome (Feb 12, 2010).

That original post offered new work suggesting that the virus XMRV is not associated with chronic fatigue syndrome (CFS). That contradicted earlier work showing that the virus is associated with the disease. The post discussed some possible reasons for the discrepancy, and suggested that further work would sort it all out.

We now have "further work" -- but no resolution. We have two papers, one on each side of the controversy. Interesting!

To make things a bit more interesting... Both of the new papers are from US government agencies. When this was noticed, both papers were put "on hold". One has since been published; the other is apparently getting further review. Is this suspicious, or just good -- if awkward -- science? I think we'll understand that better later, when more information is available. The fun of science is in finding out new things, and sometimes that involves serious controversy.

News story: Delay in Release of Study on Chronic Fatigue Syndrome Prompts an Outcry. (New York Times, July 14, 2010.) It links to the new article, from the CDC, that was published recently; that article is freely available. The introductory Background section may be a useful overview for some people. Otherwise, unless you are very much into virology or have a special concern about the issue here, it may be best to just smile and enjoy the controversy. My comments in the earlier post still stand.

Hexaflexagon -- make one for yourself, to honor Martin Gardner

July 26, 2010

Martin Gardner died in May -- at age 95. Gardner was the long time "puzzle" columnist for Scientific American. More broadly, he promoted recreational mathematics to the general public for many decades. In fact, he submitted a column for one publication just a few days before his death.

What is a hexaflexagon, and what is the connection to Martin Gardner? Well, why don't we just say that a hexaflexagon is a toy. If you go beyond that idea -- if you find yourself trying to figure it out, that is up to you. Gardner did much to popularize the hexaflexagon, going back to the 1950s. The other name commonly associated with this toy is Richard Feynman, who was fascinated by it. So, this is a toy promoted by Gardner and Feynman. That should whet your appetite.

There are many web sites with information on flexagons. I'll list a couple here, but you can explore and find more. I do suggest that you start with a template, provided on some sites. Making a flexagon from scratch is a bit tedious. If you start with a template, you just fold and label -- and flex.
The Fabulous Flexagons. Includes templates.
Hexaflexagon Toolkit. Includes movies.

Martin Gardner obituary -- A pioneering science and maths writer, and populariser of ingenious puzzles and games. (Guardian, May 27, 2010.)

Gardner's autobiography, published in 2013, is listed in my page of Book Suggestions: Gardner, Undiluted Hocus-Pocus -- The Autobiography of Martin Gardner.

A post from another good math writer: Pi (November 10, 2014).

There is more about math on my page Internet resources: Miscellaneous in the section Mathematics; statistics. It includes a listing of related Musings posts.

A better way to deliver a vaccine?

July 25, 2010

This was a big news story last week. The idea is to deliver a vaccine by use of a skin "patch" that carries tiny "needles". Applying the patch, with a little pressure, causes the needles to penetrate the skin, and deliver the vaccine into the skin. Delivery of drugs with patches is already a standard and accepted procedure. However, there is a difference here. Vaccine molecules are large. Simply applying them to the skin surface is not enough; you do need to inject them.

Interestingly, the vaccine is not delivered through the needles. The vaccine material is incorporated into the needles, which dissolve in the skin. The vaccine is liberated as the needles dissolve. (Perhaps it would be better to think of the needles as pins.)

Microneedles for vaccine delivery; dissolving over time. The figure shows part of a patch, at various times after being applied to (cadaver) pig skin.

Main points:
* You can see what the needles look like. They are about 0.6 millimeters (1/40 inch) long -- very tiny to the naked eye.
* You can see that they disappear (dissolve) within a few minutes.

This is part a of Figure 2 from the paper.

There are multiple advantages to this system -- if it really works.
* It is easy to administer. The patches are stable, and could even be mailed to people. You give yourself the vaccine, simply by applying the patch.
* It is almost painless. The needles are so small that one does not feel them -- even though there are 100 of them.
* There is no problem of needle disposal, since the needles dissolve.

What have they actually done? They have worked out a way to make the patches, and studied how they work when applied to pig skin (very similar to human skin). Then they did extensive testing using the patches to vaccinate mice; this work shows that the patches are at least as good as the traditional method for delivering vaccines. They have not yet done testing with humans, but they seem to be at that stage. That's a slow careful process, of course, so it will be a while before this is ready for the real world.

News story: New Flu Vaccines Made Into Patches with "Microneedles". (Daily Tech, July 19, 2010.)

The article: Dissolving polymer microneedle patches for influenza vaccination. (S P Sullivan et al, Nature Medicine 16:915, August 2010.) A very readable paper. If you are interested in the biology of the immune response, you may want to look through the paper. Remember, the work here is with mice; we learn how humans respond to a procedure by testing with humans.

Another approach to vaccines without needles: Aerospace engineers develop explosive device for supersonic delivery of vaccines (August 2, 2011).

More on vaccine development: Silk: Stabilizing vaccines and drugs (July 29, 2012).

Silk-clothed electronic devices that disappear when you are done with them (October 19, 2012). Another problem for which "dissolve it" may a good answer.

More on medical use of microneedles: A smart insulin patch that rapidly responds to glucose level (October 26, 2015).

More on needles: How porcupine quills work (January 5, 2013).

More on vaccines is on my page Biotechnology in the News (BITN) -- Other topics under Vaccines (general).

Posts on flu and flu vaccines are listed on the page Musings: Influenza (Swine flu).

Vodka chemistry

July 23, 2010

One of you sent me an item about vodka, with the comment "Don't know if this is news to you, but the study linked to below seems to confirm what my Slavophile mouth has been telling me for many a year - there is a difference between vodkas." Now, I know nothing about vodka, beyond popular culture, but the work is not only some interesting chemistry, but also has some interesting historical aspects.

Vodka is made by a process that starts like that for other alcoholic beverages: fermentation of sugars to make alcohol. However, much purification is done, and the final product is generally considered to be simply alcohol plus water -- about 40% alcohol (by volume). Thus it follows that vodka is colorless and tasteless. Or is it? People claim they can tell the difference between vodka brands.

The new work is logically simple: they examine the structure of the liquid in detail. The problem is that liquid is the most difficult form of matter when it comes to studying structure: it involves interactions, but they change rapidly. Nevertheless, various methods allow one to look at the collection of interactions. Their major conclusion is that the liquid structure does vary among vodkas. In particular, they find that some ethanol molecules are inside "cages" of water molecules, and that this varies from one vodka to another.

The historical aspect is that studying the unusual structure of water-alcohol mixtures dates back to Dmitri Mendeleev, better known as a key developer of the periodic table. The introduction to the article discusses this, and generally gives a nice readable overview. (The news story also notes the work of Linus Pauling, though this seems not to be mentioned in the article. It may refer generally to Pauling's work on hydrogen bonding.)

There are some important things they do not do here. Let's note them, because the simple summary, such as in the news story headline, may be misleading.
* They do not show that the structural differences they observe are related to perceived "taste". (I put "taste" in quotes there because there is no assurance that the perception of differences between samples is mediated by the ordinary taste receptors.)
* They do not show why the structural differences occur. They suspect that minor impurities in the vodka are relevant.

Their suggestions make interesting hypotheses, which presumably can be tested in later work. For example, if they can show that adding certain chemicals to the samples results in certain structures, then they can do controlled taste testing and see if the structures -- or the added chemicals -- are responsible for the tastes. In the meantime, the work is an interesting step in understanding solutions involving water and alcohol.

The news story that was sent: Vodka's Tasty Secret Revealed in Special Chemistry. (Live Science, June 9, 2010.)

The article: Structurability: A Collective Measure of the Structural Differences in Vodkas. (N Hu et al, J Agric Food Chem 58:7394, June 23, 2010.) We should note that the work was supported, in part, by a company that makes vodka.

We have discussed "molecules in cages" -- sometimes called clathrates -- before. In particular, we have discussed methane hydrates, where molecules of methane (CH4, natural gas) are trapped in water cages. A recent post related this to the BP spill: BP oil spill incident: the methane hydrate crystals (May 18, 2010). That refers to earlier posts, including the possibility of harvesting natural gas from natural deposits of methane hydrates.

Added January 22, 2017. More molecular cages: Hydride-in-a-cage: the H25- ion (January 22, 2017).

Sleepy teenagers

July 23, 2010

I heard about the new work noted here on the BBC Radio news. The topic is one that has come up in various private discussions.

The work here is straightforward. A high school adjusted standard school time by starting school a half hour later. Testing showed improvement not only in sleep, but in various measures of mental health. After what was supposed to be a two month test, the school -- students and staff -- chose to stay with the new schedule.
Cartoon, sleepy student

This is consistent with other studies, and consistent with what we know about sleep physiology. Sleep is a biological necessity, even if we do not understand why. People vary in the natural sleep rhythm of their body. However, there is a general point that hormonal changes cause some predictable changes in natural sleep behavior in teens -- high school-age teens. Most people of that age have great trouble falling asleep early; getting up early is not natural for them.

News story: Delayed School Start Time Associated With Improvements in Adolescent Behaviors. (Science Daily, July 5, 2010.) (October 30, 2011: The story listed previously is no longer available.)

* Editorial accompanying the article: School Start Time and Sleepy Teens. (K Wahlstrom, Arch Pediatr Adolesc Med 164:676, 7/10.) This brief editorial puts the new work in some perspective. It notes the issue of whether the adjusted start time affects academic performance; the short answer is that it is not clear. It also addresses the barriers faced when trying to implement such a change.
* The article: Impact of Delaying School Start Time on Adolescent Sleep, Mood, and Behavior. (J A Owens et al, Arch Pediatr Adolesc Med 164:608, 7/10.)

The article is also accompanied by a one-page item labeled "Advice for patients". It summarizes some recommendations; it also links to other such pages of advice from the journal, and to other sleep resources, such as the Stanford Sleep Clinic. This item, and other such advice pages, seem to be freely available. New Information About Adolescent Sleep. (M A Moreno et al, Arch Pediatr Adolesc Med 164:684, 7/10.)

This is part of a larger topic of sleep biology and natural sleep patterns. There really are "morning people" and "night owls"; people vary in their natural sleep rhythms. There is work showing that working "graveyard" (night) shift is not good for most people. There is even speculation about whether the ready availability of artificial lighting may be bad for us, by allowing (encouraging?) us to not respect our natural biological rhythms. Jet lag is another manifestation of the issue of natural sleep rhythms; use of the hormone melatonin can help.

Societal function seems to impose some time requirements on us. But it really would be best if you listen to your own body rhythms and respect them as much as possible. And remember that other people may be different; let's try to minimize imposing our perception of a daily life cycle on others.

* * * * *

More on sleep and body rhythms:
* Added April 15, 2016. The genetics of being a "morning person"? (April 15, 2016).
* How caffeine interferes with sleep (December 11, 2015).
* Sleep and the brain drain (November 17, 2013).
* Does it matter what time of day you get a vaccine? (October 26, 2012). The effect of circadian rhythm on the immune system.
* Light-dark (day-night) cycles affect pregnancy (August 10, 2012). The effect of circadian rhythm on pregnancy.
* Does it matter when you eat? Or whether you leave a light on at night? (December 1, 2010).

Circadian rhythms in "lower" animals: Melatonin and circadian rhythms -- in ocean plankton (November 24, 2014).

July 21, 2010

Smart dust: A central nervous system for the earth

July 20, 2010

Thien sends: 'Smart dust' aims to monitor everything. (CNN, 5/3/10.)

The general theme is that technology is giving us smaller and smaller and cheaper and cheaper devices. We can thus imagine, at some point, being able to mass produce huge numbers of tiny sensors at negligible cost, spread them around, and measure "everything everywhere". Thus the idea of "smart dust".

As a dream, it has been around for a while. The reason it comes up now is that Hewlett Packard (HP) has announced an implementation, which, while small, is very much in the spirit of smart dust. While this specific application is small, HP's plans are not: they talk of building a "A central nervous system for the earth". The immediate plan is to implement a dense array of motion sensors over a small area being investigated by an oil company.

(MEMS = Microelectromechanical Systems. I've avoided the term so far, but ...)

More... (Skip around as you wish. The last * item is probably the most fun.)
* A Central Nervous System for Earth: HP's Ambitious Sensor Network. (New York Times, 11/18/09.)
* HP Enables Better, Faster Decision Making with Breakthrough Sensing Technology -- Ultrasensitive inertial MEMS accelerometers benefit applications such as bridge, infrastructure and seismic monitoring. (HP, 11/5/09.) An HP press release. It has useful information and links to other HP info.
* Shell and HP to Develop Ultrahigh-resolution Seismic Sensing Solution -- A leap forward in oil and gas exploration. (HP & Shell, 2/15/10.) Another press release.
* The original CNN item, above, attributes the idea of smart dust to Kris Pister, at UC Berkeley. Here is Pister's web page on the subject. It's an old page, perhaps of some historical interest for the early ideas. Smart dust: Autonomous sensing and communication in a cubic millimeter. (K Pister.)
* A news story on Pister's work from a UC Berkeley College of Engineering newsletter. It's fairly old, but has some delightful content. Recommended! Robugs: Smart Dust Has Legs. (D Pescovitz, Lab Notes, Sept 2003.)

Here is a recent scientific paper by the same people in the topic area. It is not directly on the current issue, but is an example of the work being done by HP and Stanford, along with others. A Method for Wafer-Scale Encapsulation of Large Lateral Deflection MEMS Devices. (A B Graham et al, Journal of Microelectromechanical Systems 19:28, 2/10.)

Also see:

Dust (February 19, 2011).

More from the same Berkeley department... A box that will fold up upon command -- heat- or light-actuated switches (September 3, 2011).

An application of MEMS accelerometers... The Quake-Catcher Network: Using your computer to detect earthquakes (October 14, 2011).

More microscale technology: Windmills for your cell phone? (January 21, 2014).

Mice with human brain cells (April 13, 2013).

Neglected tropical diseases: How should we approach them?

July 20, 2010

The journal PLoS Medicine published an exchange of views on the problem. The Scientist magazine published a nice overview of that exchange, as a news story. The topic may interest some of you -- and the underlying issues are perhaps of broader interest. I encourage you to have a look; it is all quite short -- and of course over-simplified.

News story: Neglected diseases: Teach or treat?. (The Scientist, May 18, 2010.)

The article: The PLoS Medicine Debate: Which New Approaches to Tackling Neglected Tropical Diseases Show Promise?. (J M Spiegel et al, PLoS Medicine 7:e1000255, May 18, 2010.) The various viewpoints, each with identified authorship, are all together under this one umbrella title. The article is freely available -- as with all articles from PLoS.

Boiled batteries

July 19, 2010

It is a common school experiment: insert two different metals into a fruit (or vegetable), and watch the current flow. The current comes from the chemical reaction involving the two metals; the fluids of the fruit provide electrolyte (ions) to conduct current between them.

A simple version of such a battery uses copper and zinc rods in a potato. New work shows that it works better if you boil the potato first. Why? It is probably simple: boiling breaks down the cells (especially the membranes), allowing better flow of the electrolyte.

Potato battery; Fig 1 Potato battery. The Figure shows the basic design. In this case, the potato battery is powering two white LEDs.
   Bigger picture [link opens in new window].

   This is reduced from Figure 1 of the paper listed below.

What makes this more than simply fun is that they argue that the boiled potato battery may be a practical alternative to common commercial batteries. There are applications that depend on batteries; these include providing low but useful levels of electricity to areas not connected to a modern electricity grid. They calculate that the cost of the boiled potato battery is several fold less than common D-cells; the main cost is the zinc, which is consumed by the reaction. They also calculate that lighting based on the system shown here is cheaper than using kerosene lamps.

News story: Boiled potatoes produce more juice. (Energy Research News, June 9, 2010.)

The article: Zn/Cu-vegetative batteries, bioelectrical characterizations, and primary cost analyses. (A Golberg et al, Journal of Renewable and Sustainable Energy 2:033103, June 7, 2010.)

More about potatoes... Tracking the pathogen of the Irish potato blight (June 25, 2013).

More about batteries...
* A battery for bacteria: How bacteria store electrons (May 2, 2015).
* Science: virus-battery (April 15, 2009).

There is more about energy on my page Internet Resources for Organic and Biochemistry under Energy resources. It includes a list of some related Musings posts.

* * * * *

Borislav noticed a draft of this item, and suggested the following additional site, which is worth it both for the picture and for the discussion: Spud; now archived. It also reminds me to note another advantage of the new proposed procedure: it prevents the batteries from sprouting.

The . song

July 18, 2010

The . song.

As a bit of background... There is a well known quote from the artist Paul Klee: "A line is a dot that has gone for a walk." Here, a group of science students have built on that, with both original and compiled contributions.

Thanks to Gunjan for the contribution.

More on song: Introducing Supersonus -- it stridulates at 150,000 Hz (June 16, 2014).

What does blue light smell like?

July 18, 2010

Some wiseacre out there is probably going to suggest that it smells like a banana. And those who have come across the new work discussed below will say that blue light smells like a banana, too -- because that is what they found. At least, that is what they found in some cases -- because that is how they designed the system.

What they did was, logically, very simple (though technically quite complex to carry out). They engineered fruit flies (Drosophila) so that their olfactory (odor) neurons had a receptor for blue light. When they shined blue light on the larvae, thus activating those particular neurons, the larvae crawled toward the light. That is not what normal larvae do; in fact, normal fly larvae crawl away from the light. But in these larvae, the light is acting like an odor -- an odor of food. The light activates a receptor. It is a light receptor, of course, but its neuron is a food-odor neuron.

When we see a light, the light activates visual receptors in our eyes; that sends a signal to the brain, and our brain says "light". That's nice. But it is important to understand the two-step process. If you get poked in the eye, in total darkness, your brain will report that you have seen light. Why? The poke activates your visual receptors, and the brain interprets signals from those receptors as light. The brain does not know whether you saw light; it only knows that the visual receptor was activated.

Another example... In previous work, scientists cross-wired taste receptors in mice, so that the "bitter" receptor was wired to the "sweet" neurons. These mice were attracted to bitter tastes -- since their brain said "sweet".

Some people have what appears to be cross-talk between the senses. For example, a person might see the letter A as inherently red. This is a fascinating topic, and not well understood; after all, we can not usually explore the neuron connections in live humans. The broad phenomenon is called synesthesia; the Wikipedia page is a reasonable -- and fairly lengthy -- introduction: Wikipedia: Synesthesia.

News story: Gene Causes Blue Light to Have a Banana Odor in Fruit Flies. (Science Daily, 5/26/10.)

The article, freely available at: Optogenetically induced olfactory stimulation in Drosophila larvae reveals the neuronal basis of odor-aversion behavior. (D Bellmann et al, Frontiers in Behavioral Neuroscience 4:27, 6/10.)

* * * * *

More about synesthesia:
* Can people learn to be synesthetic? (January 7, 2015).
* Synesthesia: the good side? (January 14, 2012).

Another example of studying the senses in fruit flies: A human protein that can sense magnetic fields (July 15, 2011).

More on the interrelationships of the senses: Connecting the senses (April 26, 2011).

More about bananas... Measuring radiation: The banana standard (April 17, 2011).

More about smelling:
* Added October 10, 2016. Copper ions in your nose: a key to smelling sulfur compounds (October 10, 2016).
* What happens if you block the left nostril of a mole's nose? (April 19, 2013).

More about flavor (taste + odor): How a cork causes an off-flavor in a beverage (October 21, 2013).

Are the corals listening to the shrimp?

July 16, 2010

Corals get a lot of attention. However, we often think of the coral reef, rather than the animal -- the coral -- that builds the reef. The coral, in its early stage as a larva, is a free-swimmer -- obviously an animal. Somehow, the coral larva settles down at some point, often on a pre-existing reef. How does a coral larva find a reef? Although there is some evidence for chemical attraction between reef and larva, that seems to be an insufficient explanation. New work raises the possibility that the coral may find a reef by sound.

Corals approach the sound. Their key result... The coral larvae were in a 1 meter long tube, with a sound source 1 meter from the right hand end. The sound source broadcast "reef sounds". The graph shows the number of corals at different regions along the tube. You can see that the corals tended to be at the right hand end of the tube -- closest to the sound source. (The picture may be a bit confusing. The sound source shown gives an idea what it looks like, but the position shown there is wrong. The sound source is over here in this text somewhere -- off to the right.)

This is Fig 2A from the paper.

In another part of the experiment, they showed that if the sound source was above the tube, the corals tended to collect at the upper surface of the tube, closest to the sound, even though corals usually tend to swim downward.

Let's be cautious in interpreting this. What they do show is that the coral larvae respond to sound. This opens up the possibility that the larvae use acoustics as one clue in finding a home. However, there are things they do not show here:
* They do not show that there is any specificity in the response. That is, can the coral tell Mozart from McCartney -- or reef shrimp from who knows what? Perhaps specificity is not required, but it seems something one would want to check.
* More importantly, they do not show that the response to sound plays any role in nature. This is going to be harder to test! They make it plausible, by showing that the corals can "hear", but that does not mean it is relevant in nature.
* Further, they do not show the mechanism of the response to sound. They suggest that it is mediated by cilia on the larval surface, and may be detecting particle movement rather than acoustic waves per se. Of course, clarification of the mechanism can come later.

News story: Study links coral growth to sound. (Los Angels Times, 5/20/10.)

The article, which is freely available: Coral Larvae Move toward Reef Sounds. (M J A Vermeij et al, PLoS ONE 5(5): e10660, 5/14/10.)

More about corals: File dates and human settlement in Polynesia (November 16, 2012).

Corals are in the same animal phylum as the jellyfish and sea aenmones: the cnidarians. Jellyfish eyes were discussed in the post How many eyes does it have? (March 12, 2010). (How do you pronounce cnidarians? The initial c is silent; it is like the initial k in knife.)

Added November 15, 2016. And something perhaps related to hearing in sea anemones... Restoring lost hearing: lessons from the sea anemone (November 15, 2016).

July 15, 2010


July 14, 2010

Volcano Picture of the Week -- Capturing the Power and Beauty of Volcanoes & Geothermal Areas.

This picture (at right), full size and with caption, is at VPOW: 2010 #25. As to the caption, I will note here only that the reddish large object, center right, is about the size of a car. This page does not link to anything else. Use their home page, below, for navigating the site.

Their home page, which defaults to the "current" picture: VPOW home page. Clicking on Archive is a good way to explore.
VPOW 2010 #25

For more on volcanoes and geothermal areas:
* Lakes that explode (10/13/09).
* What happened to the Neandertals? (October 8, 2010).
* Did life start in a geothermal pond? (February 28, 2012).
* Reasons to hide tonight? (February 11, 2013).

Restoring sight by use of stem cells to regenerate a new cornea

July 13, 2010

A spectacular result! Yet, one that is also a good lesson in how progress is often made in small logical steps.

The cornea is the outer layer of the eye. It serves as a protective layer, and also as an initial lens. One key property is simply that it is transparent. The cornea is maintained by growth from special cornea stem cells. If these stem cells are lost, the cornea is not properly "refreshed"; it can become opaque, causing loss of vision.

The basic story here involves patients who had severe corneal injuries, such as chemical burns from strong alkali, with resulting loss of vision due to the cornea becoming opaque. The rest of their visual system, including the retina and optic nerve, is ok. What is done is to find small reservoirs of cornea stem cells (perhaps in the other eye), "expand" them in lab culture (that is, grow more of them), and then transplant them into the bad eye. About 3/4 of the time, the transplants "take", and a new transparent cornea develops. Since the vision loss was due to the bad cornea blocking the light, successful transplants that lead to new corneas restore substantially normal vision. If the transplant seems ok after one year, it seems to last indefinitely; one patient has been followed for ten years.

Eye before and after.

A good feature of the method is that the donor stem cells are autologous -- the patient's own -- so it avoids issues of immunological rejection. A limitation is that the patient must have some stem cells; the method will not work if all corneal stem cells have been lost on both sides. Of course, other work on stem cells might lead to being able to make corneal stem cells from other cells. The post Do you need some new brain cells? (3/22/10) is an example of this type of work; the post discusses some of the options. But note an important difference between the work reported there and here. The current work reports real medicine; real people have benefited from the stem cell work reported here. It is simple, and has limitations -- but it works. Now. The previous post discusses approaches that are being developed.

News story: Stem Cells Return Sight to Burn-Damaged Eyes. (MedPage Today, 6/23/10.)

The article: Limbal Stem-Cell Therapy and Long-Term Corneal Regeneration. (P Rama et al, New England Journal of Medicine 363:147, 7/8/10.) The picture above, showing an example of the results, is from Figure 3B of the paper.

Thanks to Borislav for alerting me to this story.

* * * * *

Nature has also published a superb news story on this work. Recommended! Regenerative medicine: An eye to treating blindness. (E Ezhkova & E Fuchs, Nature 466:567, July 29, 2010.)

Also see: Therapy based on embryonic stem cells: the first clinical trial (October 23, 2010).

More on restoring sight:
* A camera-based device to restore vision (February 25, 2013).
* Connecting the senses (April 26, 2011).

There is more on stem cells on my page Biotechnology in the News (BITN) - Cloning and stem cells.

A bio-ethics controversy: HIV-TB interaction

July 13, 2010

Here is a short news story from Science, on an ethical debate. I encourage you to read it, and think about the implications. What is "the answer"?
AIDS research: Bioethicists Assail a Celebrated TB/HIV Treatment Trial. (J Cohen, Science 328:799, 5/14/10.)

As you think about this, I might suggest the following "guidelines"...
* For simplicity, accept what is written there as substantively factually correct. If you have specific concerns, ok. But obviously there is a lot of background behind this. It doesn't help much here to hide behind not knowing that background.
* Would it work to move away from trying to judge whether what people did in this case is "right" or "wrong" to focusing on how subsequent questions should be considered?
* Remember, if it weren't controversial, it probably wouldn't be worth discussing!

Some other posts on the complexity of HIV issues:
* Why are HIV-infected people more susceptible to Salmonella infection? (5/21/10).
* HIV vaccine trial -- and quibbling about statistics (11/2/09).

Other posts on TB include...
* How did tuberculosis get to the Americas? (January 24, 2015).
* Rats, bananas, and tuberculosis (March 11, 2011).

My page for Biotechnology in the News (BITN) -- Other topics includes sections on Ethical and social issues and HIV.

Can the Staph solve the Staph problem?

July 12, 2010

Staph infections are a serious medical problem. People can die from them. Here, "Staph" refers to Staphylococcus aureus bacteria. The emergence of methicillin resistant Staphylococcus aureus (MRSA) just makes it worse, because of the greater difficulty of treatment. So where do these Staph come from? How do they get started in your body? Is there anything we can do about it?

What's interesting is that Staph is rather common in us. About a third of people carry it -- in the nose, with no ill effect. Somehow, occasionally, Staph turns from residing peacefully in the nose to causing a serious problem.

Would keeping Staph aureus out of the nose reduce the chance of Staph illness? Perhaps. And how might we do that? Perhaps we should turn to its cousin, Staphylococcus epidermidis. This related bug also is commonly found in your nose, and seems quite harmless. Interestingly, some strains of Staph epidermidis (the harmless bug) seem to inhibit Staph aureus (the potential pathogen). New work suggests how it does that, and might lead to a useful treatment. (Note that we are now using the simple term "Staph" as shorthand for Staphylococcus, but also, alone, as a term for Staphylococcus aureus.)

The new work shows that those strains of Staph epidermidis that do inhibit Staph aureus make a particular enzyme: a protease (enzyme that degrades protein) known as Esp. What the enzyme does is to inhibit Staph aureus from making a biofilm; the protease can even break up existing biofilm. The biofilm is a collective structure of bacteria, with many many cells joined together -- and attached to the surface (your nose, in this case). The biofilm of Staph aureus is the form that allows the bug to maintain itself in the nose. How it gets from there, where it seems to have no ill effect, to occasionally causing disease is still unknown. But now we know its enemy, and even understand how it works. We can now consider using Staph epidermidis as a "probiotic" (a "good" bug), or even treating people with the enzyme. It's Staph vs Staph -- in your nose.

Biofilm disruption An example of their results; the figure is part c of Figure 1 of the paper.

In this experiment, they use biofilms of Staph aureus growing on petri dishes in the lab. After the biofilms are established, they add increasing amounts of the culture fluid from Staph epidermidis, and test how much biofilm remains after 6 hr The x-axis shows the amount of culture fluid added; the y-axis shows the amount of biofilm remaining.

The black and white bars are for two strains of Staph epidermidis. The results show that the black-bar strain disrupts pre-existing Staph aureus biofilms, whereas the white-bar strain has no effect.

In another experiment, they showed that swabbing the black-bar strain into the noses of people with Staph aureus reduced the level of Staph aureus colonization over several days. This effect could also be achieved using the purified Esp protease isolated from that strain.

Blog entry; rather informally written, but generally a good presentation of the work: Fighting bacteria with bacteria -- common nose germ provides new weapon against superbugs. (E Yong, Not Exactly Rocket Science (blog, now at National Geographic), May 19, 2010.)

The article: Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization. (T Iwase et al, Nature 465:346, May 20, 2010.)

Added October 9, 2016. More about Staph interactions: Staph in your nose -- making antibiotics (October 9, 2016).

Also see How probiotics work: a clue? (October 11, 2010). This deals with the more common type of probiotics, which work in the gut.

For another probiotic story, see the post: Designing a probiotic that fights cholera (December 13, 2010).

More about the microbiota...
* A bacterial cocktail to fight Clostridium difficile (January 19, 2013). Gut.
* A virus that could treat acne? (October 21, 2012). Skin.

More about Staph infections...
* Does Triclosan in antibacterial soaps promote infection? (May 19, 2014).
* Killing persisters -- a new type of antibiotic (January 3, 2014).

More on biofilms...
* Shark skin inspires design of a new material to reduce bacterial growth (March 13, 2015).
* On sharing electrons -- II (June 9, 2013).

More on antibiotics, and the broad topic of reducing bacterial growth, is on my page Biotechnology in the News (BITN) -- Other topics under Antibiotics. It includes a list of related Musings posts.

Flow centrality: the key to a scientific analysis of the soccer game

July 11, 2010

The Germany-Spain game An analysis of the championship game of the 2008 European Cup tournament.

Each node (circle) represents a player. The size of the node reflects the player's performance; the color of the node reflects the player's z-score, a measure of passing accuracy (redder the better). Lines between nodes represent passes between the two players. Line width reflects the number of passes; line color reflects the normalized arc flow centrality (darker the better).

News stories:
* Researchers Use Science to Identify Soccer Stars. (National Science Foundation, 6/16/10.) From the funding agency.
* Using Science to Identify True Soccer Stars -- Researchers find a new approach to ranking and rating soccer players. (Northwestern University, 6/16/10.) From the lead institution; the first author is also associated with a university in Spain. (The senior author is originally from Portugal -- which is a relevant fact.)

The paper, which is freely available: Quantifying the Performance of Individual Players in a Team Activity. (J Duch et al, PLoS One 5(6):e10937, 6/16/10.) The figure above is part of Figure 5 of this paper.

It's a nice readable paper, with clear presentations of the problem and the approach. Although there is some math, much of it is fairly basic, and clearly presented; if the content interests you, go slow, and I think you will find at least some of the analysis accessible. They show that the statistical measures they develop correlate well with game results. What they do not do here is "prospective" testing: using statistics on the players to predict the outcome of games to be played.

At the end of the paper, they suggest that their general method may apply to other situations involving people working together. As an example, they analyze the relationships among authors for some papers. See Figure 6 of the paper. They do not show that anything is served by this analysis.

Incidentally, the final score was Spain 1, Germany 0. (And that was the score in their World Cup game this year, too.)

More about sports: Baseball physics (July 31, 2011).

Added March 20, 2017. More about getting the ball to the goal: Bumblebees play ball (March 20, 2017).

More from Spain: DNA from a 400,000-year-old "human" (December 9, 2013).

More from the World Cup... The brain-machine interface -- at the World Cup (July 2, 2014).

Older items are on the page Musings: archive for January-June 2010.

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Last update: March 26, 2017