Musings: January-June 2010 (archive)

Musings is an informal newsletter mainly highlighting recent science. It is intended as both fun and instructive. Items are posted a few times each week. See the Introduction, listed below, for more information.

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June 30, 2010

Butterflies and UV vision

June 29, 2010

Heliconius butterflies have two traits not found in related butterflies:
* They have improved vision in the ultraviolet (UV) region;
* They have an novel wing pigment that is distinctive in the UV.

The scientists stumbled onto this when they found that the genome contained a duplication of the usual UV receptor. This second UV receptor turns out to have a different UV response, so the presence of the two UV receptors gives these butterflies improved UV vision. They then found that the wing pigments also differed. A common yellow pigment was present in an altered form, which also absorbs in the UV. Here is an example of their data...

Spectra of butterfly wings.

The figure shows that butterflies with and without the second UV receptor in their eyes have differing patterns of UV pigments in their wings.

Part A (top) shows several species of Heliconius butterflies (all with H. to start their names). All but one of these have the second UV receptor in their eyes. Part C (bottom) shows several species of other (non-Heliconius) butterflies (none with H. to start their names). None of these have the second UV receptor in their eyes.

The curves show a measurement of the wing color; each curve is for one species. The key region is the UV, at the left below 400 nm. The key result is the big pattern, so don't worry if you can't read all the details. The key pattern: butterflies in part A, (mostly) with 2 UV receptors, have wings that look very different in the UV; butterflies in part C, not having 2 UV receptors, have wings that look very similar in the UV.

The figure is part of Figure 3 of the paper.

Thus this seems to be an example of two traits evolving together. Both traits are genetically simple, and neither is likely to have any disadvantage if it were present alone for a while. Presumably there is an advantage to the butterflies in having this extra UV-feature on the wings plus the vision capability to see it. They hypothesize that it is involved in mate selection, but there is no direct evidence on the behavioral aspect at this point.

News story: Butterfly Vision, Wing Colors Linked. (Science Daily, 3/1/10.) Caution... They over-state some of the interpretations, but the key facts are fine.

The article: Positive selection of a duplicated UV-sensitive visual pigment coincides with wing pigment evolution in Heliconius butterflies. (A D Briscoe et al, PNAS 107:3628, 2/23/10.)

Other posts on animal vision include:
* Color vision: an overview (December 1, 2014).
* How can the mantis shrimp see so many colors of UV? They use filters (August 30, 2014).
* Why might it be good to put lights on fish nets? (September 9, 2013). An application.
* An unusual eye? (June 6, 2012).
* Aedes aegypti mosquitoes do not respond to polarized light when trying to land on water (May 22, 2010).
* How many eyes does it have? (March 12, 2010).
* The vision thing (July 3, 2008).

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

More on wings:
* Introducing Supersonus -- it stridulates at 150,000 Hz (June 16, 2014).
* Wings for better walking (November 5, 2011).

More on UV: Fair skin and cancer: What is the connection? (March 12, 2013).

Do carnivorous plants attract insects that can see UV light? Carnivorous plants: A blue glow (March 16, 2013).

There is a section of my page Internet resources: Biology - Miscellaneous on Medicine: color vision and color blindness.

Another example of the co-evolution of a pair of traits: The iron war (May 17, 2015).

The 35 most famous xenon atoms

June 29, 2010

The Kavli Foundation has just announced the awarding of the 2010 Kavli prize for Nanoscience to Don Eigler and Nadrian Seeman.

IBM, Eigler Don Eigler has long worked at Almaden. Not the winery, but the Almaden lab of a well known company (in San Jose, here in the San Francisco Area).

Don is something of a doodler. And one day -- some 20 years ago -- he managed to write out the name of his company. It was quite a sight, and quite an achievement -- worthy of publication in the prestigious journal Nature.

Don's drawing is shown at the left.

To see a sequence of shots during the process of making this drawing... Figure 1, from the Nature paper [link opens in new window]. (Start at upper left, and go down. The small figure above is frame f, at the lower right.)

So, what's the big deal? Why has this figure become a standard in even introductory chemistry books? (I've told Don Eigler's story to many many beginning chem students, who are both impressed and amused.)

Each "dot" in the figure is a single atom of xenon. The drawing was made by picking up individual atoms and moving them around as desired. 35 atoms of xenon, properly positioned, and we have IBM. (I'm not counting the stray atoms in the figure.) This was done using the scanning tunneling microscope (STM) -- which had been invented at IBM's Swiss lab just a few years earlier. One can quibble about what it means to "see" atoms; arguably, the STM allowed us for the first time to see individual atoms. Eigler not only saw atoms, but picked them up and moved them around -- individual atoms. That had never been done before.

For more...
* The Kavli announcement: 2010 Nanoscience Citation. (Kavli Foundation, June 2010.)
* The Nature paper: Positioning single atoms with a scanning tunneling microscope. (D M Eigler & E K Schweizer, Nature 344:524, 4/5/1990.)
* A gallery of STM pictures, from the IBM Almaden lab: STM Image Gallery: Atomilism. Now archived. For the current picture, scroll down to "The Beginning". But there is much more, and more pages linked there.

A previous Musings post on observing atoms and molecules: Seeing molecules under a microscope (September 19, 2009). It links to more. [Scanning tunneling microscopy (STM) and atomic force microscopy (AFM) are closely related technologies. In fact, STM is a type of AFM.]

* * * * *

As noted at the top, the prize was shared by Don Eigler and Nadrian Seeman. Here is an item about a recent Seeman paper: Nanorobots: Getting DNA to walk and to carry cargo (August 7, 2010).

More on STM...
* Making triangulene -- one molecule at a time (March 29, 2017).
* Progress toward an ultra-high density hard drive (November 9, 2016).
* The smallest electric motor (September 26, 2011).

More xenon: A new sensor for barium ions -- could it lead to a better understanding of neutrinos? (September 20, 2020).

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.

Magnetic field perception

June 16, 2010

Many organisms respond to magnetic fields. How they do it is generally not clear.

The best understood case is with simple organisms: bacteria. In 1975 Richard Blakemore noticed that some bacteria he was observing under the microscope kept moving to one side. After much adjusting of the conditions, including lighting, he realized that the bacteria were going north. Study of these magnetic bacteria showed that they have tiny iron oxide (magnetite) magnets in them. Similar magnetic materials are found in some animals, but this is almost certainly only part of the story. The possible role of special pigments in the visual system is still being debated.

The article here is a nice Q-&-A introduction to bio-magnetism, especially in animals. Animal behaviour: Magnetic-field perception. (K J Lohmann, Nature 464:1140, 4/22/10.) Worth a browse! The first page contains some nice pictures of magnetic animals.

The article notes that cows have been found to align themselves in the earth's magnetic field -- as noted in the Musings post Electric cows (April 1, 2009).

Also see:
* The nature of a bio-compass? (June 10, 2016).
* A human protein that can sense magnetic fields (July 15, 2011).

A new example... Can blind rats learn to use a geomagnetic compass? (June 29, 2015).

More about magnetite... A battery for bacteria: How bacteria store electrons (May 2, 2015).

How arsenic works against a cancer

June 16, 2010

Arsenic is probably best known as a poison, though it has been used in medicines from time to time. In fact, the first synthetic agent used to treat microbes was an arsenical.

In 1992 it was found that a simple arsenic compound, arsenic trioxide (As2O3), was effective in treating one particular kind of cancer: the type of leukemia known as acute promyelocytic leukemia (APL). New work has uncovered how it works.

Cancer is, in general terms, a condition where cells grow without the proper regulation that is supposed to keep cells "in order". The loss of regulation often involves mutations in genes for proteins that regulate cell growth. APL is due to a specific type of mutation; that mutation leads to a specific defective regulatory protein, which allows excessive growth. The new work shows that the arsenic compound binds specifically to this defective protein, and leads to the degradation of that protein. Clearly, causing loss of the mutant protein should be good, since that protein is causing the excessive growth.

For those with some chemistry or biochemistry background... The arsenic compound binds to some sulfur atoms -- which are grouped together in protein motifs known as zinc fingers. Why it binds to these specific S atoms is not at all clear; zinc fingers are common in cells. So, the new work shows that the As is having a specific effect on a specific protein -- rather than being a general metabolic inhibitor. However, the basis of that specific interaction is not entirely clear.

News story: Arsenic used to treat leukemia. (Medical Xpress (Phys.Org), April 12, 2010.)

* News story accompanying the article: Medicine: Poisonous Contacts. (S C Kogan, Science 328:184, April 9, 2010.)
* The article: Arsenic Trioxide Controls the Fate of the PML-RARα Oncoprotein by Directly Binding PML. (X-W Zhang et al, Science 328:240, April 9, 2010.)

More on the biology of arsenic:
* Rice and arsenic: a follow-up (January 8, 2012).
* For a report of a bacterium growing with arsenic replacing phosphorus in general metabolism, see: NASA: Life with arsenic (December 7, 2010).
* A report of a bacterium that seems to use arsenite as the reductant in photosynthesis: Arsenic and photosynthesis (September 9, 2008).

More on zinc finger proteins: Gene therapy: Curing an animal using a ZFN (August 9, 2011).

How to talk to yourself

June 11, 2010

Borislav sends...

Do you talk with yourself?

Don't worry, we all do. It is a pleasant thing to have a conversation with someone who always agrees, and has exactly the same views.

Fun aside, psychologists lately have shown that the manner in which a person talks with self can influence one's actions. The key is in what you say to yourself when you are thinking about doing something.

Results show that if you ask yourself if you would do something, instead of declaring that you will do it, you are more likely to actually do it. The difference is in "Will I?" against "I will." Try it, it works!

Example, Fig 2. An example...

As a preliminary to a puzzle-solving session, one group of participants was told to write "Will I" 20 times; another group was told to write "I will" 20 times. After this writing exercise, all participants worked on solving some puzzles. The graph shows the scores for each group. The "Will I" group did better!

This is part of Experiment 2 from the paper; the graph is part of Figure 2.

News story: How do you talk yourself into something? What should you tell yourself to get motivated to act? (Psychology Today, 5/5/10.)

The article: Motivating Goal-Directed Behavior Through Introspective Self-Talk: The Role of the Interrogative Form of Simple Future Tense. (I Senay et al, Psychological Science 21:499, 4/10.)

More from the same journal: Child development: nature vs nurture? Year 2 as a window of opportunity. (March 5, 2011).

Jupiter injured again!

June 11, 2010

Last week. This time, the actual collision event was recorded live.

News story: Amateur astronomer spots another Jupiter strike (w/ Video). (, June 4, 2010.) [June 2022: replacement for story listed previously.] The story contains a video, showing the collision event. The video is 25 seconds; the relevant action is quite fleeting within the video. (The video is "real time", I think.) If you don't see the event after a couple of tries, here is a hint... Put your cursor over the word hint. (Do not click.)

The video itself is also at YouTube: YouTube video of Jupiter event. I encourage you to read the story above. But you may also want to check this site; there may be other good stuff here.

The story above discusses both this event and the one from last year. The pictures at the start are from last year's event; they include a nice sequence showing the scar and its healing. Musings presented that event in the post Collision! Jupiter injured (7/24/09). That post links to others on solar system collisions.

Also see: Rendezvous with Lutetia (August 14, 2010).

June 9, 2010

Hydrogen fuel cell cars

June 8, 2010

Nature recently ran a news feature on the status of hydrogen fuel cell cars. Some of you may enjoy looking it over, as an update. It seems to be freely available: Fuel of the Future? Hydrogen fuel-cell vehicles, largely forgotten as attention turned to biofuels and batteries, are staging a comeback. (J Tollefson, Nature 464:1262, 4/29/10.)

Jakub, with a background working with hydrogen fuel cells, offers some additional comments:

My personal opinion is that fuel cells would would be here soon if they would get a focused support and realistic milestones. The problem is that the government is doing everything to stall fuel cells development and make public skeptical. Bush's announcement of fuel cell funding before his elections was a joke. The funds got dispersed so much that about $200 million actually was dedicated to fuel cell research.

Ok, let's look at milestones now.

"In order for a fuel cell to be practical it has to operate at least 40,000 hours between major maintenance periods and 4,000 hours between inspections". These are generally accepted government milestones.

It is not too too bad, right? I mean, 4,000 hours is roughly half a year and 40,000 hours is roughly 5 years. I mean if a fuel cell can't make that it is junk, right? Ok, my car's on board computer showed 36 mph average speed (I checked today. It is mostly city with some highway). Let's make it 30 mph to give old combustion engines a little head start. My car requires oil change and an inspection at 3,000 miles. This is only 100 hours of driving!!! Major inspection is 60,000 miles, 2,000 hours. And I don't really expect it to perform well for more than 150,000 miles, when I will probably junk it - 5,000 hours. In between, you've major maintenance, which would be eliminated with fuel cells, such as spark plugs, timing belts, injector cleaning etc.

If you take fuel cell life requirement of 40,000 hours and multiply it by an average 30 mph, you get 1,200,000 miles per car, when a fuel cell stack will probably have to be replaced. That is when government says it makes sense... (and by the way, I'd love to see a car sale flyer saying "Good deal, Low miles - only 800,000" ;-)

Finally, environmentalists harm themselves with crying out whenever hydrogen is produced from hydrocarbons and CO2 is released. Of course, you will always have CO2 emissions whenever hydrocarbons are used. But fuel cells are more efficient than ICE, so less equivalent CO2 is released per mile and I'd say that is a good start.

In the end, I think it is good that such articles are published. However, public have such a poor practical understanding of technical issues that these reports tend to make people more skeptical.

A previous post on this topic, about a year ago: Hydrogen cars? (June 24, 2009).

Also related are some posts on electric cars:
* A new electric car (July 11, 2009).
* For an analysis of the benefits of electric cars... Electric cars and pollution (April 5, 2011).

Also see: The hydrogen economy -- in the mid-Atlantic (August 30, 2011).

A post about making hydrogen: An artificial forest with artificial trees (June 7, 2013).

More about fuel cells: A robot that can feed itself (February 3, 2017).

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.

Why are musical instruments featured on the cover of EID?

June 7, 2010

EID cover, May 2010, trimmed. Boy Playing the Flute, a painting from the 1630s, shown on the cover of the May 2010 issue of Emerging Infectious Diseases (EID).

Why? Well, it led to a nice essay with historical, musical and health content. Have a look; link here is to the article via PubMed Central: About the cover: The Whole Heaven a Musical Scale and a Number. (Polyxeni Potter, EID cover story, 16:905, May 2010.)

EID, published by the US Centers for Disease Control and Prevention (CDC), is probably one of the scariest scientific journals around. Just browse the Table of Contents -- if you dare. EID is freely available online.

The next Musings post about music: Frequency-notched music: a treatment for tinnitus? (August 17, 2010).

Another EID cover story: Musici Ambulanti: Ancient art and ancient microbiology (January 17, 2012).

There is more about music on my page Internet resources: Miscellaneous in the section Art & Music.

Killer chickens -- follow-up: some progress

June 7, 2010

The Musings post Killer chickens (December 2, 2009) discussed the problem of birds (chickens and turkeys) being contaminated with bacteria (Salmonella and Campylobacter). Contaminated birds in the US food supply are a major source of food poisoning, and a significant cause of deaths.

The USDA (United States Department of Agriculture) has announced new regulations concerning the allowed levels of bacterial contamination in birds.

If you look at the details of the regulations, you may think they are too lax; they certainly sound lax. Remember, that both sets of regulations are better than the current regulations. For Campylobacter, this is the first set of regulations at all. Further, they are considered practical or achievable. For example, the new Salmonella standard is set to what is now the average. That means that many plants are already meeting the new standard; the goal is to bring the plants that are now the poorest up to at least "medium". The regulations are accompanied by guidelines of good practices, to help achieve the desired goals.

In making the above point, I am not trying to defend the specific choices they made as optimal. I am simply trying to note that there are practical considerations in setting the goals. (And yes there are political considerations, too.) Could they have pushed for more stringent regulations? I don't know. But what seems most important to me is that the regulations represent progress. If these regulations are enforced and achieved, there will be a health benefit. Further tightening of the regulations can be considered later.

News story: Chicken, turkey may sicken 55K fewer under new USDA rules. (USA Today, May 11, 2010.)

The USDA press release: USDA Announces New Performance Standards for Salmonella and Campylobacter. (USDA, May 10, 2010. Now archived.)

Also see: Killer eggs: The American egg problem (September 8, 2010).

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

UCA passes test

June 6, 2010

All life on earth has descended from a common ancestor -- our universal common ancestor (UCA). That is a basic tenet of biology, one of the "big ideas". But how well do we really know that? Is it a well documented "fact", or more of a good working hypothesis? In some ways, it is a simple idea: Occam's razor, or parsimony, leads us to UCA as the simplest explanation for a unified view of how organisms are related. On the other hand, it is so big that it is hard to test. Impossible to test, it might seem.

There is much we know that supports the idea of UCA. The common basic biochemistry of all organisms is most simply explained by common ancestry. The genetic code is a particularly important example. No one has made any convincing case for why the genetic code is what it is, but it is almost universal. A locked-in accident is the simplest interpretation. Attempts to understand the ancestry of specific groups of organisms typically leads to the idea of a common ancestor, but that is a limited context. Further, such statements are often not rigorous tests, with no other hypotheses being considered. What about the big picture? In fact, some microbiologists have proposed that horizontal gene transfer (HGT; gene transfer by a method other than from parent to offspring) predominated in early life forms, thus obscuring any role for a UCA. We noted this briefly in the post Horizontal gene transfer: the web of life? a challenge to evolutionary theory? (March 26, 2010).

So what's new? A report of a new test of UCA. The biggest test ever done. What made this possible was the explosion of genome information in recent years. We simply have more data. The new testing pitted UCA against various other models. In each case, the data overwhelmingly supported UCA. At one point, the author concludes that "... UCA is at least 102,860 times more probable than the closest competing hypothesis". 102,860 is the kind of number that makes "astronomical" numbers seem small!

What is the significance of this new work? The simplest point is that it supports what we already "knew", that all life we know has a common ancestor, referred to as UCA; it is the best test of UCA so far, and UCA looks good. However, I think the more important significance is that it opens up a new era of testing UCA. Others can critique and build on this work. They can suggest alternative types of statistical testing. They can suggest additional models. And of course, more and more data will become available.

News story: First Large-Scale Formal Quantitative Test Confirms Darwin's Theory of Universal Common Ancestry. (Science Daily, 5/17/10.) A good, readable overview of what was done.

* News story accompanying the article: Origins of life: Common ancestry put to the test. (M Steel & D Penny, Nature 465:168, 5/13/10.)
* The article: A formal test of the theory of universal common ancestry. (D L Theobald, Nature 465:219, 5/13/10.) The article itself is difficult reading!

More on horizontal gene transfer (HGT): An extremist alga -- and how it got that way (May 3, 2013).

More about extrapolating backwards from current genomes to look for ancestors: When did the SARS-2 (COVID-19) virus arise? A window into how a zoonosis starts (June 22, 2021).

Posts about Darwin and Darwinism include... Finding a gene behind the beak diversity of Darwin's finches (July 14, 2015).

High-tech medicine: good or bad?

June 4, 2010

Sometimes I post items on controversial issues. The point is often as much to stimulate some thinking about the issue as to suggest any particular answer. A recent book review on the high cost of medical care in the US struck me as a good item to post in this context. It is probably more important for the issues it raises than for its answers. Then, on the next page was an article about medical care in Cuba -- just to rub it in.

Have a look...

Book review: Medicine: The Costs of Innovation. (B L Benderly, Science 328:571, 4/30/10.) It is a review of the book Taming the Beloved Beast -- How Medical Technology Costs Are Destroying Our Health Care System by Daniel Callahan, 2009.

"Policy forum": Global health: Fifty Years of U.S. Embargo: Cuba's Health Outcomes and Lessons. (P K Drain & M Barry, Science 328:572, 4/30/10.)

The picture is not directly related to the above items, but happens to be on the same page as the book review, with its own text. If you look at the pdf file for the book review, you will see the picture. Otherwise, you can find it at: picture source.

Other posts on health care:
* POCDx -- What's the barrier? (January 29, 2013).
* Maternal mortality (May 7, 2010).
* Healthcare costs (June 18, 2009).

Which end of the ant should you eat first?

June 4, 2010

In the work noted here, two main types of experiments were done. In one, subjects were fed one end or the other of ants, or whole ants. Subjects that ate the front ends grew better, and suffered lower mortality, than subjects that ate whole ants or the back end (the gaster). In the other, the scientists simply observed how the subjects ate whole ants, and found that they ate the front end first. So, it would seem that the front end is more nutritious, and the subjects knew that.

If the idea of eating an ant that has been cut in half does not appeal to you... They compensated some for this, by gluing together two front ends (or two back ends), to make pseudo-whole ants.

Here is a photograph of one of the subjects "at work".

Figure 1. Survival vs body parts eaten An example of their data.

The graph shows the fraction of the subjects that survive, on the various diets. Best survival -- the top curve -- was with eating "2 Foreparts" (front ends).

This is Fig 1 of the paper.

Why did they do this? The spiders studied here eat a restricted diet: just a particular type of ant. How do they balance out their nutritional needs with only one food source? That's the motivating idea for the work, and they discuss the results in terms of the nutritional content of ant body parts.

The article: Specialist ant-eating spiders selectively feed on different body parts to balance nutrient intake. (S Pekár et al, Animal Behaviour 79:1301, 6/10.)

The action photo included above is from a brief mention of this article in Nature. Wildlife biology: fussy eaters. (Nature 464:1248, 4/29/10.)

A previous post on how spiders eat... The vegetarian spider (10/21/09).

June 2, 2010

Red and green aphids

June 2, 2010

Red and green aphids There they are: aphids, mostly red with an occasional green one.

The color of the aphids is due to carotenoids. You know about carotenoids: familiar ones include the orange β-carotene in carrots and the red lycopene in tomatoes. Many plants and microbes make various carotenoids. But animals don't. So, what about these aphids? How do they get colored with carotenoids?

Well, perhaps they get them from their food -- just as we get our vitamin A, a related chemical needed for our visual pigment, from our food. Good idea, but it just isn't so. Maybe the microbes in the aphids make carotenoids for them. Good idea, but it just isn't so.

Recently, the aphid genome was sequenced. And there they were: genes for making carotenoids! But are they real genes? Do these genes really function? An answer to that was provided by looking carefully at the key gene for the last step, making the red pigment from the yellow (or green) one. The red aphids had a complete version of the gene, and green aphids had a defective version. That is, the appearance of the aphids correlated with their genes, thus supporting that these aphid genes really were responsible for the aphid color.

So it seems that the aphids make their own carotenoids -- the first animal found to do so. But where did those genes come from, if no other animals have them? Well, they looked at the carotenoid genes more closely, comparing them with the known carotenoid genes from other organisms. It seems rather likely that they are fungal genes. Thus we have a new example of horizontal gene transfer (HGT): aphids with fungal genes for their color. [A recent post about HGT was: Sushi, seaweed, and the bacteria in the gut of the Japanese (4/20/10).]

News story: First Case of Animals Making Their Own Essential Nutrients: Carotenoids. (Science Daily 4/30/10.)

* News story accompanying the article: Evolution: A Fungal Past to Insect Color. (T Fukatsu, Science 328:574, 4/30/10.) The figure at the start of this post is from this new story.)
* The article: Lateral Transfer of Genes from Fungi Underlies Carotenoid Production in Aphids. (N A Moran & T Jarvik, Science 328:624, 4/30/10.)

For those who would like a little chemistry... Here is a figure that shows some of the key carotenoids that are involved, and a likely pathway for synthesizing them. Carotenoids [link opens in new window]. Torulene is a major pigment of red aphids. Green aphids lack the enzyme that leads to torulene, labeled as "desaturase"; they accumulate the various carotenes. (The figure is Figure S1 from the Supporting Online Material for the article; it is freely available from the web page for the article, listed above.)

* * * * *

More about aphids and their carotenoids: Are aphids photosynthetic? (September 17, 2012).

More about carotenoids:
* Red color vision in dinosaurs? (October 17, 2016).
* Golden rice as a source of vitamin A: a clinical trial and a controversy (November 2, 2012).

More about aphids...
* The aphid-bacterium symbiosis: a step toward manipulating it (May 15, 2015).
* Underground messaging between bean plants (July 29, 2013).

More about tomatoes: The chemistry of a tasty tomato (June 18, 2012).

Also see...
* A case of horizontal gene transfer from plant to insect; exploiting it for insect control (April 18, 2021).
* A better understanding of the basis of color vision (February 1, 2013).

Personalized medicine -- and the entering students at UC Berkeley: addendum

June 2, 2010

Original post: Personalized medicine -- and the entering students at UC Berkeley (5/25/10).

I have added an additional web site, the site of the project. It includes much information, including a FAQ, which attempts to address concerns that have come up. I hope that the page is actively maintained.

Globalization: A Croatian song about Obama and Bush

June 1, 2010

Borislav sends...

Here is something local, by members of a popular old rock band, and a couple of comedy actors. It involves Obama and Bush, and is actually a parody love song.

The video originally included here, at, is no longer available.

Obama and Bush appear at around 2:30 into the video. The main repeating sentence is in Bosnian dialect (regarded as extremely funny in all ex-Yugoslavia countries, though don't ask me why), and it says "I think you don't love me".

Other posts about Obama:
* Quiz: Barack Obama and polar bears (July 20, 2011).
* Nobel Peace Prize (October 25, 2009).

Stanford scientists discover that ink sticks to paper

May 29, 2010

A nanotechnology paper that starts by discussing papyrus.

Think about it... You have a new type of ink. You'd like to write with this ink on a solid surface -- a thin solid, one that can be easily bent, even rolled up. You have available some glass, some plastic sheets, and some ordinary paper. What would you choose as your writing surface?

Folks, if you actually try this, be real careful bending that piece of glass.

Ok, you suspect there is a catch? Well, yes and no. I did leave out one test. You are to not just write on the surface but completely coat it -- and then test that the material will conduct electricity. But it doesn't really matter, in some ways. If the goal is to make the surface conducting, that certainly affects our choice of ink. Let's use a suspension of carbon nanotubes (CNT) (with some detergent, to keep the CNT suspended); I said the ink was novel. Beyond that... Well, paper is porous; inks absorb onto it. Very well -- for a wide variety of inks. And it is flexible. And well understood. And cheap.

So what did they do? They coated paper -- ordinary copier paper -- with CNT, and tested the electrical properties of the coated paper. They say the process is simpler than using a plastic surface, and that the results are better. They think it is rather good; we'll see.

News story: Battery made of paper charges up. (BBC, 12/8/09.) There is some confusion here. There seems to be an emphasis on "battery". Indeed they do some battery work, but the coated paper itself is not directly involved in the battery reactions. The results of interest deal with conductivity (or resistance), or with capacitance.

The article: Highly conductive paper for energy-storage devices. (L Hu et al, PNAS 106:21490, 12/22/09.)

More about porous materials: Upsalite: a novel porous material (September 6, 2013).

More about carbon nanotubes: Characterization of carbon nanotubes (December 3, 2013).

Hobbit DNA?

May 28, 2010

Just a tidbit here... The "hobbits" are the small humans found on the Indonesian island of Flores. There is considerable debate about what they are. Obviously, DNA could help. This came up at a recent seminar, and the speaker noted that people have tried (people from the foremost lab in the field, which he represented), and have been unable to get any usable DNA sequence. This was not too surprising, as the "storage" conditions for the samples in Indonesia are not conducive to DNA survival. He did note that some people are going to continue trying; perhaps new excavations will yield better samples. (He also noted that they are working on producing nuclear DNA sequence for the Siberian finger sample.)

* The little people of Indonesia (5/14/09).
* Hobbits: an update (5/1/10);
* The Siberian finger: a new human species? (4/27/10).

Complex tool use by birds

May 28, 2010

How do you (the bird) get the food, which is at "4"?

The stick "2" is not long enough to reach the food. But stick "2" is long enough to reach stick "3", and stick "3" can reach the food.

If you're having trouble figuring it out... Go look at the movie, noted below. The movie is clearer, and quite delightful!
The tool problem

News story: Clever New Caledonian crows can use three tools. (BBC, 4/20/10.) The figure above is trimmed from a figure in this item; it is also similar to Fig 1 of the paper.

The article: Complex cognition and behavioural innovation in New Caledonian crows. (A H Taylor et al, Proc. R. Soc. B 277:2637, September 7, 2010.)

The journal page given above links to a movie. Just click on "Data Supplement". You should have access to the movie, regardless of access to the article. The movie is also at Movie posted at YouTube.

* * * * *

Tool use, and animal behavior in general, is often fun. It is also instructive to learn what diverse members of the animal kingdom can do. Here are some posts in this broad area.
* Cultural transmission of fishing techniques among dolphins (September 13, 2011).
* The octopus and the coconut (December 28, 2009).

Bird brains...
* Ravens: planning for the future? (September 11, 2017).
* Bird brains -- better than mammalian brains? (June 24, 2016).

More on bird behavior: Bird theater (October 19, 2010).

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

The book Marzluff & Angell, Gifts of the Crow -- How perception, emotion, and thought allow smart birds to behave like humans (2012), is a delightful introduction to these intelligent birds. For more about the book, see my page Books: Suggestions for general science reading, for Marzluff & Angell, Gifts of the Crow.

May 26, 2010

Personalized medicine -- and the entering students at UC Berkeley

May 25, 2010

Students entering UC Berkeley this coming Fall will get something a bit unusual in their welcoming package: a cotton swab (a Q-tip). They are to swab the inside of their cheek, and send the swab -- with cheek cells, containing a sample of their DNA -- back to the University.

The project was described in a news release from the University: L&S Program Asks Students to Bring Their Genes to Cal -- Exploring personalized medicine with Jasper Rine. (May 13, 2010; now archived.)

An article in the school paper is also useful: Research & ideas: L&S freshmen can have their DNA analyzed. (Daily Cal, 5/17/10.)

This is not part of a university medical screening or such. It is part of a project where the students will learn about the emerging field of personalized medicine. Only a few simple traits are being tested, and only the students will know the personal results. Their participation in the testing is voluntary. The project involves students in L&S (Letters and Sciences), not the whole university.)

The plan has resulted in some questions, perhaps even controversy. An example is in a subsequent article from the school paper: Freshman Genetic Testing Program Draws Criticism. (Daily Cal, 5/24/10.)

An additional web site, the site of the project. It includes much information, including a FAQ, which attempts to address concerns that have come up. Now archived: "On the same page" project: Bring your genes to Cal.

UC Berkeley announces changes to the program, in response to concerns raised. Musings post: Personalized medicine -- and the entering students at UC Berkeley: follow-up (August 27, 2010).

One of the first Musings posts about personalized medicine: Personalized medicine: Getting your genes checked (10/27/09). This links to several others in the broad area.


May 25, 2010

I just want to be sure that we establish the importance of bears. It is not a frivolous topic.

Let's start with the flag of the state of California.

On June 16, 1846, California declared its independence from Mexico. The flag of the new California Republic was its great symbol -- and perhaps its only accomplishment. 26 days later it was conquered by the armed forces of the United States of America -- by a force of 60 soldiers. The current state flag, shown here, was modeled on the flag of that independent republic.

California state flag

From: Wikipedia: Flag of California.

Bear exploring car. Car damaged by bear.
Bears are still an important part of California culture.

These two pictures shows two stages in an all-too-common interaction. (They are, of course, independent pictures -- different situations.) They were probably taken in Yosemite National Park. They are from: Bears. This web site is from Mary Donahue at De Anza College, in the Silicon Valley town of Cupertino, California. Much more here, both pictures and information. (Now archived.)

Even more important is Oski.

For more: Wikipedia: Oski.

(You should know that the sports teams of UC Berkeley are known as the Bears -- more formally, the Golden Bears.)

   Source for this figure? Not sure; probably an old page, which is not available.


Other posts on bears include:
* Trains, grains, and bears (May 24, 2017).
* Bears hibernate -- but stay warm (April 30, 2011).
* Polar bears: ABC (May 11, 2010).

Obesity, gut bacteria, and the immune system

May 24, 2010

Is there a connection between those three topics listed in the title? Maybe.

Is it possible that our gut bacteria cause obesity? Maybe.

A recent post was about a role for our gut bacteria in the proper functioning of the immune system: Is Arthromitus a key bug in your gut? (January 16, 2010). Now we have more.

Let's start with a simple description of the key new work. They used mice: a strain of mice deficient in a specific immune system protein. The mice had a defective TLR5, a protein of the innate immune system that recognizes bacterial flagella; we call them TLR5- (which you can read as "TLR5 minus" or "TLR5 negative"). The first finding was simply that the TLR5- mice were obese, and had other characteristics of what we call "metabolic syndrome", a precursor of diabetes.

Why did the defect in the innate immune system cause these metabolic disturbances? Well, they treated the mice with antibiotics, to kill the gut bacteria. This reversed the metabolic syndrome. In another experiment, they transferred the bacteria from the obese TLR5- mice to other mice, which were wild type (normal; TLR5+). These recipient mice became obese, and developed the metabolic syndrome. Sandoval & Seeley (see below) summarize it: "Thus, the gut microbiota in the obese mice was both necessary and sufficient for the resulting obesity."

So, summarizing, we see that two distinct types of events caused the metabolic problems. One, with the first mice, was the immune system defect. The second was the bacteria themselves, as shown by the transfer experiment. There has already been some work showing that people with metabolic syndrome have different gut bacteria than "normal" people. The new work suggests that the bacteria may be the cause of the metabolic problem, not the other way around. What causes the change in the bacterial population in people is not known. But the new work makes it important that these clues are followed up in humans.

News story: Intestinal Bacteria Drive Obesity and Metabolic Disease in Immune-Altered Mice. (Science Daily, 3/8/10.)

* News story accompanying the article: Medicine: The Microbes Made Me Eat It. (D A Sandoval & R J Seeley, Science 328:179, 4/9/10.)
* The article: Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5. (M Vijay-Kumar et al, Science 328:228, 4/9/10.)

More on gut bacteria:
* Breastfeeding and obesity: the HMO and microbiome connections? (November 14, 2015).
* Antibiotics and obesity: Is there a causal connection? (October 15, 2012).
* Your gut bacteria: where do you get them? (July 30, 2010).

More on the innate immune system and TLRs:
* Why vaccine effectiveness may vary: role of gut microbiome? (February 27, 2015).
* Why mice don't get typhoid fever (November 26, 2012).

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

The Scientist: open access (temporary)

May 22, 2010

The Scientist is a news magazine. It is for biologists, largely molecular biologists, though the coverage is somewhat broader at times.

The Scientist has announced a temporary change so that the magazine is now entirely freely available (OA = open access), both current and archive. I encourage those with biology interest to take this chance to look over the magazine. At least, browse the contents for some recent issues.

Examples of articles from the May issue:
* C Bode, Dangerous liaisons. Discusses the complex issue of drug interactions, and some approaches to uncovering them.
* J Davies, The garden of antimicrobial delights. An essay on the problem of the shortage of antibiotics. Julian Davies says we just need to look.

The Scientist.

December 2012: Their access policy varies over time. For now, it seems quite freely available.

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

Aedes aegypti mosquitoes do not respond to polarized light when trying to land on water

May 22, 2010

A negative result. So, why would we feature a negative result? Because the result is rather surprising: this is the first case found where an insect that needs to land on water (to lay eggs) does not respond to polarized light. Anyway, the whole topic is fun, and maybe even important.

The topic of animals responding to polarized light came up in the chemed discussion group, and led to some useful private discussion. I think it is likely that most of us did not realize how common it is for animals to respond to polarized light. Among animals that must recognize the surface of water, including many insects and birds, it may be normal. The light reflected off a water surface is polarized, and is a good signature of a body of water.

The article, via abstract at PubMed: Polarized light and oviposition site selection in the yellow fever mosquito: No evidence for positive polarotaxis in Aedes aegypti. (B Bernáth et al, Vision Research 48:1449, 2008.)

A news story on the broader topic of how polarized light affects animals: Polarized Light Leads Animals Astray: 'Ecological Traps' Cause Animal Behaviors That Can Lead To Death. (Science Daily, 1/7/09.) A good place to start! It offers examples of how manmade objects create a distorted environment, and how such distortions affect animals.

The review that the above news story refers to: Polarized light pollution: a new kind of ecological photopollution. (G Horváth et al, Frontiers in Ecology and the Environment 7(6):317, 2009.)

It's beyond the immediate topic, but I'm sure some will ask... Can humans detect polarized light? The answer seems to be yes, with limitations. As an introduction, have a look: Wikipedia: Haidinger's brush.

A subsequent post on animal vision: Butterflies and UV vision (June 29, 2010).

A post on how a nocturnal animal finds water: Water: a bat's view (December 3, 2010).

Stripes protect zebra against horseflies -- another story of polarized light (February 26, 2012).

More about Aedes mosquitoes:
* A mosquito map for the United States (October 3, 2017).
* Why don't black African mosquitoes bite humans? (December 19, 2014).

Why are HIV-infected people more susceptible to Salmonella infection?

May 21, 2010

The answer to the title question might seem obvious enough: HIV-infected people have defects in the immune system, and so they don't make antibodies against the invading bacteria. A reasonable hypothesis. And apparently wrong.

Imagine the following experiment... Infect two people with Salmonella bacteria: one who is infected with HIV (HIV+) and one who is not (HIV-). Allow some time for an immune reaction to develop. Take their blood, and see if the blood kills Salmonella in the lab. Your predictions?

Well, the blood from the Salmonella-infected HIV- person kills Salmonella in the lab. The blood from the Salmonella-infected HIV+ person does not. Ok, that is probably what you predicted. So far, so good. But what if we add the blood from both people together to some Salmonella bacteria in the lab? Kill or not? Your prediction? Why?

If you use the model stated at the top of this post, you might expect that the mixture of bloods would kill. After all, the model says that the HIV- blood contains antibodies against the bacteria, and the HIV+ blood does not. But that is not what they found! They found that the mixture of two bloods did not kill the bacteria. It is as if the blood from the HIV+ person contained something that prevented killing, that protected the bacteria.

If your prediction was wrong, that's fine. What's important is that you thought about it and made the best prediction you could, given the information you have. I often tell students that the only time you learn something new is when your prediction is wrong. That's how science makes progress, discovering things that don't fit with what we already know -- or think we know.

They investigated further, and found that the HIV+ people actually made plenty of antibodies against the Salmonella. But -- and this is the key point -- those antibodies failed to promote killing of the bacteria. In fact, they protected the bacteria, and prevented the "good" antibodies, from HIV- people, from killing. Why this happens is not yet known, but it certainly opens up new perspectives on how the immune system is working.

The story serves to emphasize some things about the immune system that reveal how it is more complex than our simple views. We sometimes think about the immune system attacking things that are bad, such as pathogens. But the immune system really does not know good from bad. If it did, we would not have autoimmune diseases, in which the immune system attacks our own body. The post Can you die from an infection without being infected? (3/19/10) presents a recently discovered example of how the immune system gets "confused". The immune system has "learned", in the evolutionary sense, what to attack -- but its rules are imperfect. Further, we sometimes think than an immune response leads to killing the invader. Maybe it does, maybe not. The story here shows that some antibodies against a particular invader lead to killing it, while others actually protect it. This is a situation very familiar to people who study viruses. It is common to find that some antibodies to the virus "neutralize" the virus, whereas other antibodies do not.

News story: HIV Patients Hold Clues to Salmonella Vaccine Development. (Science Daily, 4/29/10.)

* News story accompanying the article: Immunology: Salmonella Susceptibility. (S Moir & A S Fauci, Science 328:439, 4/23/10.)
* The article: Dysregulated Humoral Immunity to Nontyphoidal Salmonella in HIV-Infected African Adults. (C A MacLennan et al, Science 328:508, 4/23/10.)

Some other posts on the complexity of HIV issues:
* A bio-ethics controversy: HIV-TB interaction (7/13/10).
* HIV vaccine trial -- and quibbling about statistics (11/2/09).

More about Salmonella (from the same lab)... Towards a better understanding of Salmonella infections (May 25, 2012).

More examples of the immune system causing a problem...
* What's the connection: Narcolepsy and the flu vaccine (or getting the flu)? (October 3, 2015).
* Dengue fever -- Two strikes and you're out (August 10, 2010).

The following post might fit with both of the previous two paragraphs... Why did the HIV vaccine work for some people? Follow-up (May 1, 2012).

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

May 19, 2010

Do you make morphine?

May 18, 2010

Morphine is a powerful and useful pain killer. It is also an addictive substance. Morphine is made by the opium poppy; it can be converted into illicit drugs, such as heroin. Society has complex reactions to this mix of properties. Now, a new twist: Is it possible that humans make morphine? That morphine is a normal part of the human body? The answer is "maybe". Circumstantial evidence has been accumulating for a few decades suggesting that we make morphine, and a new paper lends substantial -- but incomplete -- support. Not surprisingly, it has been getting attention!

What's the evidence? Well, there has been considerable evidence that humans -- and other mammals, including rodents -- excrete morphine in the urine. Morphine has also been found in various tissue samples and lab cultures. The amounts are typically low, and the origin has been unclear. The new work? They fed "labeled" precursors to mice, and showed that the label ended up in morphine. That is, chemicals known to be converted into morphine were actually converted into morphine in the mice. Since the precursors used were already known to be normal body chemicals, it seems clear that the mice contain the entire pathway for making morphine.

So, what do we do with this new information?
* Importantly, at this point, the information should have no effect on anything we do. There is nothing in what has been shown so far that should affect our medical use of morphine, and nothing that should affect our view of it and related chemicals, as illegal drugs.
* The current work is in mice. We do not know it is true for humans. Now, I suspect it will be found for humans, too. There is already circumstantial evidence that it holds for humans.
* Let's assume for the moment that the new result does hold for humans. What will be important is to try to establish what role the endogenous morphine plays. For example, do people vary in how much they make? If so, does it correlate with sensitivity to pain? Do people make more of it in situations of pain? Can we control the amount of endogenous morphine they make? Would a drug that affects endogenous production of morphine be a useful drug? Useful in treating pain? Useful in treating addiction? effective? safe?

So for now this is simply a new bit of information. It may fascinate us, but it should not have any immediate impact on us, simply because the current story is so incomplete. On the other hand, the biology community should find this of considerable interest to follow-up -- to make the story more complete.

News story: Human Bodies Make Their Own Morphine. (National Geographic, 4/26/10. Now archived.)

The article: Urinary excretion of morphine and biosynthetic precursors in mice. (N Grobe et al, PNAS 107:8147, 5/4/10.)

More about pain: Alcohol consumption, an "ethnic" mutation, and a possible new drug (October 28, 2014).

More about opioids...
* Lesson from a worm: An endogenous anti-opioid system? (January 5, 2020).
* I feel your pain -- how does that work? (March 4, 2017).

A laser-based missile-defense system to bring down mosquitoes

May 18, 2010

A recent post was about a new approach to reducing disease-carrying mosquitoes: Mosquitoes that can't fly (May 3, 2010). That item involved the genetic modification of mosquitoes to produce flightless females, which can neither bite nor mate. I have since received some alternative suggestions. Here is one of them.

Jakub, whose engineering expertise is in areas other than genetic engineering, sends: Backyard Star Wars -- Build your own photonic fence to zap mosquitoes midflight. (J Kare, IEEE Spectrum, May 2010.) Includes a movie.

Edward Teller must be smiling in his grave.

More on controlling mosquitoes...
* A mammalian device for repelling mosquitoes (December 10, 2018).
* Can Wolbachia reduce transmission of mosquito-borne diseases? 1. Introduction and Zika virus (June 14, 2016).

More about fences: Security fences at national borders: implications for wildlife (August 29, 2016).

BP oil spill incident: the methane hydrate crystals

May 18, 2010

One part of the story of the current BP oil spill incident relates to an interesting Musings post from last year. Let's make the connection.

BP tried to put a containment dome over a leaking pipe at the ocean floor. They soon reported that the attempt was foiled by "crystals" forming, blocking the exit pipe from the containment dome. News coverage of the nature of the crystals varied quite a bit, but the crystals were methane hydrate (also called methane clathrate).

Methane hydrate was introduced here in the post Ice on fire (August 28, 2009).

News story on methane hydrate in the BP incident: Did Deepwater methane hydrates cause the BP Gulf explosion? (Guardian, May 20, 2010.) I encourage you to look over both this item and the earlier Musings post. (This is a replacement news story; the original is no longer available.)

The Wikipedia page on methane hydrate is useful, and even notes the BP story; see the section there on Blowout recovery (or search the page for BP). Wikipedia: Methane clathrate.

Also see...
* Oil in the oceans: made there by bacteria (January 3, 2016).
* A biodegradable agent for herding oil slicks (September 18, 2015).
* Fire from ice: is it practical? (May 13, 2013). A first effort to harvest methane from hydrate deposits.
* Vodka chemistry (July 23, 2010).

Making biofuels from cellulose

May 17, 2010

This item is part of the broad subject of energy sources. More specifically, it is on a process for converting cellulose (such as wood) to biofuels (such as ethanol). I think I have largely avoided this topic -- one that I worked on in my biotech days. Why do I avoid it? There certainly are plenty of papers reporting one or another technical advance. However, there is still no economically practical process for converting wood to useful small molecule fuels. Why? Because that is nature's plan. The "purpose" of cellulose is to be non-degradable. We've been nibbling around the edges of the problem, but have not succeeded in overcoming it. Further, most papers reporting technical advances fail to provide any realistic evaluation of the overall real world situation.

So, what now? A paper with an interesting technical advance, involving some interesting -- and even fairly simple -- chemistry. In addition, they provide a good discussion of the overall process they envision, and they address quite critically what needs to be done to make it work.

The work builds on the finding that cellulose will dissolve in some ionic liquids -- a finding that Jai called to my attention some time ago. However, attempts to degrade the cellulose in the ionic liquid solvent led to excessive degradation. A key finding here is that the excessive degradation is due to lack of water! They then develop a process -- a practical process, they think -- for maintaining the right amount of water. Too much water, and the cellulose is not soluble; too little water, and the resulting glucose degrades. They plan out a complete process, from wood to alcohol. Their analysis raises some questions about its limitations; for example, can the relatively expensive solvent be recycled with high enough efficiency so that solvent cost is not a barrier? The paper is worth reading over as much for this overall view of the process as for the specific advance.

Flow chart of proposed process Flow chart of proposed process; Fig 5 of the paper.

Corn stover is what's left of the corn plant after harvesting the ears of corn. It is an example of an agricultural waste material, rich is cellulose.

[EMIM]Cl is the ionic liquid: 1-ethyl-3-methylimidazolium chloride.

The news release from the university: From raw biomass, chemical process produces simple, fermentable sugars. (University of Wisconsin, Madison, 3/9/10.)

I also found the following news story. I know nothing of the source. The story is somewhat sloppily written, but overall does a good job of presenting the issues. University of Wisconsin Team Develops High-Yielding Chemical Hydrolysis Process to Release Sugars from Biomass for Cellulosic Fuels and Chemicals. (Green Car Congress, 3/11/10.)

The article, which is freely available: Fermentable sugars by chemical hydrolysis of biomass. (J B Binder & R T Raines, PNAS 107:4516, 3/9/10.)

Also see:
* Engineering E coli bacteria to convert cellulose to biofuel (December 13, 2011). This also makes use of an IL to dissolve the cellulose.
* Cellulosics for energy: an update (October 30, 2010). Overview of the use of cellulosics -- and the slow progress being made.

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.

Let parents decide

May 14, 2010

Musings has posted items on personalized medicine. Among the issues are getting the information, and then deciding what to do with it.

The article listed below deals with one specific situation, which has been "real" for several years now. It involves the issue of examining a fertilized egg before implanting it in the mother's uterus, and then deciding what to do. This procedure is called preimplantation genetic diagnosis (PGD).

Rather than me "explain" further, with the risk of editorializing, let me simply offer the article. It is labeled as an Opinion piece, and it is by an expert in the field -- in fact one of the developers of PGD.

The article: Opinion: Let parents decide. (A Handyside, Nature 464:978, 4/15/10.)

If anyone would like to post an article with a differing view, let me know. If you want to write something yourself, try to keep it short; focus on a small number of key points you want to make. (I'm happy to post such replies anonymously.)

One of the first Musings posts about personalized medicine: Personalized medicine: Getting your genes checked (October 27, 2009). This links to several others in the broad area.

A post on developments in evaluating the quality of fertilized eggs: In vitro fertilization: an improvement and a Nobel prize (October 15, 2010).

Another post on IVF ethical issues: Medical ethics: pregnancy reduction (August 20, 2011).

Genome sequencing of a human fetus (August 25, 2012). Another new technology forces us to consider ethical issues.

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

Making replacement insulin-producing cells: another way

May 14, 2010

A new paper suggests a novel approach to making insulin-producing cells: convert nearby cells to become insulin-producing.

They have a model system with mice. They inactivate the insulin-producing cells. Over time, the mice acquire new insulin-producing cells. More detailed analysis suggests that they are coming from nearby cells that had been producing another hormone (glucagon). Further, they suggest that it is a direct conversion, not requiring new cell growth.

A brief tour of your pancreas.

The α (alpha) cells make glucagon; the β (beta) cells make insulin. These two hormones have opposing effects on metabolism of glucose.

Pancreas diagram, showing alpha and beta cells.
From How stuff works: Diabetes.

That seems so simple! But if this really happens, why doesn't it happen in people who lose their β cells? They address this; they suggest that there is evidence it does happen -- at a very low level, and especially in very young children. Perhaps, then, it can happen; the issue is learning how to make it happen at a useful level. With this view, what they have done is to open up a new line of work: learning to control the process of converting α cells to β cells. Time will tell whether this turns out to be useful.

News story: Some Cells in Pancreas Can Spontaneously Change Into Insulin-Producing Cells, Diabetes Researchers Show. (Science Daily, April 6, 2010.)

* News story accompanying the article: Diabetes forum: Extreme makeover of pancreatic α-cells. (Two short items: K S Zaret, M F White, Nature 464:1132, 4/22/10.)
* The article: Conversion of adult pancreatic α-cells to β-cells after extreme β-cell loss. (F Thorel et al, Nature 464:1149, 4/22/10.)

The general goal here is replacement of a missing body function. The approach here is one of several that are competing toward the goal. Others that have been noted in Musings include:
* Print yourself new body parts (April 16, 2010);
* Do you need some new brain cells? (March 22, 2010);
* Pigs as organ donors for humans (February 16, 2010);
* Prosthetic arms (September 16, 2009).

There is more about regeneration and stem cells on my page Biotechnology in the News (BITN) for Cloning and stem cells. It includes an extensive list of related Musings posts.

For more about insulin... Insulin as a treatment for Alzheimer's disease? (January 28, 2012).

For more about diabetes... What color is your rice? Rice, diabetes, and arsenic. (December 12, 2010).

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

May 12, 2010

Breeding plants to be more nutritious

May 11, 2010

This item starts with a post to the Nutrigenomics list; that post refers to an article on the criteria used for plant breeding. The essence of the article is that most plant breeding has been done to improve yield or cost of the plant product, rather than to provide optimum nutrition. This applies broadly to plant breeding, whether by traditional means or by modern "genetic modification" (GM) approaches. Of course, changing this requires that we have specific nutritional goals in mind, and the authors discuss numerous examples.

A complication in all this, beyond having a good understanding of the underlying nutritional issues, is that the emphasis is on individual foods, not on whole diets. It is the overall diet that really matters. We need to at least consider that a good way to remedy the nutritional deficiency of one food is to combine it with another food. However, we also realize that some societies depend heavily on certain individual foods.

Corn (maize) is one example that gets much attention in the article. It is a staple food for some people, but a seriously deficient food. Corn protein is seriously deficient in essential amino acids, and corn contains high levels of phytic acid, a chemical that renders important minerals unavailable to us.

I encourage you to read at least the Nutrigenomics post; it includes the abstract of the article, plus some useful commentary. If you want more, you can wander around individual parts of the article as you wish. I think it is important to separate their general point from any specific detail. The general point is to begin to think explicitly about the nutritional content of plants. People will argue about which nutritional points are most important; getting that argument started is good.

Nutrigenomics post: Crops: Nutrition or yield (May 1, 2010). This item is no longer available; I have no substitute news story.

The article, which is freely available via abstract at PubMed: Elevating optimal human nutrition to a central goal of plant breeding and production of plant-based foods. (D C Sands et al, Plant Science 177:377, November 2009.)

Other posts related to nutrition include...
* Fructose; soft drinks vs fruit juices (November 7, 2010).
* Is folic acid good for you or bad for you? (April 10, 2010).

For more on GM crops, see my page BITN: Agricultural biotechnology (GM foods) and Gene therapy.

My page Internet resources: Biology - Miscellaneous contains a section on Nutrition; Food safety. It includes a list of relevant Musings posts.

Polar bears: ABC

May 11, 2010

There seems to be a fascination with bears -- even if we stretched the idea a bit with our recent post on the subject. Lazy Polar Bears
Bigger picture [link opens in new window].

Ok, so we now understand the fascination part.

So, what's new on the polar bear front? Turns out that the family history of polar bears has not been well established, but we now have some nice progress.

A new fossil was discovered recently. It was clearly from a polar bear, not from the closely related brown bear. Amazingly, scientists were able to extract DNA, and sequence the mitochondrial DNA. The sequence analysis, taken along with that of other bears, showed that the fossil is from very near the time when the polar bears split off from the brown bears. Thus it is a very early example of a polar bear. Coupled with the dating, they are able to estimate when the polar bears split off: about 150,000 years ago. This is a much better estimate than anything previously available.

ABC? The polar bears seem to be most closely related to a particular group of brown bears, found only on Admiralty, Baranof, and Chichagof islands, in Alaska.

That story may sound familiar. It is very much the same kind of story we had with the Siberian finger: an old fossil, which yielded mitochondrial DNA that could be compared with an array of samples from related organisms to determine a family tree. [The Siberian finger: a new human species? (4/27/10).] Again, a caution: the data so far is limited. The family tree drawn in this paper is more detailed than what came before. But new samples and new sequences will undoubtedly refine it further.

News story: One small fossil, one giant step for polar bear evolution. (UC Berkeley, 4/10.) This page is intended as a resource for teachers, but it well serves the role of a news story. It includes a picture of the fossil jawbone, and a nice diagram of the family tree. It also includes links to the article, and to other resources.

The article, which is freely available: Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. (C Lindqvist et al, PNAS 107:5053, 3/16/10.)

The picture above is found at various sites, which come and go. Here is one, from a blog post: Polar bears losing in the game of life? (May 26, 2010)

* Previous item on bears: A space-faring bear that survives the vacuum of space -- and lay eggs normally (4/30/10).
* And then... Bears (5/25/10).

For more about bears, also see:
* Killer chickens - follow-up (12/9/09).
* A new flute -- 35,000 years old (7/1/09).

* * * * *

We noted above that the story of the origin of the polar bear given here is probably incomplete. Indeed, we have more...
* Quiz: Barack Obama and polar bears (July 20, 2011). Check the answer.
* A polar bear update (June 3, 2012).

The miracle of Methylomirabilis

May 10, 2010

Methylomirabilis is a type of bacteria. Its key features include:
* It grows on methane, CH4.
* It metabolizes the methane by the "usual" pathway: the first step is using oxygen, O2, to oxidize the methane, CH4, to methanol, CH3OH.
* It grows anaerobically (without oxygen).

Ok, let's pause a moment. Are you confused? If you aren't confused, please go back and read that again.

For a long time, it was thought that the only pathway for growing on methane used O2. All known methanotrophs (organisms growing on methane) were aerobes, and they all had the key enzyme methane mono-oxygenase (MMO), which uses O2 and leads to methanol.
CH4 + O2 + 2 [H] --> CH3OH + H2O. (The [H] is a shorthand to show that some source of H atoms is needed, but without specifying the details. A good example of a biological source of [H] would be the cofactor NADH.)

Then people found an anaerobic methanotroph. It turned out to be a complex story -- in more ways than one. Briefly, it involved a consortium of microbes (bacteria and archaea), with the overall result that sulfate was oxidizing the methane. Then people found another anaerobe that oxidized methane; it seemed to be using nitrite ion, NO2-, as the oxidizing agent -- but something just wasn't right.

So, what now? They determined the genome (DNA) sequence for this new bug. The genome sequence revealed that this anaerobe has a typical MMO -- that oxygen-dependent enzyme for using methane. The sequence revealed other clues, too. Just briefly... It shows no evidence to support the complex process found in that other anaerobe, noted above. And it shows no enzyme for another property of this bug: it makes nitrogen gas, N2 -- but has no recognizable gene for doing that.

The situation is clear: The bug requires oxygen, but grows without it. Now, that is a paradox. From such paradoxes come new discoveries. And the name Methylomirabilis.

The resolution? Methylomirabilis makes its own oxygen! The nitrite ion is easily converted to nitric oxide, NO. Methylomirabilis seems to have a novel enzyme, which "splits" NO to form nitrogen and oxygen. 2 NO --> N2 + O2. Note that this reaction explains not only the ability to do the O2-requiring reaction anaerobically, but also the unexplained production of N2.

The biological production of oxygen is not completely new. In fact, one type of biological production of oxygen is well known: common photosynthesis. This process, carried out by all higher plants as well as by many photosynthetic microbes, is thought to be the original source of the oxygen in our atmosphere. That's a lot of O2 -- but it is due to one reaction. Beyond that one reaction, there is little evidence for the biological production of oxygen.

News story: New oxygen producing mechanism proposed. (PhysOrg, March 25, 2010.)

* News story accompanying the article: Biogeochemistry: NO connection with methane. (R S Oremland, Nature 464:500, March 25, 2010.)
* The article: Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. (K F Ettwig et al, Nature 464:543, March 25, 2010.) This is actually a quite delightful article. Those who have a bit of background in microbial metabolism may enjoy it. Much is based on genomics, but the story is well told. Further, it includes some interesting points of history about the idea of microbial oxygenesis, and some thoughts about the implications.

Another post that introduced the idea of reactive H being shown as [H]: Photosynthesis that gave off manganese dioxide? (July 21, 2013). Interestingly, this post also involves an oxygen mystery.

More about bacterial growth on hydrocarbons: Polystyrene foam for dinner? (October 19, 2015).

Posts about nitric oxide include... SNO and the higher prevalence of Alzheimer's disease in women (January 14, 2023).

More about the biological use of sulfate as an oxidizing agent:
* Microbes that make elemental carbon (November 27, 2021).
* Nuclear-powered bacteria: suitable for Europa? (March 27, 2018).

This post is noted on my page Unusual microbes.

Racial stereotyping reduced with Williams syndrome

May 10, 2010

Williams syndrome (WS) is a genetic disease. One distinctive feature of people with WS is that they lack "social fear": they are overly friendly -- even with strangers. In a new paper, it is reported that WS children show greatly reduced stereotyping by race, but normal stereotyping by gender.

Fig 1B: stereotyping by WS children Graph of key results; Figure 1B of the paper.

For sex role stereotyping, both control and WS children showed about the same level of stereotyping.

For racial attitude stereotyping, WS children (black bar) showed a considerably lower level of stereotyping than did the controls (gray bar). (50% on the graph represents "no" stereotyping.)

The simple interpretation is that the WS genetic defect is reducing racial bias. Further, one might suggest that the racial bias effect is related to the general lack of social fear. Of course, this is a single result, on a complex issue. I think it is better for now to see the result than to spend too much time trying to analyze it here. I'm sure people will be following up on this, including questioning the details of the procedure and considering alternative interpretations. Think about... What questions does this raise in your mind, both about the testing and about human nature?

Both the news story and paper listed below are short and readable. I encourage you to read both of them.

News story: When Social Fear Is Missing, So Are Racial Stereotypes, Shows Study of Children With Williams Syndrome. (Science Daily, 4/12/10.)

The article: Absence of racial, but not gender, stereotyping in Williams syndrome children. (A Santos et al, Current Biology 20:R307, 4/13/10.)

For another aspect of fear and related emotions, see the post A person without fear -- due to a brain lesion (January 18, 2011).

Maternal mortality

May 7, 2010

This has been a big news story, and is actually both important and interesting.

One of the United Nations Millennium Goals is to greatly reduce maternal mortality: death due to being a mother. The specific numeric goal is a 75% reduction from 1990 to 2015 of the maternal mortality ratio (MMR; given as maternal deaths per 100,000 live births). A major status report has just been announced. Some highlights of the findings...
* As of 2008, there has been a 22% decline, worldwide, since 1990.
* There are huge differences between countries in the actual MMR. Some countries have ratios below 10, and some are above 1000.
* There are huge differences between countries in the progress so far. The average rate of change of the MMR within a country varies from better than -8% per year (i.e., an 8% decline) to "positive" (MMR is increasing). We'll come back to this below, but in some ways it is encouraging: it shows that rapid progress is possible.

This item continues on the supplementary page Musings: Maternal mortality.

The problem of human birth (July 8, 2011). This post deals with the timing of human birth, both compared to other animals and the problem of premature birth.

For more on health care:
* POCDx -- What's the barrier? (January 29, 2013).
* High-tech medicine: good or bad? (June 4, 2010).

More about maternal care: The earliest known example of maternal care? (May 2, 2016).

Posts on premature birth include... Kangaroo mother care for premature babies: start immediately (June 27, 2021). Links to more.

May 5, 2010

Your waste body heat

May 4, 2010

The way you metabolize (burn) your food is, overall, very much like how wood burns. And it produces heat, just as the burning wood does.
CH2O + O2 --> CO2 + H2O + heat. (CH2O is the empirical formula for sugar and its polymers; thus this equation describes the overall reaction both of us eating our food and of burning wood.)

So, what do you do with that heat? Well, you use some of it to maintain your body temperature. But beyond that? You just waste it? Well, you use some of it to warm the room you are in. We all know that a cool room can get noticeably warm after people have been in it for a while -- burning their food. (Of course, in warm weather, this is not helpful!) But beyond that? You just waste it?

Some people in Sweden now collect their excess body heat, and use it to heat a nearby office building.

The idea is simple enough; it's just a matter of doing it -- and making sure it makes economical sense. The room where the crowds are gets warm from all the people; that heat is used to heat water. The water is then transported to the other building, as a source of heat. Engineers design such heat transfer steps into all sorts of industrial processes, with considerable energy savings.

Here is a short news story, which is all I have: Going Green -- Body Heat: Sweden's New Green Energy Source. (Time, April 15, 2010.)

That story will also reveal another recycling that the Swedes are doing for energy.

A recent post on energy recycling: MIT invents a better bicycle wheel (April 24, 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.

A gene for breast cancer: what does it do?

May 4, 2010

Some types of cancer run in families. Two genes that affect susceptibility to breast cancer have been identified: BRCA1 and BRCA2. Women with mutant alleles (forms) of these genes have a high chance of developing breast cancer at some point. Such mutations for cancer susceptibility should offer some clues as to how cancers develop.

The picture that is emerging is that BRCA1 affects cancer rather indirectly. That is, BRCA1 is not a key gene for breast cancer; in fact, BRCA1 mutations are not particularly common in breast cancers in women who lack such mutations initially. Instead, it seems that BRCA1 affects the general accumulation of mutations.

As an analogy, let's look at the role of UV (ultraviolet) light in causing mutations. If a naive observer does simple experiments with E coli bacteria, it may seem that UV causes mutations. However, as one does more work, with various organisms and with E coli mutants, one is led to a somewhat different -- and more complex -- model. That should not be a surprise; more knowledge should lead to a more complete view, and a more complete view is likely to be more complex. We now prefer to say that UV causes damage to DNA -- causes lesions in the DNA. Various things may happen to those lesions. Sometimes, nothing happens, and the cell dies from the damage. Sometimes, the lesion is repaired -- accurately; in such cases, the UV-induced lesions have no effect. In other cases, the lesion is repaired, but "sloppily" -- and mutations result. Thus we see that the UV per se does not cause mutations. Rather, it causes lesions; the lesions may have various fates, one of which may lead to mutations.

Why would a cell use a "sloppy" (or, as we say, error-prone) repair system, if an accurate one is also available? Because sometimes the accurate one is unable to work properly, and the error-prone one is the only way to avoid death. It is better -- perhaps -- to make an attempt to repair the damage than to make no attempt, and die.

It now seems that BRCA1 is involved in a similar choice between accurate and inaccurate repair of damage. Apparently, the normal (wild type) BRCA1 protein helps promote accurate repair. Loss of BRCA1 leads to more error-prone repair, thus allowing mutations to accumulate faster, and cancer to appear sooner. The new finding (see below) is that one can add a compensating mutation, which tips the balance back toward more accurate repair -- and less cancer, despite carrying the BRCA1 mutation.

The new work is in lab mice. The specific technique used to compensate for the BRCA1 mutation would not be directly applicable to real humans. However, the result increases our understanding of how BRCA1 acts. Perhaps alternative approaches to restoring the normal balance between accurate and error-prone repair can be developed.

News story, from NIH: Pathways that can repair BRCA1 cancer gene mutation clarified in mice. (NIH, April 1, 2010.) For the most part, this NIH news release does a good job of presenting the story. However, we should explicitly note a problem with the title. (Remember, headlines are often written by someone other than the author.) The pathway revealed here does not repair the mutation; rather, it compensates for it. The original mutation, a change in the DNA, is still there. Conceptually, this is an important point.

The article: 53BP1 Inhibits Homologous Recombination in Brca1-Deficient Cells by Blocking Resection of DNA Breaks. (S F Bunting et al, Cell 141:243, April 16, 2010.)

Thanks to those who called this item to my attention. It is fine when you tell me of items I have noticed, too; it is sort of like getting extra votes for an item. The NIH mailing list is a good source of information! And because of the complex options, different people will get -- and notice -- different items.

* * * * *

The BRCA1 and BRCA2 genes are the genes that are the subject of the patent dispute that was discussed in the item Can genes be patented? The Myriad case (April 2, 2010).

More BRCA1:
* Distinguishing pathogenic and benign BRCA1 mutants: a high-throughput test (January 26, 2019).
* BRCA1 (the breast cancer gene) and Alzheimer's disease? (February 8, 2016).

More on genes that affect cancer: Fair skin and cancer: What is the connection? (March 12, 2013).

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Cancer. It includes a list of related posts.

Also see: Nobel notes (October 13, 2015).

Mosquitoes that can't fly

May 3, 2010

Now, that sounds like a good idea.

There is a lot of interest in developing better mosquitoes. Better from our point of view: less able to transmit diseases. The proposal here is logically straightforward, and may be practical. The idea is to make the females unable to fly. How do they do this? By introducing a mutation that interferes with the development of flight muscles in the wings of the females. The males carry the mutation, which then spreads as the males reproduce.

Making the females flightless serves two purposes. First, if they can't fly, they probably won't bite you. Second, they are unable to mate. Why can't they mate? Because flying together is a part of the mating ritual. We had a Musings post on this point some time ago -- an item that was presented largely because it was fun, but maybe it is also important. Science: Love songs (March 26, 2009).

One might think of this as a variation on the sterile male approach. The traditional sterile male approach has not worked well with mosquitoes, for reasons having to do with practical aspects of mosquito biology. In the article, they note why their procedure may work better. For one thing, they can mate the males in the lab, and then release the eggs into the wild; this may work better than the usual approach of releasing males.

What have they actually accomplished so far? Proof of principle, we might say. They have introduced the mutation, and shown that the resulting females don't fly. See the company web site, below, for more information, including some preliminary testing of the ability of the mutation to lead to population reduction.

News story: Flightless Mosquitoes Developed to Help Control Dengue Fever. (Science Daily, 2/23/10.)

The article, which is freely available: Female-specific flightless phenotype for mosquito control. (G Fu et al, PNAS 107:4550, 3/9/10.)

Movies are available -- showing that the females don't fly. Go to the link given above for the article, and click on Supporting Information. There are two movies, one each for males and females. You can tell which is which. That's the point.

The paper is from a company, Oxitec, plus two academic labs. (Interestingly, the authors declare no financial interests in the paper. Odd.) The company web site is: Oxitec. Look under "Products"; it is called OX3604C... You will see that it succeeded in eradicating the wild type mosquitoes in a small scale lab test, and that a test in "large scale outdoor cages" is planned for 2010. Perhaps they are on track to "real world" testing.

* * * * *

Another way to modify mosquitoes was introduced in the post The flying vaccinator (April 13, 2010).

Other posts that may of interest...
* Can Wolbachia reduce transmission of mosquito-borne diseases? 1. Introduction and Zika virus (June 14, 2016).
* Mosquitoes are delectable things to eat (August 21, 2010). A serious discussion of the good and bad of mosquitoes. Good perspective.
* A laser-based missile-defense system to bring down mosquitoes (May 18, 2010). An alternative approach.

More about flying... What is the proper shape for an egg? (September 18, 2017).

More about muscles: Making better artificial muscles (March 13, 2018).

A Bird puzzle

May 3, 2010

Can you find the Bird in the following picture?

Bird, with bird

The animal at the right is Dr David Bird, now retired. He was a professor at McGill University and Director of the Avian Science and Conservation Centre there. And he has written a couple of books, on ... Well, just check out his web page: Bird. (The picture above is one from this page. Look around for more information.)

Hobbits: an update

May 1, 2010

Original post: The little people of Indonesia (5/14/09).

Briefly, this is about fossils of small humans, referred to as "hobbits", that were discovered on the Indonesian island of Flores. These may represent a new species of human; this is controversial, and people continue to collect data -- and to argue.

Some new work on the hobbits was presented at a meeting of the American Association of Physical Anthropologists on April 17. Here is a news story summarizing some of that meeting: Hobbit debate goes out on some limbs. (Archaeology Daily News, April, 22 2010. Now archived; scroll down through considerable empty space.) It's a nice article as an update. There are no clear conclusions.

Another Musings post on other human species: The Siberian finger: a new human species? (4/27/10).

A bit more on hobbits: Hobbit DNA? (5/28/10).

A space-faring bear that survives the vacuum of space -- and lay eggs normally

April 30, 2010

One of the wonderful aspects of science is how interconnected things are. That shows up in discussions, as one thing leads to another. So... This is a follow-up to the post on rotifers: Lesbian necrophiliacs (March 8, 2010). One of the points there was that rotifers can survive desiccation (drying). That is a fascinating trait among animals, partly because it is so unusual. The rotifer post noted how resistance to desiccation is important in their normal habitat.

In following up on the rotifers, Borislav found that another group of desiccation-resistant animals has been subjected to "outer space" -- and survived. These are the tardigrades.

An example of a tardigrade is shown at the right. The size is not given, but adult size is typically about 1 millimeter.

If you think it looks somewhat like an insect or such -- the phylum of arthropods... Not exactly. The tardigrades are considered a distinct, but perhaps closely related, phylum.

Bears? Well, the tardigrades are commonly called water bears -- following on the original observations, in the 18th century. That description is supposed to reflect the rather lumbering walking style. So these are "bears" that aren't really bears. The word tardigrade means "slow walker".
A tardigrade

The figure is from Wikipedia: Tardigrade

In 2007, a number of studies of tardigrades were done on the FOTON-M3 mission of the European Space Agency. Among other things, tardigrades were exposed to the space vacuum -- for ten days, which of course, caused them to become desiccated. These space-exposed tardigrades revived almost as well as control samples that had been desiccated in the lab on earth. Another result is shown in the figure below.

Egg-laying by tardigrades exposed to space vacuum. This graph shows how well eggs hatched from animals that had been exposed to space vacuum, vs the controls (desiccated in the lab). The actual extent of egg-laying was similar for both samples.

Results are shown for two tardigrade species.

In each set, the left bar (black) shows the hatching rate for the eggs from the control animals; the next bar (light; "SV") shows the hatching rate for the eggs laid by the animals that had endured space vacuum. For each species, the sample and control gave similar hatching rates.

For one species, a few animals survived the even more extreme treatment of being exposed to both the space vacuum and the full spectrum of Sun's radiation. The right hand bar (medium gray, "UVAB") shows that the few animals that did survive were able to lay good eggs.

This is Figure 1C from the paper listed below.

The article: Tardigrades survive exposure to space in low Earth orbit. (K I Jönsson et al, Current Biology 18: R729, 9/9/08.)

Movies, to show how tardigrades walk: walking movies. This is part of a larger site all about tardigrades, from Bob Goldstein, University of North Carolina.

* * * * *

More... How the tardigrades resist desiccation (April 10, 2017).

Next item on bears: Polar bears: ABC (May 11, 2010).

April 28, 2010

Near-death experiences: the CO2 connection

April 28, 2010

Some people who experience a near-fatal heart attack report a consistent set of experiences, including seeing lights. The phenomenon is termed near-death experience (NDE); it has long intrigued biologists.

Now, scientists have observed a group of such patients; they tried to correlate the results of several physiological measurements with the patients' own report of NDE. The main finding is that high levels of carbon dioxide (CO2) correlate with the report of having an NDE. The results here are entirely correlation, with no information on causality. However, they note independent work suggesting that high CO2 may cause such effects.

This should certainly be taken as preliminary, but it seems to offer some clues that can be followed up. The news story below is, for the most part, a good overview of the main ideas, including the reservations. The article itself starts with a good overview of the problem.

News story: New light on near-death flashes. (BBC, April 8, 2010.)

The article, which is freely available online: The effect of carbon dioxide on near-death experiences in out-of-hospital cardiac arrest survivors: a prospective observational study. (Z Klemenc-Ketis et al, Critical Care 14:R56, April 8, 2010.)

More about NDE: Near-death experiences: are the memories real? (August 11, 2013).

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

The Siberian finger: a new human species?

April 27, 2010

The heart of the story is simple -- and remarkable. A "human" finger bone, found in a cave in Siberia dated at around 40,000 years, yielded DNA that was of good enough quality it could be sequenced. It wasn't long ago we were marveling that people (the same people, incidentally) were getting genome sequence data for Neandertals -- of about the same age. Yesterday's technological breakthrough has become routine! Well, not routine; it is still challenging, but people are doing it.

The result? Well, the DNA sequence suggests it is not modern humans (Homo sapiens) or Neandertals. Taken at face value, it appears to be a new species of human. But here is where we need to be cautious. So far, we have only mitochondrial DNA sequence, a single sample and a single sequence. Further, the dating is not well documented. These are solvable problems. We can offer some tentative interpretations based on what we have so far, but let's remember that they are very tentative at this point, pending further work. The advance news story by Dalton, below, is good at dealing with this -- both what has been found, and the uncertainties surrounding it.

Assuming, for now, that the interpretation holds up, there are a couple types of important implications:
* First, a technical point -- an exciting technical point. This would be the first time that a species of human is identified by genome, rather than morphology. Over the long term, we want to understand the relationship between genome changes and morphology changes, but the former is more fundamental.
* Second, if this new species is confirmed, it may mean that around 40,000 years ago there were four species of humans on earth. And three of them (sapiens, Neandertal, and the Siberian finger folks), all found in the same region, might have interacted with each other. (The fourth human species of that era would be the "hobbits"; see The little people of Indonesia (May 14, 2009).)

A tree, showing how the Siberian finger sample fits with modern and Neandertal humans. A "tree of life" showing how the sample from the Siberian finger bone ("Denisova hominin") fits with modern and Neandertal humans. Relative distances are based on the differences in the mitochondrial DNAs. The new sample has about twice as many differences from modern humans as do the Neandertal samples. Calibration to years is based on archeological information.

News story: DNA identifies new ancient human dubbed 'X-woman'. (BBC, 3/25/10.)

Here are two news stories from Nature. One was published in advance -- actually at the time the article was officially published in online form. The second accompanied the article in print. Both are good, and they complement. I think that some will find the first one a good place to start, and perhaps better balanced in the interpretation.
* Advance news story: Fossil finger points to new human species. (R Dalton, Nature 464:472, 3/25/10.) (If you read the pdf, note that the article covers the top of two pages; when the article seems to stop, in mid-sentence, scroll down to the next page.)
* News story accompanying the article: Human evolution: Stranger from Siberia. (T A Brown, Nature 464:838, 4/8/10.) (The figure above is from this article.)

The article: The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. (J Krause et al, Nature 464:894, 4/8/10.)

Major follow-up post on the Siberian finger sample: a complete genome sequence, and its implications. The Siberian finger: a new human species? -- A follow-up in the story of Denisovan man (January 14, 2011).

And... Denisovan man: beyond Denisova Cave (May 7, 2019).

A previous post on Neandertal DNA sequence: Did Neandertal children hate broccoli? (November 22, 2009).

A Musings update on the Hobbits: Hobbits: an update (May 1, 2010).

A bit more on both the Siberian sample and the hobbits: Hobbit DNA? (May 28, 2010).

A post about the demise of the Neandertals: What happened to the Neandertals? (October 8, 2010).

More ancient biology resurrected from the arctic: A 30,000 year-old plant, with an assist from a squirrel (March 10, 2012).

Science magazine included the broad topic of sequencing ancient DNA as one of its Insights of the Decade. It also specifically noted the sequencing of the Neandertal genome as one of the highlights of 2010. Science: highlights of the decade (January 25, 2011).

More about ancient Siberians: The First Americans: the European connection (February 8, 2014).

Another genome story: Comparing woolly mammoth genomes over time (June 1, 2015).

What if there were no bones at all... Is there useful ancient DNA in the dirt? (August 8, 2017).

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

BOB 2.0

April 26, 2010

Borislav sends the following site: BOB V2.0. And he quotes from it:

BOB had quite a few flaws and drawbacks, so I have now improved BOB in a few ways. (He? It?) now has better:
   Stamina (improved power system)
   'Vision' (extra sensors)
   'Nerves' (connections are made more securely)
   Brainpower (different microcontroller)

* * * * *

The site includes a picture of BOB 2.0.

Folks, if you do work on this, please get "Step 4" of their instructions right.

Borislav's previous attempt to dehumanize me: Cannibalism (4/27/09).

Plants and climate change

April 25, 2010

I recently received the following e-mail announcing a seminar:

Climate science seminar, Tuesday, April 13, 2010

Speaker: Jung-Eun Lee, University of Chicago

Title: Plant hydraulics across geologic time scales: Implications for climate

Movement of water from soil to atmosphere by plant transpiration can feed precipitation, but is limited by the hydraulic capacity of plants, which have not been uniform through time. The flowering plants that dominate modern vegetation possess unique transpiration capacities dramatically higher than any other plants, living or extinct. Transpiration operates at the level of the leaf, however, and how the impact of this physiological revolution scales up to the landscape and larger environment remains unclear. Here, climate modeling demonstrates that angiosperms help ensure a seasonally high levels of precipitation in the modern tropics. Most strikingly, replacement of angiosperm with non-angiosperm vegetation would result in a hotter, drier, and more seasonal Amazon basin, decreasing the overall area of ever-wet rainforest by 80%. Thus, flowering plant ecological dominance has strongly altered climate and the global hydrological cycle. Because tropical biodiversity is closely tied to precipitation and rainforest area, angiosperm climate modification may have promoted diversification of the angiosperms themselves, as well as radiations of diverse vertebrate and invertebrate animal lineages and of epiphytic plants.

Another example of the complex interactions in the natural world!

I checked to see if I could find more about this. The speaker's web site shows that papers are in progress, but I don't see anything that is yet published. So, for now, we have an idea, but without the supporting story.

Angiosperms are the flowering plants. As she notes above, they are now the dominant plant type on land. Another major group of complex plants is the conifers, such as pine trees.

More about angiosperms: Did the earliest dinosaurs like flowers? (October 14, 2013).

More about transpiration: Water loss from irrigated lawns (June 21, 2017).

* * * * *

More, June 7, 2012...

The article on this work has been published: Could Land Plant Evolution Have Fed the Marine Revolution? (C K Boyce & J-E Lee, Paleontological Research 15(2):100, June 2011.)

MIT invents a better bicycle wheel

April 24, 2010

The idea is simple enough. When you brake, capture the energy that would otherwise be wasted, and store it for later use. It's called regenerative braking. The Prius uses it. Now MIT engineers have designed a regenerative braking system for bicycles. A good idea? That's not so clear.

The news story discusses the development, with its pros and cons -- and some other ideas on making better bicycles: For Bicyclists Needing a Boost, This Wheel May Help. (New York Times, 12/14/09.)

A news story from MIT... It has additional info -- for better or worse. MIT's big wheel in Copenhagen -- New bicycle wheel not only boosts power, but also can keep track of friends, fitness, smog and traffic. (MIT, December 16, 2009.)

The project site at MIT... It doesn't have much more at this point, but might be a page to watch if you want to follow this project. Copenhagen wheel.

A subsequent post on energy recycling: Your waste body heat (May 4, 2010).

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

More about braking... A better way to make chocolate, inspired by brake fluid (August 23, 2016).

More about inventions... National Inventors Hall of Fame: 2014 inductees (March 11, 2014).

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.

On his right side, he is female

April 24, 2010

Chicken: female on right, male on left. That's a chicken. Female on his right side, male on her left side.

Note that "right" and "left" are shown on the figure, to avoid the ambiguity of whose right or left is being talked about. The chicken's.

This is Fig 1 from the paper listed below. For more detail: bigger picture [link opens in new window]

In humans, sex is determined by the "sex chromosomes". Males are heterogametic (XY, i.e., one copy of each an X and a Y) for the sex chromosomes, whereas females are homogametic (XX). We have learned that the key is the Y chromosome, which directs maleness. (Rare individuals who are XO -- having one X but no second sex chromosome) are female. Further, we have learned that the Y chromosome determines maleness largely through a single gene, called SRY, which sets in motion the pathway toward maleness. It is generally believed that once the pathway is initiated, sexual development depends primarily on hormones; thus the entire body, sharing the circulating hormones, develops as the same sex.

The chicken pictured above clearly violates this. What's going on?

This chicken is a chimera: it consists of two genetically distinct types of cells. Such chimeras occur naturally, at low frequency, for various reasons. For example, it is possible that the bird is actually a pair of twins that fused early in development. In this case, the two cell types differ in their sex chromosomes: one cell type is male and the other is female. (Birds have a chromosome system of sex determination, as we do, but it is somewhat different in detail.) In fact, the cells on one side are predominantly male, and the cells on the other side are predominantly female.

It is also a gynandromorph: it consists of male and female structures. On the side where the cells are mainly male, the bird developed male characteristics. But this violates what we said earlier, that circulating hormones determine the sexual development, and the animal should be uniform. In fact, the major conclusion from this work is that our simple view is not entirely correct, at least for chickens. It seems here that sexual development is "cell autonomous": each cell develops according to its own genetic complement. Of course, it may well be more complicated, a mix of both systems. That is, what happens is due both to circulating hormones and to local genes.

News story: Scientists Solve Puzzle of Chickens That Are Half Male and Half Female. (Science Daily, March 11, 2010.)

* News story accompanying the article in Nature: Sex determination: An avian sexual revolution. (L A Barske & B Capel, Nature 464:171, 3/11/10.) This article discusses some of the various results that are obtained -- with various organisms and various ways of establishing the chimerism. It is not simple!
* The article: Somatic sex identity is cell autonomous in the chicken. (D Zhao et al, Nature 464:237, 3/11/10.)

For more about chimeras... The first chimeric monkeys (February 5, 2012).

More about unusual sexual development: The basis of intersexuality in moles (November 28, 2020).

Another animal with a 2-sex appearance -- for a completely different reason: Deceiving a rival male (August 28, 2012).

Also see...
* Men are losing their Y chromosomes, and some men are losing them faster than others -- does it matter? (February 25, 2020).
* Can chickens prevent malaria? (August 12, 2016).
* Twenty percent of the females are genetic males (October 6, 2015).
* How flippase works (September 25, 2015).

April 21, 2010

Chemical element #117 -- follow-up

April 20, 2010

Original post: Chemical element #117 (April 13, 2010). The post noted that the new element had been made by fusion of nuclei of elements #20 and 97 -- calcium and berkelium. An astute reader quickly noted, then, that we might refer to the new element #117 as Cal-Berkelium. (She is not from Cal Berkeley, but has visited.) Thanks for that!

Sushi, seaweed, and the bacteria in the gut of the Japanese

April 20, 2010

A recent post was about a role for our gut bacteria in the proper functioning of the immune system. [Is Arthromitus a key bug in your gut? (1/16/10).] It is also clear that a major role of the gut bacteria is digesting food, especially complex carbohydrates that human cells cannot digest. The post here shows that people who eat a particular unusual carbohydrate have special bacteria to digest that carbohydrate. Further, it is possible to propose a simple story about how they acquired those bacteria.

The food in question is a seaweed (a red alga, genus Porphyra), commonly used by the Japanese to wrap sushi. The seaweed contains an unusual carbohydrate polymer (a polysaccharide), called porphyran. (The item here has nothing to do with the meat part of the sushi, only the seaweed.)

There are two key points made in this work.

First, the Japanese have an unusual enzyme that can degrade the porphyran. More specifically, the enzyme is in bacteria in the gut. (The enzyme, of course, is called a porphyranase.)

This first story is fairly straightforward. When a population has a particular digestive need, they (may) evolve a solution to it. It is analogous to a few populations where dairying is common; they have evolved the ability to digest milk (more specifically, the milk sugar, lactose) -- even as adults. There is a difference: humans evolved the ability to use lactose as an adult by a genetic change in the human genome. Apparently, the Japanese evolved the ability to use porphyran by a genetic change in their gut bacteria. That's fine. We know that gut bacteria are important in digesting food, and we increasingly recognize that our gut bacteria are an integral part of us.

The second story is how this porphyranase enzyme got into those gut bacteria. It is in a type of bacteria that is well known -- very common in human gut. However, no one had ever seen this enzyme in those bacteria before. In fact, no one had ever seen this enzyme much of anywhere before -- except in bacteria in the ocean around the algae. That makes some sense: it is an uncommon polymer, and bacteria that can eat it are found only where the polymer is -- in this one type of algae.

A key finding is that the enzyme in the gut bacteria is very similar to the enzyme in the marine bacteria. This similarity led the authors to propose how the enzyme got into human gut bacteria. A "simple" hypothesis: people (in Japan) ate the algae -- raw; thus they ingested the associated bacteria along with the algae. That's how the marine bacteria got into the human gut. But we don't find the marine bacteria in the gut; we find regular gut bacteria -- with the extra enzyme. Somehow, the gene for the enzyme got transferred from the marine bacteria to the gut bacteria -- where it is "useful", in the evolutionary sense. The gene transfer? Well, it seems to be another example of horizontal gene transfer (HGT): transfer from one organism to another (not via parents). HGT is considered relatively common in bacteria, so this is quite plausible. [A recent post about HGT was: GEBA: B -- revisited     or     Horizontal gene transfer: the web of life? a challenge to evolutionary theory? (March 26, 2010).]

In thinking about this story, be sure to distinguish what is "fact" and what is "hypothesis". The facts are that an unusual enzyme is found in two places: marine bacteria associated with the algae, and gut bacteria of people who eat those algae -- but not the equivalent gut bacteria in populations that do not eat the algae. The hypothesis is that the gene was transferred from the former to the latter by HGT, quite possibly in the human gut. A reasonable hypothesis, perhaps the simplest hypothesis (with only limited data available at this point).

The work raises some interesting questions, which should be addressable experimentally. One is what happens to people who change culture -- say from not eating sushi (or algae) to eating it. The whole question of how we acquire our gut bacteria is poorly understood; here we have a case of a specific bacterium with a specific function.

The other question is whether we might be able to demonstrate the HGT of the gene -- perhaps even in an animal gut. When we say HGT is "common", let's remember the power of natural selection in amplifying rare but useful changes. It's likely that a single HGT event, some thousands of years ago, was responsible for all we now see here. But maybe the event can be re-created. It might be interesting to see if it could be shown in humans, but we do not make good experimental animals. I have a hunch that we are going to read about a lot of mice being fed sushi.

News story: How Gut Bacteria Evolved To Feast On Sushi. (NPR, 4/7/10.)

* News story accompanying the article: Microbiology: Genetic pot luck. (J L Sonnenburg, Nature 464:837, 4/8/10.)
* The article: Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. (J-H Hehemann et al, Nature 464:908, 4/8/10.)

Posts about plant-bacteria associations:
* A new organelle "in progress"? (September 13, 2010).
* Plants need bacteria, too (October 9, 2010).

Science magazine included the broad topic of the role of microbes in our body as one of its Insights of the Decade. Science: highlights of the decade (January 25, 2011).

Next post on sushi: In what year was the word "slavery" most used in books? (February 23, 2011).

and... DNA evidence in restaurants: is the fish properly labeled? (June 5, 2017).

Also see:
* The biological basis of sanguivory (March 2, 2018).
* Red meat and heart disease: carnitine, your gut bacteria, and TMAO (May 21, 2013).
* Getting along: animals and bacteria (August 6, 2012).

Turkey stories

April 19, 2010

An ancient bowl features a turkey "An ancient bowl features a turkey, originally raised for feathers and ritual use, not meat."

Figure and above caption text are from the news story listed below; the figure here is reduced.

Did you know that the turkey commonly grown in the US for food came here from Spain? It was originally from what is now Mexico, but came to the US via Spain.

The new finding is that the turkey was domesticated twice in North America -- the Mexican bird, mentioned above, and once in what is now southwest US (Four Corners area).

How does one learn all this? By studying the DNA in near-fossilized bird droppings.

News story: Turkeys domesticated not once, but twice. (Los Angeles Times, 2/3/10.) "New research indicates that the birds were tamed in Mesoamerica and what is now the Southwestern United States, with the poultry we eat today descending from the former region."

News release from Washington State University, where the work was done... DNA Analysis Finds Earliest Example of a Domesticated Bird in U.S.. (2/1/10 -- though the page seems to be undated. Now archived.) It links to more at the University.

The article is freely available: Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication. (C F Speller et al, PNAS 107:2807, 2/16/10.)

For a delightful essay about another American icon in the skies: Eagles (November 10, 2008).


April 19, 2010

A commercial -- as social commentary: Priest-off.

The human genome - 10 years on

April 16, 2010

2010 marks the tenth anniversary of the first announcement of the human genome. The event being commemorated was perhaps rather contrived (politics!), but still it is a time for some reflection on what has happened, and some predictions about what the future may hold.

Musings has posted numerous items in this broad area. Among them...
* Personalized medicine: Getting your genes checked (10/27/09). It links to some others items on the use of genomic information.
* Inuk, a 4000 year old Saqqaq from Qeqertasussuk (March 1, 2010). An example of sequencing of human genomes.

Nature devoted a substantial part of its April 1 issue to this human genome anniversary. It is at: The Human Genome at 10: Growing pains of the genomics age. (Nature, 4/1/10.) Some articles are freely available. There is quite a range of short essays. Look around, and try some of them. I might especially recommend...
* the Feature "Life is complicated"
* and the pair of Point-Counterpoint essays by two MIT cancer biologists on the merits of hypothesis-driven vs data-driven research.

At about the same time, National Geographic posted a nice page with brief discussions of five advances from this ten year period of the human genome, plus five predictions for the next ten years. This is a nice overview with lots of good ideas presented concisely. Human genome at ten: 5 Breakthroughs, 5 Predictions. (National Geographic, 3/31/10. Now archived.)

Also see: How many human genomes have been sequenced? (November 30, 2010).

There is more about genomes on my page Biotechnology in the News (BITN) - DNA and the genome.

Print yourself new body parts

April 16, 2010

Burns can be a serious medical problem. Perhaps it is only with severe burns that we appreciate the importance of skin -- the largest organ in the body, and our first line of defense against infection.

The proposal here is to replace missing skin with skin cells, sprayed on to the wound using something very much like an inkjet printer. This works better than skin grafts -- in the preliminary work done so far with mice.

We don't have much information at this point. The work has been presented at a meeting, and briefly covered in the news media. The idea is intriguing, but until it actually gets tested in humans, it is not much more than a proposal. Certainly an interesting proposal.

It is unclear to me who the donor would be. In the mouse work discussed here, apparently human cells were used. I suspect the mice were immune-deficient. In real use, would the donor be the patient? In that case, time is needed to prepare the cells. Or would some foreign donor be used, perhaps providing only a temporary barrier until the patient regenerates his own skin? These are just some examples of questions that need to be answered before we claim this actually works.

News story: Inkjet-like device 'prints' cells right over burns. (Reuters, April 8, 2010.)

Update February 2020... The original post, as shown above, does not include an actual scientific article. Since the topic of this post came up again, and the new post refers to this one, I checked for an article. I don't see an article focusing on the work noted here, but a review article the following year probably includes it reasonably. Drop-on-demand inkjet bioprinting: a primer. (K W Binder et al, Gene Therapy and Regulation 6:33, 2011.) Check Google Scholar for a freely available copy.

* * * * *

Another post on printing cells onto burns: A handheld printer that can print cells onto a severe burn (February 16, 2020). A decade later, the technology is better.

Other items exploring ways to make replacement body parts...
* Next: Making replacement insulin-producing cells: another way (May 14, 2010);
* Previous: Do you need some new brain cells? (March 22, 2010);

More complex applications of printing body parts:
* 3D printing of human tissues: the ITOP (May 24, 2016).
* 3D printing: simple inexpensive prosthetic arms (January 29, 2014).

More on wound healing: Targeting growth factors to where they are needed (April 21, 2014).

There is more about regeneration and stem cells on my page Biotechnology in the News (BITN) for Cloning and stem cells. It includes an extensive list of related Musings posts.

April 14, 2010

The flying vaccinator

April 13, 2010

If that conjures up an image of a jet-set doctor flying to distant lands delivering polio vaccine... no. The flying vaccinator here is a natural-born flier. And very tiny. And female. And well-known for delivering things to us. Usually diseases. But it has occurred to scientists that perhaps we could get it to deliver a drug -- or a vaccine -- along with the disease, or maybe even instead of the disease.

The idea here is actually quite simple in principle -- but quite a technical achievement. Jitesh Dundas noted the announcement that scientists have genetically engineered mosquitoes to make specific proteins in their saliva. (Getting genetically engineered proteins to be made in a specific organ is always an important issue in any kind of "gene therapy".) And if the mosquitoes make a protein in their saliva, they will deliver it to you -- when they bite you.

The scientists engineered mosquitoes to make a protein that is being considered as a vaccine against another protozoan disease, leishmaniasis. The mosquitoes make the protein in their saliva. Lab mice that were bitten by these mosquitoes developed antibodies to the protein. At some level, that is proof of principle.

With luck, you have some doubts about the practicality of this approach. The news stories below discuss some of them, as does the article itself. In reading this item, you need to separate several issues, including the scientific accomplishments and the specific application that seems to be emphasized.

The news story that Jitesh first noted: Researchers Engineer Mosquitoes into "Flying Vaccinators". (GEN, 3/19/10.)

A more thorough discussion: Researchers Turn Mosquitoes Into Flying Vaccinators. (Science Now, 3/18/10.) (I suggest that you not click on the link just above the figure.)

The article: Flying vaccinator; a transgenic mosquito delivers a Leishmania vaccine via blood feeding. (D S Yamamoto et al, Insect Molecular Biology 19:391, 6/10.)

Those who need a picture can click on Genes that protect against malaria (January 19, 2010) for your fix.

For another way -- perhaps a better way -- to modify mosquitoes: Mosquitoes that can't fly (May 3, 2010).

More on gene therapy: Gene therapy: Curing an animal using a ZFN (August 9, 2011).

Science in Asia-Pacific region -- as ranked by Nature

April 13, 2010

A recent issue of Nature had an insert: the Nature Asia-Pacific Publishing Rankings 2009. Since several people here are in or from that region, I thought this might be of interest.

The simple story is that the folks -- or the computers -- at Nature have sorted through all the papers in the Nature family of journals, 1998-2009, and determined how many are from each country. (They also do a "correction", to allocate multi-country articles to the various countries.)

"Asia-Pacific" here seems to be Asia from India eastward, plus Australia and nearby countries. (Russia is not included.) The 12 countries listed -- apparently the only 12 countries in the region to have papers in a Nature journal in 2009 -- are (in alphabetical order): Australia, China, India, Indonesia, Japan, New Zealand, Papua New Guinea, Singapore, South Korea, Taiwan, Thailand, Vietnam. (Cambodia has now joined the list, in 2010.)

Their system provides a simple objective way to watch the development of science in this region. More important than the rankings, perhaps, is simply the information. Those looking for schools in the region may find the lists of specific institutions of interest.

Update, March 10, 2016. Web site for Nature Asia-Pacific Publishing Index: That page is no longer available, but has been superseded by: Nature Index.

There are many lists of universities by various criteria; caution should be used with any such list. The one from the Shanghai Jiao Tong University has a world perspective and a good reputation. It offers lists of the "top 500" universities in the world, based on their graduate programs in various fields: Academic Ranking of World Universities. [The ARWU site is also noted on my page Internet resources: Miscellaneous under Colleges and universities (local, and beyond).] The Wikipedia page about this site has a lot of information, and could be a good place to start: Wikipedia: Academic Ranking of World Universities. (Click on a country on the map to bring up a list of ranked universities for that country.)

Nature's "Top 50" institutions for scientific research (May 9, 2011). This is, in part, a follow-up post.

Chemical element #117

April 13, 2010

A new chemical element has been reported. Element #117 was made by bombarding a target of berkelium (Z = 97) with calcium nuclei (Z = 20). Occasionally, fusion of Bk and Ca nuclei occurs, giving a nucleus with 117 protons. Such events are identified by following their decay products. Six atoms of the new element were detected -- over about two months.

Until it is confirmed and formally accepted, the new element will be known as ununseptium (Uus).

Assuming that all the tentative reports are confirmed (elements 113-118), there are currently no gaps in the periodic table. Elements 1-118 have all been reported.

Students ask why we are so interested in making these new heavy elements and heavy isotopes. Of course, the usual scientific curiosity is one good reply. But in addition, heavy isotopes are helping us to answer questions about the structure of the nucleus.

Our understanding of nuclear structure is incomplete. Theories predict that at some point, heavier isotopes should be more stable than lighter isotopes. Different theories predict different specifics, and one use of the data on heavy isotopes is to help choose between -- and refine -- the theories of nuclear stability. Some theories even make the tantalizing prediction that there may be very heavy isotopes that are stable enough to "hang around", and maybe even be useful.

Half-lives vs N The graph at the left shows evidence that heavier isotopes are indeed more stable. Each dashed line shows the data for one element (111 to 115). Each point shows the observed half life, for alpha decay, as a function of the number of neutrons in the nucleus. For example, look at the line for element 111. The half-life increases from about a millisecond at N = 167 to about 2 minutes at N = 170. What if we could check even heavier isotopes? And that's the problem: the technical difficulty of making the isotopes increases with increasing N -- making the most interesting regions of these curves inaccessible so far. Nevertheless, the graph shows that there is a trend toward greater stability with higher N.

The graph is Part B of Figure 3 of the paper listed below. For our purposes here, ignore the left side, with N ≤ 165.

News story: International team discovers element 117. (ORNL Review Vol. 43, No. 2, 2010.) This is from the Oak Ridge National Laboratory (ORNL), one of the institutions doing the work. A version of this was originally a news release dated April 7, 2010.

* "Viewpoint" story accompanying the article, freely available at: Exploring the island of superheavy elements. (S Hofmann, Physics 3:31, April 9, 2010.)
* The article is freely available -- if you use the journal's special link: Synthesis of a New Element with Atomic Number Z = 117. (Yu. Ts. Oganessian et al, Physical Review Letters 104:e142502, April 9, 2010.)

* * * * *

There is a follow-up post: Chemical element #117 -- follow-up (April 20, 2010). This post suggests a name for the new element.

* * * * *

* Previous post on the chemical elements: Element #112: Copernicium (July 15, 2009).
* Next: Chemical elements 114 and 116 officially recognized (June 8, 2011).
* And... Glenn Seaborg centennial (April 18, 2012).

This news was also presented on my page of Internet resources for introductory chemistry: Element #117. Also see other sections on that page on the newer chemical elements.

Added February 7, 2024. This post is listed on my page Introductory Chemistry Internet resources in the section Lanthanoids and actinoids. This listing reflects the use of Bk in the work.

He hi - ha - he

April 10, 2010

What do you think that title represents?

A laugh, or giggle? Good. But did you recognize it as a laugh, or "giggle call", from a laughing hyena? A subordinate laughing hyena? And did you know that the University of California, Berkeley, maintains a colony of these hyenas on campus?

Berkeley researchers have analyzed the giggles from several members of the colony, with the goal of understanding what role these vocalizations play in the life of these highly social animals. They conclude that the sounds convey social status; they probably serve as key indicators that help maintain the strict social structure.

A hyena

Both items below include sounds clips of giggles from various members of the UC Berkeley community.

News story: Giggles give clues to hyena's social status. (UC Berkeley, 3/30/10. Now archived.) The picture above is from this story. I do not know if it is an individual from the Berkeley colony.

The article, which is freely available: What the hyena's laugh tells: Sex, age, dominance and individual signature in the giggling call of Crocuta crocuta. (N Mathevon et al, BMC Ecology 10:9, 3/30/10.)

Some bad news... The Berkeley hyenas (March 20, 2012).

More Berkeley wildlife... Berkeley wildlife (September 3, 2010).

Folding towels

April 10, 2010

News story: Researchers enable a robot to fold towels. More than just a household convenience, the project is a step forward in the robotic manipulation of non-rigid objects. (UC Berkeley, April 2, 2010.) It includes a video. It also links to a paper, which is to be presented at a meeting in May. (I presume that the paper is not peer-reviewed or otherwise published at this point.) A direct link to the paper, which is freely available at the authors' web site: Cloth Grasp Point Detection based on Multiple-View Geometric Cues with Application to Robotic Towel Folding. (J Maitin-Shepard et al, paper to be presented at the International Conference on Robotics and Automation, May 2010.)

Robot seeks towel corners. The robot is trying to find two adjacent corners of the towel. It will.

This is from Fig 2 of the paper; that figure shows a flow chart of how the robot works, and a series of stills, such as this one, from one sequence. The sequence is from the video in the news story.

* Among recent Musings items on robots: Synthetic brains (January 25, 2010).
* Previous Musings items on towels: none.

* Next Musings item on robots: Nanorobots: Getting DNA to walk and to carry cargo (August 7, 2010).

More folding stories:
* A robot that can fold itself up (December 9, 2014).
* How to fold a bag (May 13, 2011).

Another laundry story: When the laundry piles up... An econophysics critique of smart meters (December 6, 2015).

If anyone wants to post a video of you carrying out this activity, please let me know.

Is folic acid good for you or bad for you?

April 10, 2010

The emerging answer is: Yes.

A deficiency of folic acid in early pregnancy leads to birth defects (neural tube defects, such as spina bifida). There is no question that providing adequate folic acid to women in early pregnancy is worthwhile. There has been a demonstrable decrease in birth defects from the attention given to folic acid.

One approach to making sure that pregnant women get enough folic acid is that many foods are now supplemented (fortified) with it. Since the critical period for the folic acid effect is very early in the pregnancy, it is not sufficient to wait until the woman knows she is pregnant. Folic acid supplementation of foods serves the population of those who might become pregnant. It also serves everyone else. Is this really a good idea?

There has long been some concern that high folic acid intake could mask a deficiency in vitamin B12. This is a fairly specific issue, and can be dealt with. Beyond this, the common view has been that folic acid is generally safe. But now we are beginning to question that. There is increasing evidence associating high folic acid intake with increasing incidence of cancer.

What's the take home lesson from this? I honestly don't know. I think I would encourage you to be cautious in reaching conclusions. A given chemical does not have to be "good" or "bad"; it is fine for it to be both, under one situation or another. A single report of an effect -- or lack thereof -- is not a final answer. Small effects can be hard to document in any case. And if there really is more than one answer, depending on conditions, many studies, especially early ones, may not properly take that into account. There does seem little doubt that having adequate folic acid during early pregnancy prevents neural tube birth defects. Beyond that, maybe the best answer is that we do not know. At least, some good questions are now being asked.

If the role of folic acid in causing cancer is supported by further work, how do we deal with it? How do we balance the benefit of folic acid -- on the next generation -- with possible risk to the mother? With possible risk to the general population? Would reducing the level of folic acid supplementation be sufficient? Or will we need to change the strategy, targeting the supplements only to those who have a specific need?

The following two items are from the same issue of the Journal of the National Cancer Institute (JNCI). The second is a report of the effect of folic acid on certain cancers. The first is an editorial, discussing this paper, and also giving something of a broader view of the role of "nutritional supplements" or "micronutrients" on cancer. I strongly encourage you to read the editorial, for general perspective. Both items are freely available at the JNCI website.
* Editorial: Nutritional Prevention of Cancer: New Directions for an Increasingly Complex Challenge. (A R Kristal & S M Lippman, J Natl Cancer Inst 101:363, March 18, 2009.) Read it!
* Article: Folic Acid and Risk of Prostate Cancer: Results From a Randomized Clinical Trial. (J C Figueiredo et al, J Natl Cancer Inst 101:432, March 18, 2009.)

Here is a somewhat older news story on the same general issue. It discusses different data, but with the same general concern: folic acid may be both good and bad. Folic Acid Linked To Increased Cancer Rate, Historical Review Suggests. (Science Daily, 11/5/07.)

There is a special twist to the folic acid story. Sometimes one hears a debate about whether synthetic and natural forms of a chemical are the same. Of course they are -- if they really are the same chemical. Vitamin C (ascorbic acid) is a good example; natural and synthetic are the same. But folic acid is different. There are actually various chemical forms of what we generically call "folic acid". The form of folic acid used as a supplement is not one of the major natural forms. So when you see people talking about a difference between the effects of food folic acid and supplemental folic acid, that is indeed plausible -- though there are other possibilities, too.

Disclaimer... The usual. I do not give medical (or nutritional) advice. (I have no formal qualifications to do so.) There is always more to the story than can be presented here. Sometimes what is presented here is obviously only part of the story. In this case, I have suggested that I have given some overall sense of the field. Maybe I have done that well, or maybe not. Read what I wrote, read some of my sources; read more. If you think you have something different worth presenting, let me know.

Despite the Disclaimer... I do hope that one of the big general messages here is to be cautious about food supplements. There is much hype about them, and they are poorly regulated. Vitamins may be essential, but that does not mean "more is better". Some are well known to be toxic at high does (e.g., vitamin A). In other cases, claims are made that are not substantiated. There is no convincing evidence that vitamin C has any benefit against colds or cancer. There is no convincing evidence that supplemental anti-oxidants have any benefit; indeed clinical trials of beta-carotene have even shown an increased incidence of cancer in some situations.

A previous post on food supplements: Omega-3 fatty acids; fish oil (March 29, 2010).

Another example of the difficulty of determining a suitable dose for a nutrient... Vitamin D: How much is too much? (July 9, 2013).

And more generally... Should you take a vitamin (or mineral) supplement? (July 14, 2014).

* How vitamin C kills cancer (December 15, 2015).
* Anti-oxidants and cancer? (October 18, 2015).

Other posts related to nutrition include...
* Rice and arsenic: a follow-up (January 8, 2012).
* Fructose; soft drinks vs fruit juices (November 7, 2010).
* Breeding plants to be more nutritious (May 11, 2010).

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

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

April 7, 2010

How fish rot -- and the implications for studying fossils

April 6, 2010

Scientists in the Department of Geology at the University of Leicester have reported the results of their study of how fish rot.

Ok, now that you have crossed off the Leicester Geology Department from your list of schools to attend...

The results were reported in Nature, which means someone thinks they were important results. In fact, there is one major conclusion, one that has implications for how we read the fossil record. They found that fish decay non-randomly. For example, in the study of one particular kind of larval fish, which took about 200 days to completely decay under their conditions, the buccal tentacles were always gone by day 3, the heart by day 11, and the dorsal fins by day 90. There was a pattern to decay. Further, there was an evolutionary issue: body parts that are considered more recent, in evolutionary terms, tended to decay first. That is, as the animal decays, it looks more and more like a more ancient animal. This last point is particularly important, as it suggests there is a bias in judging the evolutionary age of a fossil.

The problem occurs for soft tissue, not for bones. They are studying primitive chordates -- at the root of the branch that led to vertebrates, including humans. Soft tissues fossilize poorly, in any case, and interpretation of fossils at the chordate base is often contentious. The new work increases our understanding of such fossils -- but also means that some previous interpretations will need to be re-examined.

News story: Rotting Fish Spoil Ideas about Early Life-Forms' Simplicity. (Scientific American, 1/31/10.)

* News story accompanying the article in Nature: Palaeontology: Decay distorts ancestry. (D E G Briggs, Nature 463:741, 2/11/10.)
* The article: Non-random decay of chordate characters causes bias in fossil interpretation. (R S Sansom et al, Nature 463:797, 2/11/10.)

More about processes that can affect the fossil record: What did Osedax worms eat before there were whales? (May 30, 2015).

More about rot: Better violins through better fungi? (March 4, 2013).

The cow ate the data

April 6, 2010

Science occasionally publishes short letters which are simply funny incidents.

Life in science: The cow ate my fieldwork. (B L Madsen, Science 327:1079, 2/26/10.)

Remember, cows -- or, rather, the microbes in their gut -- can digest paper (cellulose).
cartoon: The cow ate the data

Genome sequencing to diagnose child with mystery syndrome

April 5, 2010

A sick child does not respond to standard treatments. Doctors are baffled. They make a list of all the genes they can think of that might be involved -- about 2000 of them, about 10% of his genes. They check the genome sequence of all these, and find nothing. Finally, they check the genome sequence of all the child's genes -- and find what is wrong.

News story: Doctors use genetic code to make groundbreaking diagnosis. (Journal Sentinel (Milwaukee), March 27, 2010. Now archived.) Read it!

That news story is about all we have at this point. We have little basis for evaluating the details. Was this the proper, cost-effective treatment for this child at this time? Will the child be effectively treated? Who knows. That really misses the point, in the big picture.

This is a remarkable -- and historic -- event. For the first time, a human being is diagnosed based on a large scale genome sequencing to see what is wrong. The information base for this was developed only within the past decade. The technical tools to allow it to be done for the indicated cost have only been developed within that same decade. Improvements in both the information base and in the sequencing technologies will continue. Stay tuned.

There is a major update to this story: Genome sequencing to diagnose child with mystery syndrome -- follow-up (May 17, 2011).

Is whole genome sequencing a useful medical tool? (November 9, 2011). The cost of genome sequencing continues to drop. Will it become common in medicine?

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

Implications... More genome sequencing for newborns? (September 17, 2013).

More... The emerging role for genome sequencing of sick babies (October 27, 2014).

A major step: Project Baby Bear: Is it worthwhile to sequence the genomes of babies with mysterious ailments? (October 18, 2021).

Recall previous discussions of personalized, genome-based medicine, such as: Personalized medicine: Getting your genes checked (October 27, 2009). The new work falls under this umbrella, but is distinct in scope.

Perspective... DNA sequencing: the future? (November 7, 2017).

Another case of a bold pioneering treatment for a sick child: Gene therapy and stem cells: A child gets new skin (January 22, 2018).

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

A dinosaur in color

April 5, 2010

Dinosaur, in color

The figure, of course, is an artist's conception of what this dinosaur looked like, based on analysis of fossil samples. What's neat is that the colors shown here are based on evidence. They analyzed the structure of the melanosomes (cells that produce melanin pigment) in fossil feathers, and compared the dinosaur melanosomes with those of modern birds and their fossils. Thus they inferred the color of the feathers in particular parts of the dinosaur.

News story: True-Color Dinosaur Revealed: First Full-Body Rendering. (National Geographic, 2/4/10. Now archived.) Includes an animation, which shows you the dinosaur through a 360° rotation.

The article: Plumage Color Patterns of an Extinct Dinosaur. (Q Li et al, Science 327:1369, 3/12/10.) The figure above is Fig 4 of the paper. The figure legend: "Reconstruction of the plumage color of the Jurassic troodontid A. huxleyi. ... Color plate is by M. A. DiGiorgio."

An earlier post was about the analysis of Dinosaur proteins (July 6, 2009). As noted there, that discovery provoked considerable controversy, but may be gaining acceptance as more information becomes available, and criticisms are addressed. It will be interesting to see how well the new findings, showing color, will be accepted. One concern here is that the analysis considers only melanin pigment; the possible contribution of other pigments is unknown.

Another, unrelated, story of color in dinosaurs: Red color vision in dinosaurs? (October 17, 2016).

More about dinosaurs: Do animal bones have something like annual growth rings? (August 7, 2012).

More about melanin: The story of the peppered moth (July 9, 2012).


April 2, 2010

The use of fingerprints is probably one of the best known applications of science in the legal system. But how scientific is it? Nature recently ran a short News Feature on this; I think you may find it fun to look over.

Science in court: The fine print. (L Spinney, Nature 464:344, March 18, 2010.) From the subtitle: "A single incriminating fingerprint can land someone in jail. But, Laura Spinney finds, there is little empirical basis for such decisions."

As a bonus... An accompanying News Feature in that issue of Nature is on DNA fingerprinting, especially a recent trend toward using it on smaller and smaller samples. Science in court: DNA'S identity crisis. (N Gilbert, Nature 464:347, March 18, 2010.) From the subtitle: "It may be the gold standard of forensic science, but questions are now being raised about DNA identification from ever-smaller human traces. Natasha Gilbert asks how low can you go?"

* * * * *

More about fingerprints: Can one tell if a fingerprint is from a male or a female? (December 4, 2015).

Can genes be patented? The Myriad case

April 2, 2010

There are follow-up posts; they are linked near the end of this item.

Jitesh Dundas just sent me the following item: Patents on Breast Cancer Genes Ruled Invalid. (GEN, 3/30/10.)

The story behind the ruling is long and messy. I have obvious strong biases -- in both directions. As a long time part of the biotech industry, I might be expected to have strong feelings for the Myriad position. As a long time member of the ACLU, I might be expected to have strong feelings against the Myriad position. So, for me to try to explain this would probably not be fruitful. The story above at least introduces some of the arguments on each side; a useful start. I would encourage you to try to emphasize understanding the issues in the dispute, rather than trying to reach any simple clear conclusion. (Unless you understand the arguments on both sides, you are not in a position to choose between them.) The purpose of a patent is to protect an inventor, and also to promote the use of the invention for the benefit of society. People disagree on the balance between those two goals -- as the Myriad case shows.

A couple of comments...
* Remember that the role of the courts is to interpret the law, not to write law. And the relevant law in this case is "old": it predates and does not anticipate "genes". (To my knowledge, there are no modern laws dealing with the patenting of genes. As with my other comments on the legal issues, this refers to US law.)
* One reason that Myriad drew so much attention is that many considered their implementation of the patent to be "outrageous". It is an interesting speculation what would have happened if Myriad had implemented a licensing plan with more modest terms and fees.

The story of the Myriad patent on breast cancer genes has been playing out for many years. The ruling here is a step. But it is not the last word.

There are follow-up posts:
* Can genes be patented? The Myriad case -- follow-up (November 8, 2010).
* Can genes be patented? The Myriad case -- legal issues (November 28, 2010).
* Can genes be patented? The Myriad case -- Reversal (August 10, 2011).
* Can genes be patented? The Myriad case: The Last Word (June 26, 2013).

This post is not specifically about the Myriad case, but about a broader framework: Commercializing the output of academic research (January 31, 2011).

Another case: CRISPR: the legal battles begin (February 1, 2015).

More about inventions... National Inventors Hall of Fame: 2014 inductees (March 11, 2014).

A post about how the BRCA1 gene works: A gene for breast cancer: what does it do? (May 4, 2010).

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Cancer. It includes a list of related posts.

March 31, 2010

The sounds of vegetables

March 31, 2010

The sounds of vegetables.

The pictures are from this site. There are videos here, too.

a carrot flute a gurkophon

I hope this is good fun, regardless of your tastes -- in vegetables or music. But it is also good science!

More about vegetables... Microbes on your fresh fruits and vegetables? (May 29, 2013).

There is more about music on my page Internet resources: Miscellaneous in the section Art & Music.

Earthquakes: increasing?

March 30, 2010

A recent post about the Chile earthquake, Chile earthquake caused the day to become shorter (3/8/10), stimulated some discussion about earthquakes. This post addresses one of the questions that came up.

There have been a lot of earthquakes in the news recently, including the major quakes in Haiti and Chile. The former resulted in a huge death toll; the latter was one of the largest quakes ever recorded. It is natural to wonder if there is some increase in earthquakes. It's actually a rather complex question, since quakes come over a range of intensities. The damage caused by a quake, whether in death toll or economic damage, is a function of location as well as intensity. In this context, "location" includes both the population density and the quality of the construction. There is one quake of magnitude ≥6 nearly every two days somewhere on earth. However, only a few of those, mainly large ones in susceptible locations, are of concern, and their numbers are too low for good statistical analysis.

Here is a recent news story which presents some analysis of the question. Not more quakes, just more people in quake zones. (San Diego Union Tribune, March 8, 2010.)

Graph showing quake intensities and death tolls, 1998-2010. This is the key figure from that story. (It is the lower part of the first figure from the story.)

The main point made here is that there is no particular trend. The left graph shows the number of quakes with magnitude of ≥6 over recent years. It fluctuates, but does not show any clear trend. (Of course, a version of this over a longer time span might be interesting. The story does say that there seems to be no trend from 1970 to the present.)

The graph at the right shows the death toll. There are two major spikes, for 2004 and 2010. Those are due to particular events: the Indonesia quake of December 2004, and the recent Haiti quake. (Much of the death toll of the 2004 event was due to the subsequent tsunami.) The years 2006-9 show a minimal death toll, and yet have a frequency of quakes that is normal, or even slightly above.

Clearly, the earthquakes that attract our attention are special cases of some unusual interest; they do not reflect any general trend toward having more quakes. However, the article also cautions us that things are not simple. There has been a burst of earthquakes in the early part of 2010 -- due to aftershocks from the Chile quake. Clearly, these are causally related. Quakes are not entirely random, at least over short distances and times.

The data on which the article is based are publicly available. If anyone sees an article they find of interest on this subject, perhaps with different approach or conclusions, I encourage you to send it to me.

* We now have two papers on this topic. See the post: Are large earthquakes occurring non-randomly? (February 10, 2012).

Other posts on earthquakes include:
* The great Tonga earthquake: how many quakes were there? (September 12, 2010).
* The Quake-Catcher Network: Using your computer to detect earthquakes (October 14, 2011).

More about tsunamis: Modeling the tsunami from the asteroid impact that caused the dinosaur extinction (October 16, 2022).

Omega-3 fatty acids; fish oil

March 29, 2010

Thien sent the following site, which provides a brief but useful overview of fish oil tablets, used to provide ω-3 fatty acids (FA). "Fish oil" site. See the following paragraph for an update.

Update, August 21, 2013... The site was originally posted as part of the UC Berkeley Wellness Guide to Dietary Supplements. It is now archived at Fish oil. Berkeley Wellness has now posted the following page, which is presumably intended as an update: Omega-3 Supplements in Question. (Berkeley Wellness, May 9, 2013. Now archived.)

What's this all about? Fatty acids are described by the chain length and the number and position of double bonds (unsaturation). One group of them has the last double bond three carbons from the end; these are called ω-3 FA, or n-3 if you want to avoid the Greek "omega". There is considerable interest in the importance of n-3 FA. One result is promoting fish oil supplements, to provide additional n-3 FA. As you read about this class of nutrients, think about two questions: One is the value of the nutrient; the other is whether, if you think it is worthwhile, it is better to get it by eating appropriate foods or by taking supplements. Of course, one issue along the way is to be careful about promotional information from those selling the supplements.

For more: Position of the American Dietetic Association and Dietitians of Canada: Dietary Fatty Acids. (J Am Diet Assoc 107:1599, 2007.) This is a technical report, for experts in the field. It is full of detailed information.

In the US, food supplements such as the fish oil tablets, are minimally regulated. They may be readily available, but no regulatory body has approved them as either being useful or safe.

* * * * *

A subsequent post on food supplements: Is folic acid good for you or bad for you? (April 10, 2010).

More about ω-3 fatty acids:
* Vitamin D, omega-3 fatty acids, and autoimmune disease? (March 29, 2022).
* Omega-3 fatty acids and the adaptation of fish to fresh water (August 3, 2019).

More fish... A connection between eating fish and skin cancer? (June 20, 2022).

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

For more about lipids, see the section of my page Organic/Biochemistry Internet resources on Lipids.

GEBA: B -- revisited
Horizontal gene transfer: the web of life? a challenge to evolutionary theory?

March 26, 2010

Original post ... GEBA: B (February 5, 2010). That post consisted entirely of one figure, with no explanation. In fact, I removed much of the descriptive text from it (and what text remained was probably not readable). At one level, I just thought it was a neat picture. It's now time to fill out the story.

Background: horizontal gene transfer (HGT). There are two items here, with the central theme of HGT. So let's review a bit what HGT is; it has come up before. The "normal" source of genes is your parents. Parents pass their genes on to their offspring; we call this vertical transmission. However, it is also possible to get genes from "others". Bacterial transformation is one example. Another example is the development of the eukaryotic cell, by some kind of fusion of a precursor cell with bacteria destined to become mitochondria. To distinguish this kind of gene transmission from the "ordinary" kind, we use the term horizontal gene transfer (HGT). Generally, HGT seems more common in microbes than in higher organisms; a recent post noted evidence for HGT in rotifers. (Lesbian necrophiliacs (March 8, 2010).)

Background: the tree of life (TOL). If you make a chart of your family, going back to grandparents, great-grandparents etc, one can arrange them in a tree structure, showing who descended from whom. We can do something similar for types of organisms (e.g., species). In this case, we don't have birth records; we rely on the observed similarities between species, and infer which types of organisms descended from which. Such a tree, showing the ancestral relationships between types of organisms, is known as a tree of life (TOL).

Genome data has revolutionized the development of the tree of life. There are two distinct reasons for this. One is that the genome is the fundamental level at which relatedness occurs. (Bats and birds both have wings, but they are not closely related.) Second, modern technology allows genome information to be obtained at ever increasing rates.

HGT & TOL. The issue is that HGT can confuse the tree of life. The existence of HGT says that our inheritance is not as simple as we thought. In fact, the extensive genome information obtained with bacteria has made some people wonder whether we might better consider a web of life rather than a tree of life. The web would show that we are interconnected, genetically, with some range of organisms, not just our parents etc. Both items here deal with this issue, and raise the question of how much HGT interferes with there being a simple tree of life. One of the stories shows that HGT does not dominate the picture, does not obscure what we might expect as the tree of life. The other suggests that it might, if we look further.


A group of researchers decided to sequence a large group of microbes -- chosen to represent a wide range. Commonly, each group sequences the organisms of particular interest to their work. The "big picture" then builds up by accumulation. This group decided to aim for the big picture, and they chose a range of bacteria intended to reflect the diversity. They sequenced their chosen organisms, and arranged them as the sequence data dictated. The result, along with other data available, is what is in the GEBA figure. It is indeed a tree. That is, there seems to be no trouble making a traditional TOL for these organisms. HGT may be a part of the full story, but it does not obscure the traditional vertical inheritance pattern. We can still tell who the parents are. If we think of vertical transmission as the normal pattern, and HGT as "noise", the noise does not obscure the normal pattern.

The article, which is freely available: A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. (D Wu et al, Nature 462:1056, 12/24/09.)

Here is the full figure, untrimmed: GEBA: B


The second item is a story in New Scientist which raises some interesting challenges about the importance of HGT, but also suffers from some sensationalism.

The key idea is that HGT may have been even more important in the early stages of evolution of life than it is now. We now recognize it as important in microbes, less important in more complex organisms. One might extrapolate backwards that it was even more important with primordial organisms, more primitive than our current microbes. That's not an argument per se, but simply some perspective. They suggest -- and even show with some computer modeling -- that high levels of HGT could help explain some aspects of what we now observe about the homogeneity of living systems. That is, the likely argument is that massive HGT helps explain what we see. It is biologically reasonable; primordial organisms were quite likely leakier than modern organisms (leakier membranes). And it fits with the trend we see now, that HGT seems to have become less important over evolutionary time.

If the idea is correct, it means that an attempt to organize primordial organisms would result in something more like a web than a tree.

Now, the sensationalism... The news story suggests that there is something non-Darwinian about the proposal. Not at all, though the claim may serve to get some attention. It may be non-Mendelian, but certainly it is compatible with Darwin. The essence of Darwinian evolution is that variation occurs, and then natural selection causes some variants to survive. Darwin knew nothing of the source of variation. (In fact, he was something of a Lamarckian.) We now understand that variation has many sources, including mutation and recombination. HGT is one of those processes, too; we have come to appreciate it more and more in recent decades. The new proposal is simply to extend its role. It makes some sense, and they have some modeling to support it. What more will come of the proposal remains to be seen. It may be a shift in our thinking, but I don't see that it actually contradicts any important things we now accept.

Here is that New Scientist story. Read it for the idea about the importance of HGT, but I suggest you downplay some of the hype about it contradicting Darwin. Horizontal and vertical: The evolution of evolution. (1/25/10.) (This article is no longer freely available.)

One key article behind that story is from Carl Woese and collaborators, from 2006. It is freely available: Collective evolution and the genetic code. (K Vetsigian et al, PNAS 103:10696, 7/11/06.) Caution... It is rather slow reading.

* * * * *

Other posts involving HGT:
* A virus with an immune system -- stolen from a host? (March 25, 2013).
* Sushi, seaweed, and the bacteria in the gut of the Japanese (April 20, 2010).

The post UCA passes test (June 6, 2010) addresses the concern that HGT may conceal the "tree" of life.

March 24, 2010

Guitar: unusual technique

March 24, 2010

Guitar video. Recorded live in London. Other videos may be available; try searching, using search terms from the story below.

For some background: Birds of a feather strung together. (2/27/10.)

Perhaps one of you near London will get a chance to see this, and give us a personal evaluation.

Lux aeterna: Mushrooms; Mozart -- follow-up

March 22, 2010

Original post: Lux aeterna: Mushrooms; Mozart (December 7, 2009)

I found an additional item which some may enjoy reading... a page at the NSF (National Science Foundation) describing the discovery: A Thousand Points of Light: Bioluminescent Fungi. (D Desjardin, August 15, 2008.)

Also, the paper has finally appeared in published form. Because of all the beautiful photos, some might want to grab yourself a copy: Luminescent Mycena: new and noteworthy species. (D E Desjardin et al, Mycologia 102:459, March 2010.)

Do you need some new brain cells?

March 22, 2010

No problem. Just take some of your skin cells, and change them into brain cells.

Science fiction? Well, it's certainly not available yet. But at least at the lab level, it has been done.

It's a stem cell story -- sort of. It does not actually involve stem cells, but the work is clearly an offshoot of some exciting stem cell work.

Stem cell biology is a field that fascinates the general public, as evidenced by the political support people have given stem cell work. It's a recent field, full of promise (of course) and hype (of course). One key kind of stem cell is the embryonic stem cell (ESC), first characterized -- in mice -- in 1981. Human ESC were discovered in 1998. The great appeal of ESC is that they are pluripotent; they can be turned into any cell type. Among the disadvantages is that they are hard to get.

In 2006 Shinya Yamanaka, now at Kyoto University (and also at the Gladstone Institute in San Francisco), revolutionized the field -- and that is not hype. He reported that he could make pluripotent cells, very similar to ESC, by treating cultured cells with a small number of specific protein factors. He found the needed factors by a combination of using current knowledge about likely candidates (24 of them), plus some clever work to sort out which were the key ones. The 2006 report was with mouse cells; the ink was barely dry before the report was confirmed, in 2007, with human cells. The cells produced are called induced pluripotent stem cells (iPSC).

A key advantage of using iPSC rather than ESC is that it avoids the need for an embryo. But more than that, it changed the whole way of thinking about stem cells. Converting cells from one type to another in the lab was now under the control of the investigator. It involved a small number of factors, whose role was at least partially understood. From one type to another? Yamanaka used factors needed for pluripotent cells, to make pluripotent cells. Why not use the factors needed for neurons -- and make neurons?

That is... The original plan might have been to take ESC obtained with great difficulty, and convert them in the lab to neurons. Yamanaka's way of making iPSC simplified the first part of that, allowing one to start with skin cells, convert them to pluripotent cells, and then to neurons. But it also opened up the possibility of simply converting the skin cells directly to neurons -- by adding what is needed to make neurons. Further, Yamanaka's work provided the approach for figuring out how to do it.

It's been done.

The figure below is a simplified flow chart of the processes considered here.

Simple flow chart, differentiation etc. The boxes represent cell types: embryonic cells at the left, two types of adult cells at the right.

The two green arrows represent what occurs during normal development of the animal. Of course, each green arrow may represent many steps. Biologists are learning to carry out these steps in the lab, too, using pluripotent cells (ESC or iPSC). The green arrows represent differentiation.

The two magenta arrows, the reverse of the green arrows, represent the reverse process. These processes do not normally occur in the animal; perhaps there are some limited exceptions. Biologists have begun to carry out this type of process, making iPSC. The magenta arrows represent dedifferentiation.

The red arrow represents the conversion of one adult (differentiated) cell type to another, without going through the intermediate stage of making pluripotent cells. There is little reason to believe this occurs in the animal. This is what is reported in the new work. The red arrow represents trans-differentiation.

Hype alert. I've used the word above, and then probably contributed to it. So let's step back. The work reported here, if it holds up, is extremely exciting science. However, if one thinks of stem cell work from the point of view of using them therapeutically, then it is but one step along a very long pathway. We need to keep those two perspectives separate. Making something that is therapeutically useful in humans requires "perfecting" it, and extensive testing. However, stem cells are becoming important research tools in the lab. The ability to make stem cells and various kinds of differentiated cells from individual patients will open up new areas of lab work.

News story: Mouse Skin Cells Turned Directly Into Neurons, Skipping IPS Stage. (Science Daily, January 28, 2010.) This is an excellent overview of the work, and its context.

* News story accompanying the article in Nature: Regenerative medicine: Cell reprogramming gets direct. (C R Nicholas & A R Kriegstein, Nature 463:1031, 2/25/10.) The figure above is a simplified version of the figure in this article.
* The article: Direct conversion of fibroblasts to functional neurons by defined factors. (T Vierbuchen et al, Nature 463:1035, 2/25/10.)

Some related posts:
* A previous post on stem cells: Growing new teeth (9/29/09).
* An alternative to the use of stem cells to make replacement tissues is transplantation; a recent item on that topic is Pigs as organ donors for humans (2/16/10).
* Print yourself new body parts (April 16, 2010);
* Making replacement insulin-producing cells: another way (5/14/10). A direct conversion of one cell type to another?
* A recent item on a stem cell success story: Restoring sight by use of stem cells to regenerate a new cornea (7/13/10).
* Therapy based on embryonic stem cells: the first clinical trial (October 23, 2010).
* Children with two fathers (January 3, 2011).
* Science: highlights of the decade (January 25, 2011).
* Using patient-specific stem cells to study Alzheimer's disease (February 24, 2012).

CSI: Microbe

March 22, 2010

It was all over the media just last week: When you use the computer, you leave bacteria from your hands on the mouse and keyboard. Since each of us has a different collection of bacteria on our hands, someone can come along, collect and identify the bacteria -- and tell who used the computer. Sounds hyped? What's the real story? Since the paper is interesting in several ways, I thought it might be good to look and see what was really done.

A short summary might be that all the ideas are right. However, the amount of testing so far is very limited; it is hard to tell how useful the test would be in the real world. It is, we might say, a "proof of principle". It's good work: it raises an idea, and provides some initial testing. Now it's on the table, and people can think about specific applications, and test them.

Fig 1A, showing clustering of data for 2 individuals.

Fig 1A, continued; the 'key'.

An example of their results.

The graph shows the data in a small experiment on three individuals -- and their computer keyboards. Each sample is the collection of bacteria retrieved by swabbing a fingertip or computer key; DNA was extracted, and sequenced for the standard small ribosomal DNA.

The data points for one person are shown as black circles -- filled and unfilled. These points happen to lie towards the right of the graph. The key point is that the data for each person form a separate cluster. That is, the data distinguish the three individuals. However, you should also note that the separation between #2 and #3 (red and blue) is not very large; surely, we must wonder how good the separation would be if many more people were involved.

It is hard to explain exactly what the points show. The points involve a statistical analysis of the DNA sequence data. Remember, each sample is not simply one organism, but a community of organisms. The idea is that samples of the bacteria for one person are more similar to other samples from that person than to samples from other people; that is what the clustering shows. If anyone is interested in the statistical tools, they are referenced in the paper. In fact, they use two comparison methods in this paper.

This is from Fig 1A of the paper.

One of the important parts of the background is that people vary in what bacteria they have on their hands, but that the population on a person's hands does not change much over time. This is part of the fascinating and emerging story of the human microbiome: the extended view of the human organism that includes our resident microbes. Is everyone's collection of skin bacteria really distinct, and over what time scale? These are questions that can only be answered with more extensive studies.

In thinking about how such a test might be used, we can distinguish different kinds of tests. For example, in one case we might have a very narrow question, about whether person X did or did not use a particular machine. If the test proposed here shows that the machine sample is inconsistent with X's finger sample, then this might be one good piece of evidence -- to be considered along with other evidence. On the other hand, sometimes there are broad questions. A sample is obtained from the park bench, and we want to know which of the many thousands of people in the community is responsible. That is a much more demanding problem. The point is, we do not simply say this is or is not a good potential test for forensic use. It may be useful in some situations. Time will tell. The idea seems sound; how useful it is in practice is something we will learn over time.

Announcement from the Howard Hughes Medical Institute (HHMI): Bacterial "Signatures" Linger on Users' Keyboards. (3/15/10.) This item is a good overview of what they did, and discusses many questions that remain.

The article: Forensic identification using skin bacterial communities. (N Fierer et al, PNAS 107:6477, 4/6/10.)

Thanks to Jitesh Dundas for sending me the HHMI story.


March 19, 2010

I received the following link by a wireless transmission, but suspect that it was sent by a piece of meat. Meat.

Can you die from an infection without being infected?

March 19, 2010

If the title has you scratching your head, you're not alone.

If you get bacteria in your bloodstream, your immune system reacts. The immune reaction itself can be life-threatening. Ok. But sometimes, after trauma, people get the same type of immune reaction -- and there does not seem to be any infection. The immune system seems to be reacting to bacteria, but there are no bacteria to be found. What gives?

One possibility is that some bacteria from your gut might have gotten into the bloodstream -- a side effect of the trauma. Ok, an idea. But testing of this idea has provided no support.

So, what other source of stimulation might be considered? What else might somehow be sending a "bacteria-alert" to your immune system? Ah, it's right there in (almost) every cell in your body. And has been there for a couple billion years. mitochondria

It has finally occurred to someone that it might be mitochondria that are causing the problem. The idea is that trauma causes an unusual degree of cell breakage, and some cell debris may end up in the bloodstream. Mitochondria are derived from bacteria, and still have some distinctively bacterial characteristics. Perhaps it is our own mitochondria -- bacterial remnants in our cells -- that trigger an immune response when they get free in the blood. This would be the innate immune system, which responds to general features. A group has proposed it, and tested it. Their evidence supports the proposal. They show that mitochondrial debris, with obviously bacterial features, is found in the blood, and can trigger the immune response.

This may well be a major discovery, with therapeutic implications. For example, if you seem to have a bacterial infection but really have no bacteria, antibiotics won't help. More importantly, drugs targeted at the immune reaction may help.

News story: Immune responses to mitochondria help explain body's inflammatory response to injury. (Medical Xpress (formerly Phys.Org), March 3, 2010.) A very good overview.

* News story accompanying the article in Nature: Clinical immunology: Culprits with evolutionary ties. (C S Calfee & M A Matthay, Nature 464:41, March 4, 2010.)
* The article: Circulating mitochondrial DAMPs cause inflammatory responses to injury. (Q Zhang et al, Nature 464:104,March 4, 2010.)

The figure above shows two mitochondria -- from rat liver. The figure is from Wikipedia: Mitochondria.

* * * * *

Other posts about mitochondria that may be related...
* Mitochondria in the blood? (April 5, 2020).
* Heart damage: role of mitochondrial DNA (June 1, 2012).

More on the complexity of the immune system... Why are HIV-infected people more susceptible to Salmonella infection? (May 21, 2010).

Also see... Origin of eukaryotic cells: a new hypothesis (February 24, 2015).

March 17, 2010

Spirit -- follow-up

March 17, 2010

This is a follow-up to Spirit (February 20, 2010).

That post presented a delightful essay about the Mars rover Spirit. As delightful as it was, it had an oddity: it sounded like an obituary, even while noting that Spirit was not dead.

I wasn't the only one to notice that oddity, of course. Among the others was Steve Squyres -- the project director, identified in the original story as one of the two fathers of Spirit. His short note to Nature was published four weeks after the initial story. No big deal, but it is fun to note -- and it was accompanied by the cartoon at right.

Spring awakening planned for Mars rover Spirit. (S Squyres, Nature 464:31, 3/4/10.)

Spirit cartoon

The answer is cereblon

March 16, 2010

Thalidomide is an infamous drug -- and yet still a useful drug. It was originally introduced as a sedative for pregnant women; testing of the drug on lab animals had failed to reveal that it caused birth defects. Thus the initial use of thalidomide, to treat a rather mild problem, led to a burst of children being born missing limbs. Other than causing birth defects, thalidomide seems to have only moderate side effects. So, when it became clear that thalidomide was useful against leprosy and certain cancers, it seemed to be a drug of choice -- except for its reputation of causing birth defects. No problem; just don't give it to pregnant women. Or to women who might become pregnant. Easier said than done, and the controversy continues.

A new report offers insight into how thalidomide causes birth defects. It shows that the primary target of the drug is a protein called cereblon (CRBN); they also provide considerable information on what CRBN does, and why thalidomide binding to it causes birth defects.

Among the evidence... In an animal model (zebrafish -- which has a transparent embryo!), they show that using an independent method to reduce CRBN causes developmental defects similar to those caused by thalidomide. Further, if the animal has a mutant form of the CRBN that cannot bind thalidomide, then the thalidomide does not cause the defects.

An example of their results. This figure shows the importance of cereblon (CRBN; in this case, the zebrafish analog, called zcrbn) for development of the pectoral fins. The pictures show the developing embryo 72 hours after fertilization. In each frame, the arrowhead points to the left pectoral fin. For scale, the embryos are about 0.5 millimeter wide. (This is Fig 4C of the paper.)

Figure 4C. Effect of inhibiting CRBN in zebrafish * Left: A normal embryo, with normal fins. ("uninj" = uninjected)
* Middle: The embryo had been injected with the inhibitor ("zcrbn AMO", an "anti-sense" drug targeted to the zcrbn gene), The inhibitor prevents making the mRNA for the zcrbn gene. The fins are absent. (Addition of the drug thalidomide gives results similar to those shown here.)
* Right: A "rescued" embryo -- a control, to show that the inhibitor was doing what we thought it was. It had been injected with the inhibitor, but also with mRNA for the gene, which should compensate for the inhibitor; it does, and the embryos have normal fins.

Why is this an important finding? Knowing the specific target of the drug -- in this case, the target for a bad effect -- can be useful in developing modified forms of the drug. A common approach to drug development is to make many variations of the candidate drug, and test them. It is much easier to test a new variation to see whether it binds to a particular protein than it is to inject it into an animal and see if it causes defects. There is no guarantee that this approach will work. We do not know that CRBN is the only target for bad effects, and we do not know what the target is for good effects (they are working on this). And we do not know that it is possible to make a drug that will have the good effects without the bad. Nevertheless, the finding reported here is a good step forward.

News story: Thalidomide effect mystery solved. (3/11/10.)

The article: Identification of a Primary Target of Thalidomide Teratogenicity. (T Ito et al, Science 327:1345, 3/12/10.)

Thanks to John for sending me this item -- the day it was published!

* * * * *

More about the usefulness of transparency: Transparent soil (October 13, 2012).

Also see:
* CISS: separating mirror-image molecules using a magnetic field? (August 7, 2018).
* Scoliosis: an animal model (July 22, 2016).
* Fish make their own sunscreen (September 29, 2015).
* Leprosy: the armadillo connection (May 14, 2011).

Black hole: simulation

March 15, 2010

Borislav sends New black hole simulator uses real star data. (New Scientist, February 9, 2010.) The page includes a video, which illustrates gravitational lensing as light passes by a black hole. It also links to a program you can download to explore the black hole on your own; see next paragraph for an updated link. You can move around the black hole, or program yourself for free fall into the black hole. The program page also includes additional movies and information. I strongly encourage you to read the article above before trying the program.

Update December 12, 2019... The program page has moved from the site given in the New Scientist story. It is now at: the simulation program; new link. (You can also get the page using the original URL at the Wayback machine. Go back to 2015; not sure of cutoff.)

Both the video and program will entertain, whether you understand much of what is going on or not. (Caution: the program is rather demanding of computer resources.)

Don't get too close.

There is an article that accompanies release of the program. Much of it is rather technical, but it also provides something of a manual for using the program. Distortion of the stellar sky by a Schwarzschild black hole. (T Müller & D Weiskopf, American J Physics 78:204, February 2010.) The New Scientist page listed above links directly to the article.

* * * * *

More on black holes...
* How would you die if you visit a black hole? (May 6, 2013).
* Mayhem at the center of the Milky Way (August 23, 2011).

Low-carb or low-fat diets: a rational choice?

March 14, 2010

The general result with diets is that they don't work very well -- especially over the long term. One particular debate among diet advocates is whether a low-carb (carbohydrate) or low-fat diet is the best approach. Testing has generally been inconclusive.

Now an answer may be emerging. And that answer is... It depends. It depends on the genes of the individual. Some people have genes that make them better candidates for low-carb dieting, and other people have genes that make them candidates for low-fat dieting.

Time will tell, but it does seem plausible. People are not the same. We know that; we know people who eat similarly gain different amounts of weight. It is reasonable that the best approach for dieting may vary for different people. The question is probably not whether that basic point is correct, but whether they have the right genes and magnitude of effect.

Caution. This is a preliminary story, with only incomplete information available. I first heard about this on the radio a few days ago. I don't take a radio news item as worth much, but it was interesting enough to try to follow up. Google led me to the news story listed below. The story notes that the work was presented at a meeting, but has not yet been published. It also notes the potential for some conflict of interest, since the work involved a collaboration with a company making a genetic test. So, again, this is preliminary; we await formal publication of a peer-reviewed paper, and then independent replication of the work with more people. We also need to learn, over time, of the long term consequences of any such diet.

Disclaimer. Again, a reminder that Musings does not offer medical advice (including nutrition); we discuss individual pieces of work, and do not know the full implications. As noted above, we have here a preliminary report of a possibly interesting finding.

News story: DNA test 'could predict most effective diet'. (BBC, March 5, 2010.) This appears to be a reasonable presentation of this preliminary story. [The news story originally listed here is no longer available. Here is a replacement; I think it is equivalent.]

This can be thought of as an example of personalized medicine, discussed here before, e.g., Personalized medicine: Getting your genes checked (10/27/09). It involves not a large scale test of your genes, but a specific test (three genes, in this case). Actually, one could make use of their basic idea without getting any genetic test at all. Simply try both diets, and see which one works best for you -- rather than dogmatically assume that one is better in general.

An anti-palindrome?

March 14, 2010

Jessica sends video. You need to read the text content of the video as you go; read it as you listen to the speaker. (It is about 2 minutes.)

She also supplied some "explanatory material". She suggests you read it (below; indented) before looking at the video; I think it may be good to check the video first -- so long as you read my one "instruction" given above. Probably no big deal either way.

A palindrome reads the same backwards as forward. This video reads the exact opposite backwards as forward. Not only does it read the opposite, the meaning is the exact opposite. Make sure you read as well as listen... forward and backward.

This is a video that was submitted in a contest by a 20-year old. The contest was titled "u @ 50" by AARP. This video won second place. When they showed it, everyone in the room was awe-struck and broke into spontaneous applause. So simple and yet so brilliant.

* * * * *


If you are unfamiliar with palindromes... the simplest ones to think about are those involving letters. For example, "Anna" is a palindrome; it reads the same forward and backward. Palindromes are an interesting issue with DNA sequences. For example, a palindromic DNA sequence produces an RNA molecule that can fold back on itself.

The main purpose here is the clever presentation. Individuals can deal with the content as they wish.

How many eyes does it have?

March 12, 2010

rhopalium. Fig 1B, 125% Let's count them.

There are two little round eyes, at the top near each side. They are known as pit eyes, and are labeled pe.

Under each pit eye is an elongated eye, known as a slit eye (se).

In the middle are two larger eyes, each of which has a true lens. These are called the upper lens eye (ule) and lower lens eye (lle).

That's six eyes -- in this picture. Six eyes in one rhopalium.

But surely you understood that my title refers to the animal. How many eyes does the animal have?

It's a little box-shaped animal, with one rhopalium on each of its four vertical sides. (Sort of like you having eyes in the back of your head -- and on each side. But not on top.) Thus, the animal has four rhopalia, each with six eyes. That's 24 eyes.

box jellyfish. Fig 1A, 125% Here is the animal. You may recognize it as a jellyfish. More specifically, it is a box jellyfish (or cubomedusae), from its distinctive shape.

The white square in this figure outlines the region that is expanded in the first figure above.

The scale bar for this figure (lower right) is 1 cm; the animal is a few centimeters across. The scale bar for the upper figure is 100 µm; the rhopalium is about a half millimeter wide.

Why? The most interesting question is why are there so many types of eyes. Little is known, but it is likely that the eyes have specialized functions. Jellyfish have a primitive nervous system, without a central brain. Processing of signals that we would do in the brain is done by simply separating them in different sensors (eyes). It will be interesting to watch as more information on this system becomes available.

What brought this up? The top picture, the rhopalium, was in Nature. They were noting a new paper on the box jellyfish visual system. The paper addresses the question of whether these jellyfish have color vision. Apparently, previous work on the question had been inconclusive. In the new paper, they analyze the visual pigments in the two lensed eyes, and conclude there is only one. That would seem to preclude color vision.

Visual pigment in the lens eyes of the box jellyfish Chiropsella bronzie. (M O'Connor et al, Proceedings of the Royal Society B 277:1843, 6/22/10.) The first page gives some interesting background material about these animals, and their visual system. The two figures above are parts of Figure 1 of the paper; that Fig also includes a part c, showing details of the retina.

For more about box jellyfish and their eyes: With 24 eyes, can they see the trees? (June 11, 2011).

A broader view of jellyfish eyes: The eyes of Cnidaria (jellyfish): the big picture (August 19, 2018).

A previous item on the diversity of animal eyes: Where are the eyes? (12/16/09).

More on animal vision:
* An eye that forms an image using a mirror (February 13, 2018).
* Butterflies and UV vision (June 29, 2010).

Eyes in non-animals? Is the warnowiid ocelloid really an eye? (October 12, 2015).

Jellyfish and corals are in the same animal phylum: the cnidarians. The possibility that corals use sound to locate their "home" is discussed in the post Are the corals listening to the shrimp? (7/16/10).

March 10, 2010

Web browsers

March 10, 2010

Borislav writes...

As I use all of the PC/Win browsers, here is my top list and some general comments on them:

* * * * *

Comment. I can't begin to offer any systematic comparison. However, I now use Opera (10.1) as the main browser on both my desktop and laptop machines (both running Windows XP). For the most part, it is fine; occasional sites don't work on it. I had tried to use Firefox (3.5) on the laptop -- as much for variety as anything. I had various general computer problems, which seem to have disappeared as I stopped using Firefox. The standard browser on the computers in the university libraries is Internet Explorer 6; it is out-of-date for some sites, but otherwise works ok.

Other comments? Especially if they offer different perspectives or issues.

Lesbian necrophiliacs

March 8, 2010

A reader sent me this fascinating item. With a title like that, the person deserves -- maybe needs -- anonymity. Actually, it is much less juicy than the title suggests, and it explores some unusual and fascinating biology. It is about
* rotifers and their fungal parasites;
* why animals have sex;
* how those first two points are related;
* and more.

The figure at the right shows a rotifer. This figure is from the ASM blog page noted below.

It is perhaps a confusing story, because there are several interrelated issues. In fact, there are two key papers here, one new and one from two years ago. So, let's go through it slowly. (If you decide you've had enough of the rotifers, skip down to the last paragraph of this post, on the supplementary page, for some music.)

a rotifer

This item continues on the supplementary page Lesbian necrophiliacs.

* * * * *

A follow-up post: The rotifers that lack sexual reproduction: what do we learn from the genome? (October 4, 2013).

A subsequent Musings item, stimulated by this one, is about another animal that shares an interesting feature with the rotifers: A space-faring bear that survives the vacuum of space -- and lay eggs normally (April 30, 2010).

And... How the tardigrades resist desiccation (April 10, 2017).

More on horizontal gene transfer (HGT):
* Briefly noted... How rotifers silence transposons (June 15, 2022).
* More on photosynthetic sea slugs (February 20, 2015).
* An extremist alga -- and how it got that way (May 3, 2013).
* GEBA: B -- revisited     or     Horizontal gene transfer: the web of life? a challenge to evolutionary theory? (March 26, 2010).

More from Matt Meselson: Speech droplets: Can you transmit an infection to someone by yelling "Stay healthy" at them? (June 14, 2020).

Also see: Bob Dylan and biomedical research (January 20, 2016).

There is more about music on my page Internet resources: Miscellaneous in the section Art & Music. It includes a list of related Musings posts.

Chile earthquake caused the day to become shorter

March 8, 2010

Jakub sends Chile Quake Shortens Length Of Day. (March 2, 2010.) The page is a transcript of a segment from National Public Radio (NPR). It includes an interview with the scientist, Dr. Richard Gross of NASA.

According to the analysis, days are now shorter by about a millionth of a second. The earthquake caused shifting of mass within the earth. This affected the speed of rotation, to conserve angular momentum. For now, this is a prediction, based on calculation. The effect on the day length has not been confirmed by observation.

A follow-up post: Earthquakes: increasing? (March 30, 2010).

Other posts on earthquakes include:
* Could we block seismic waves from earthquakes? (June 23, 2014). Links to more.
* The Quake-Catcher Network: Using your computer to detect earthquakes (October 14, 2011). The Chile quake is one example discussed here.

More about Earth's rotation:
* Briefly noted... A record short day (August 23, 2022).
* Did changes in Earth's rotation promote the rise of oxygen-evolving photosynthesis? (August 23, 2021).

More about analyzing angular momentum: There is Mozart in the air -- encoded in orbital angular momentum (April 25, 2015).

Big steps or little steps: how does evolution proceed?

March 6, 2010

This is a question that has intrigued biologists ever since they began to understand that one species arises from another. With our modern understanding of molecular genetics (loosely, DNA and how it works), the question doesn't seem as important. There is no either/or. We recognize that there is a complex relationship between genotype (the genome) and phenotype (observed characteristics). We have a good understanding of small and large steps at the genome level. And we understand how small genome changes can cause large changes in the properties of the organism (through regulatory mutations, for example).

A feature story in a recent Nature provides some interesting discussion of the question, with plenty of historical material. Non-biologists may need to skip over some details, but should still get the gist of the story.

Among the work discussed here is a project that is notable simply for its magnitude. Richard Lenski has watched a population for 40,000 generations. That would take nearly a million years with humans, but Lenski is watching Escherichia coli bacteria; the work covers about 20 years. He has watched population changes, and analyzed the genetic changes behind them.

Revenge of the hopeful monster. (T Chouard, Nature 463:864, 2/18/10.) Well, that's quite a title. It is followed by: "Experiments have revealed how single mutations can have huge effects that drive evolution. But small steps pave the way."

March 3, 2010

An electronic nose to monitor air quality on spacecraft

March 2, 2010

Our space buff sends information from the Jet Propulsion Lab (JPL) on the ENose -- their electronic nose developed to monitor air quality on the space shuttle. The home page for the JPL ENose is Welcome to the JPL Electronic Nose! The introduction continues on An Introduction to JPL's ENose.

The figure at the right shows the 3rd generation sensor unit. Volume ~820 cm3; mass ~840 g. This figure is from the home page noted above.

JPL ENose, 3rd generation.

He writes...

NASA is currently testing a device of a rather funny name - an electronic nose. However, if proved successful, that device could have very important role in future of human space flight. Nice. Now, what is the big deal? Well, it is apparently extremely complex. Sense of smell that you take for granted can get very complicated for a machine.

If a machine would like to "sense" something, it will almost always measure a difference in electrical current that occurs after a change in a specified device. A simple example is temperature: a rise in temperature will raise electrical resistance, so the machine will be able to measure that change and tie it to temperature change.

With "smell" it is much harder. The way to do it is to create special materials that can react with extremely low concentrations of specific ("smelling") molecules in air; the instrument then measures changes in the electrical properties of the materials when they react. Different materials react differently (see below), and a computer sorts out the signals. For use on a spacecraft, long term stability might be a concern. However, NASA has recently completed operating the ENose on the Space Station for about six months, apparently with good success. Click on "Flight Mission 2008-09" on one of the JPL pages listed for the page "ENose in Space", which has more information on this test.

Read more, and learn about a novel type of electro-chemistry!

* * * * *


The JPL ENose is based on the work of Nate Lewis, chemistry professor at Caltech (which is very near and administratively connected to JPL). Lewis's web page on the Electronic Nose is Lewis Research Group -- Electronic Nose.

Example of results, with 17 sensors. The figure at the left shows an example of the results obtained with such an electronic nose.

This device has 17 sensors (numbered along the bottom). Three specific odor molecules are tested; they are color-coded (and listed at the top).

The important result is that the sensors give different patterns. For example, sensor 1 responds best to methanol (red), whereas sensor 8 responds best to ethyl acetate (yellow). You don't need to make sense of the patterns; a computer does that -- and matches the pattern obtained with a real sample with its collection of knowledge about the patterns from individual chemicals.

This figure is part of Figure 3 at the Lewis page listed above.

How does the sensor work? Each sensor is a very thin sheet of plastic. (A couple of the types of plastic are labeled on the figure.) If the chemical binds to the sensor, the plastic swells. That affects its electrical properties, which are measured.

More information, including publications, is available at both the JPL and Lewis sites.

For another story from Lewis, see Joint Center for Artificial Photosynthesis (JCAP) (August 16, 2010).

More about odors...
* Bomb-sniffing grasshoppers? (November 8, 2020).
* Copper ions in your nose: a key to smelling sulfur compounds (October 10, 2016).
* Malaria-infected mosquitoes have greater attraction for people (May 28, 2013).

Should you run barefoot? -- the missing figure

March 2, 2010

Original post: Should you run barefoot? (February 22, 2010). I have added a figure.

Inuk, a 4000 year old Saqqaq from Qeqertasussuk

March 1, 2010

Eight humans have had their DNA (genome) sequenced. Jim Watson and Craig Venter are among them. Now we have the ninth -- and it is a Saqqaq from Qeqertasussuk, a Saqqaq who lived about 4000 years ago.

This is an interesting story at two rather distinct levels. One is simply doing it, and the other is the knowledge obtained from doing it -- about this person, and about human history.

At right... An artist's conception of what "Inuk" might have looked like, based on information from his genome.

The figure here is part of a featured figure in the news story listed below; another view was featured on the cover of Nature.

The story starts with some hair recovered from the permafrost in Greenland -- near a place called Qeqertasussuk. That the hair was stored so cold for the millennia was important; survival of DNA is very much affected by temperature. Still, analyzing any DNA requires great care to make sure you don't contaminate it with anything else -- including microbes in the sample and the lab workers. Analysis of ancient samples is particularly challenging, because of the quality of the DNA. It is a developing art, and it is not unknown to have serious problems, and even to decide that results already published are not of acceptable quality. The paper itself outlines many of their precautions -- including noting that all scientists who worked with the sample were Northern Europeans.

Perhaps more interesting to most people is what was learned by sequencing the DNA from Inuk's hair. In many cases, specific features of the genome sequence, when compared to known variations of modern human genomes, suggested specific characteristics of the individual. For example, his genome suggests that he had type A blood and brown eyes. The two news stories below discuss these findings very well; some of the findings are reflected in the drawing shown above. In addition to suggesting some characteristics of this person, comparison with a variety of modern humans suggested his origins, and thereby suggested ancient human migration routes. Prior to this analysis, it was commonly thought that the Saqqaq were related most closely to Native Americans, but the results here show that this person is more closely related to tribes in Siberia.

Caution... Should you take all this at face value? Well, with luck, they got the sequence right. That is experimental data. The inferences they draw are just that: inferences. They are based on what we know now about humans. Over time, we will learn more, and the conclusions will grow. For example, the paper notes that they have only one individual. We have no idea how typical he is. Many of the reservations here are similar to the reservations in another area of genome analysis, which we have discussed before, e.g., Personalized medicine: Getting your genes checked (October 27, 2009).

News story: First Ancient-Human Genome Sequence Answers Anthropological Riddle. (Wired, February 10, 2010.) [June 2022: replacement for story listed previously.]

* News story accompanying the article: Evolutionary biology: Face of the past reconstructed. (D M Lambert & L Huynen, Nature 463:739, February 11, 2010.)
* The article: Ancient human genome sequence of an extinct Palaeo-Eskimo. (M Rasmussen et al, Nature 463:757, February 11, 2010.)

Among many posts on genome sequencing...
* Ancient DNA and the archeologists (April 27, 2018).
* Identifying individuals from their genomes: a controversy (December 5, 2017).
* DNA sequencing: the future? (November 7, 2017).
* The panda genome (January 11, 2010).
* The human genome - 10 years on (April 16, 2010). Perspective.
* How many human genomes have been sequenced? (November 30, 2010).
* Ancient DNA: an overview (August 22, 2015).

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

Other arctic posts include:
* Should we geoengineer glaciers to reduce their melting? (April 4, 2018).
* Recovery of live, infectious virus from 30,000 year old permafrost (March 25, 2014).
* A 30,000 year-old plant, with an assist from a squirrel (March 10, 2012).
* Mammoth hemoglobin (February 1, 2011).
* What's a dia? Bumblebees and reindeer don't agree. (December 6, 2010).

Also see:
* Converting Type A blood so that anyone can receive it (September 17, 2019).
* Zhemchuzhnikovite: a natural MOF (August 19, 2016).
* Genes that make us human: genes that affect what we eat (February 18, 2015).
* The Iceman's blood (May 14, 2012). Another ancient human -- older than Inuk.

There's plenty of room at the bottom

March 1, 2010

The title here is the title of a famous talk by Richard Feynman. The talk was given at a meeting of the American Physical Society in December 1959. An adaptation was printed in the Caltech alumni magazine Engineering and Science (E&S) in February 1960. Thus we are at the 50th anniversary of this Feynman gem, which is often considered the seminal paper of what has become one of the major areas of modern science, nanotechnology. (The subtitle of the article is "An invitation to enter a new field of physics".)

You've probably heard the phrase, but have you read the paper? It is still worth a look, both as a touch of Feynman and an insight into nanotechnology.

Here are a couple of sources. Both include the text. The first is a pdf of the article as published in E&S; it's not a very good copy, but it does include some pictures. The second is simply the text, but is clear; it also includes some information.
* A pdf of the E&S article. Not a very good copy, but it includes some pictures.
* The text. It includes a little information at the top.

One of Feynman's challenges was to make a tiny electric motor. For an update on that story... The smallest electric motor (September 26, 2011).

More small-scale technology: Windmills for your cell phone? (January 21, 2014).

Tracking termites

February 26, 2010

Jessica has developed an interest in tracking termites. (Hm, that might be an interesting story in its own right.) She sends: New Assay Helps Track Termites and Other Insects. (Science Daily, 2/17/10.)

A simple enough idea, with a clever implementation. It is a variation of a common procedure biologists use for tracking animals. You mark them, and then follow them. Banding of birds is an example you may know. The trick is to figure out something that is practical for termites -- and other insects. Here they mark the termites with a protein, which they can then detect later. Actually, they get the termites to mark themselves. They include the marker protein in a food bait provided to the termites at certain food stations; the termites eat the food provided, and along the way get some of the marker. (What does a biologist feed termites? Cardboard.) The marking protein they use here is one often used by biologists in the lab; the news story notes that work on using cheaper proteins, such as milk or egg white, is in progress.

75% The termite plot, and some results. The Figure is Fig 1 from the paper.

The spot in the center is the "central feeding station" (CFS), where the termites were fed with cardboard that had been impregnated with the marker protein.

Around the CFS are other feeding stations, with unmarked cardboard. The outer ring of stations is 10 meters from the CFS.

At intervals, the feeding stations were checked for termites. Collected termites were analyzed for the marker.

In a particular experiment... 17 days after the initial feeding, termites were found at 11 stations (including the CFS); these are the ones shown dark in the figure. Analysis of the termites at those stations showed that at 7 stations there were some marked termites; these stations have dots around the station symbols in the figure.

(The news story, listed above, includes a good picture of the termites.)

The paper: Utilizing rabbit immunoglobulin G protein for mark-capture studies on the desert subterranean termite, Heterotermes aureus (Snyder). (P B Baker et al, Insectes Sociaux 57:147, 5/10.)

More about termites...
* What if two of the world's most destructive pests spent the evening together in Fort Lauderdale? (April 4, 2015).
* Prospecting for gold -- with help from the little ones (March 1, 2013).

For more about tracking insects...
* Radio-tagged ants (May 13, 2009). High tech. More expensive. More suitable for special lab studies than for field work. But more fun.
* Ants: nurses, foragers, and cleaners (May 24, 2013). Large scale!

February 24, 2010

Pigs as organ donors for humans -- follow-up

February 23, 2010

This is a follow-up to the post Pigs as organ donors for humans (February 16, 2010). A comment from a reader, with useful perspective...

The topic of xenotransplantation has been around a long time. I actually did a public speaking event on the topic in 2000 when I was in high school, and the topic was prevalent in publications in the 1990s through that time. The issues then, as they apparently continue to be, are antigens and the prevention of disease between the species (as mentioned in the post commentary). The idea seemed logical, which made it a good topic for debate. If we could "grow" replacement organs in an animal that also had other uses, it seemed far more efficient, at least, than regenerative approaches. But the time it takes to overcome these barriers/challenges is still a reminder that it's anyone's game in the research field. Then there are the ethical concerns to consider; a barrier that impacts most if not all these fields. The progression of the research has seemed slow and the social conflict further retards some advance. Only 10 years ago, xenotransplantation was on the verge of breaking out; yet the debate continues. As a result, I suspect the there will still be a number of years for competition. If anything, the renewed interest in the topic demonstrates its resilience and the ability for the public to become "comfortable" with the idea.

* * * * *

Response: I think it is important to emphasize that these are research topics for now. Sometimes these things get hyped, and people think that magic cures are imminent.

This prompts me to add a bit more...

I think we sometimes forget how new the whole field of transplantation is. It was only 20 years ago that the Nobel Prize in Physiology or Medicine was awarded to E Donnall Thomas and Joseph E Murray "for their discoveries concerning organ and cell transplantation in the treatment of human disease". Their work: developing bone marrow transplantation and kidney transplantation. (We might also note that bone marrow transplantation should be considered a use of stem cells.) See the Nobel site: 1990 Nobel Prize in Medicine.

The first successful kidney and bone marrow transplantations were in the 1950s. The first successful heart transplant was in the 60s. The transplantation of a baboon heart to a human was in 1984 -- at Loma Linda in California. All of these occurred within my lifetime. I have clear memories of the heart transplant events as major news stories.

In the original post, I briefly note the possibility of transplanting pig pancreas cells -- specifically, islet cells -- to humans for the treatment of diabetes. The whole subject of islet cell transplantation is an active field, with both promise and frustration. Much is done with human islet cells, but the supply is a serious limitation. Pig islet cells have been tried with a wide range of animals, and in very limited tests with humans. Official human trials are imminent. In some of this work, the islet cells are encapsulated, to prevent immune attack. A big subject -- well beyond this post. Stay tuned.

In raising the immunological issues with xenotransplantation, we should note that it is not necessary to get a perfect match. Perfect matches are rare with current transplants between humans, and the management of mismatches has become quite sophisticated. As noted before, a major immunological barrier has been removed by genetic modification of the pigs. Whether this is a sufficient reduction to make pig-to-human transplants immunologically acceptable remains to be seen.

An artificial kidney... WAK: Early clinical trial is encouraging (July 1, 2016).

There is more about regeneration and stem cells on my page Biotechnology in the News (BITN) for Cloning and stem cells. It includes an extensive list of related Musings posts.

Should you run barefoot?

February 22, 2010

A recent paper analyzed the stresses on the body in running barefoot vs wearing shoes. The first striking conclusion is that the mechanics of running are quite different in the two cases. The use of shoes -- padded shoes -- allows us to land on our heels. An important finding in the work is that this may be bad for you.

Photos of how (experienced) runners with and without shoes land. Comparison of how runners with and without shoes land.

The white circles on the leading leg are markers, used for analysis of leg motions.

Figure is from the news story in Nature; a variation of the figure is also in the Science Daily story.

* News story: Barefoot Running: How Humans Ran Comfortably and Safely Before the Invention of Shoes. (Science Daily, 2/1/10.)
* News story in Nature accompanying the article: Biomechanics: Barefoot running strikes back. (W L Jungers, Nature 463:433, 1/28/10.)
* The article: Foot strike patterns and collision forces in habitually barefoot versus shod runners. (D E Lieberman et al, Nature 463:531, 1/28/10.)

The authors have also established a web site: Biomechanics of Foot Strikes & Applications to Running Barefoot or in Minimal Footwear. (Now archived.) "This website has been developed to provide an evidence-based resource for those interested in the biomechanics of different foot strikes in endurance running and the applications to human endurance running prior to the modern running shoe."

Caution. Musings does not give medical advice. It reports, generally, on the findings in individual papers. Individual papers may be only part of the story, and sometimes are even wrong. This paper presents some interesting points about running with or without shoes. The authors explicitly note that they do not have evidence on the overall merit of one or the other.

People who run may be particularly interested in reading this story. I just caution you to not jump to conclusions based on a single report.

* * * * *

A reader response...

I have to disagree with the article you have presented.

People that train running are taught how to run, or they learn for themselves. Most important thing is to learn never to touch ground with your heels, as that is devastating to the knees, and unproductive speed-wise. The sneaker companies are basing their products on making devices that are making people using wrong technique more comfortable. Runners that use modern sneakers almost exclusively run on the front part of the leg, using heel cushioning as a gentle note how far their heel got (that also offloads part of the weight).

I am talking about this from personal perspective, as during the winters I have run a few miles every day, so I needed to learn how not to cripple myself. Additionally, running bare-foot is healthy enterprise only on natural soft surfaces. On concrete and asphalt it is idiocy.

* * * * *

A brief reply...

Interesting. Apparently, not everyone does learn. And indeed, as you suggest, shoe design (and marketing) may be part of the problem. A quick check showed that the field of shoes and running is a mess. One recent review article bluntly said there is little scientific basis for shoe design. I assume they are talking about shoes for the general consumer, not the pro.

As to running barefoot on hard surfaces, they address this. They say that habitual barefoot runners develop highly calloused feet, and run fine on very hard surfaces. How hard? Not sure. It may mean hard dirt. Concrete? Don't know, but I suspect some info might be available. Certainly, casual running on such surfaces without shoes would be painful.

* * * * *

Added March 2...
The story was featured on the cover of Nature; the cover photo was what originally caught my attention. I have since found a clean copy of the figure; it is on the authors' web page noted there, under Barefoot Running & Training Tips. Cover photo, Nature, January 28 [link opens in new window].

* * * * *

More about running...
* High-performing athletes: might they have performance-enhancing microbes in their gut? (June 28, 2019).
* Sparing glucose for athletic endurance (August 21, 2017).
* Is the Paralympics biased against left-leg amputees? (April 23, 2016).

More about knees: Using your nose to fix knee damage (January 28, 2017).

More about shoes and stresses: On the spontaneous untying of shoe laces (June 10, 2017).

Also see: A shoe (August 9, 2010).

Beware of goats bearing infections
It's one health.

February 20, 2010

Q fever incidence in The Netherlands. Q fever is on the rise in the Netherlands.

Why? Because of the goats.

From the Science magazine item listed below.

There are two levels of looking at this item. One is the specific case: how a rise of human Q fever in the Netherlands is related to what is going on in the goat herds. The other is the broader issue: the general issue of disease transmission among animals. We get diseases from other animals: sometimes from other humans, sometimes from our domesticated animals, sometimes from wild animals. By tradition, our healthcare systems for humans and for other animals are separate -- yet we are all together in one world, sharing our diseases. Part of the problem in this Q fever incident seems to be poor cooperation between these health systems. It's all one health. Something to think about.

Infectious diseases: 1) Questions Abound in Q-Fever Explosion in the Netherlands; 2) Humans, Animals - It's One Health. Or Is It? (Science 327:266, January 15, 2010.) The first deals with the specifics of the Q fever story; the second deals with the broader issue of an integrated view of health. Together, these are what brought up this item for me. As noted above, I encourage you to emphasize the second -- the big picture. (The first one will tell you the origin of the name Q fever.)

* News story: Netherlands to cull 35,000 goats in Q fever fight. (BBC, December 16, 2009.)
* An informational page from the CDC: Q Fever. (US Centers for Disease Control.) Basic background information on Q fever. (A CDC travel advisory previously listed here is no longer available.)

A reminder... humans transmit diseases to other animals, too. We're all together, and we share our infectious agents. See Both ways (November 18, 2008).

For a broader view of the One Health idea, see One health (November 15, 2010).

More on goats... Sliced meat: implications for size of human mouth and brain? (March 23, 2016).


February 20, 2010

NASA has given up on moving the Spirit rover on Mars. It's sad, but it is hard to be negative about something designed for 90 days that served for 6 years. (Hm, I wonder about its methionine content.)

Nature ran a delightful one-page retrospective on Spirit. It's cute, and actually pretty good. Have a look, at least for fun. Mars rover Spirit (2003-10) -- NASA commits robot explorer to her final resting place. (Nature 463:600, 2/4/10.)

Although the essay is generally very good, it does seem to be inappropriate in one way. As you read it, what do you think is wrong? For my view, put your cursor over the "link" It seems like ... . (Other ideas? Let me know.)

If you missed the point of my parenthetical comment near the start, see Methuselah's secret: methionine? (February 12, 2010).

* * * * *

Follow-up post: Spirit -- follow-up (March 17, 2010).

More about Mars...
* Water at the Martian surface? (August 27, 2011).

Geoengineering: a sunscreen for the earth?

February 20, 2010

One way to cool the earth would be to block the sun's rays. We know that increased levels of particulates in the upper atmosphere can do this; major volcanic eruptions lead to noticeable cooling of the earth. Some have proposed that we might dump particulates into the atmosphere intentionally, as a way to cool the earth. The general field of changing how earth works is called geoengineering; not surprisingly, it is controversial, and some is not well thought out.

Here are three short articles about combatting global warming with this type of geoengineering. These are "opinion" pieces; people are expressing their views on how we should proceed. To varying degrees, they talk about the problem in general, and the issues with this method. They talk about both scientific and political issues. Taken together, I think they offer a useful set of perspectives. I encourage you to at least browse them, with an open mind. There is no need for you to reach any conclusion at this point; just reading a bit about the issues may be useful.

* Opinion: Research on global sun block needed now. (D W Keith et al, Nature 463:426, 1/28/10.)
* Policy forum. Climate change: The Politics of Geoengineering. (J J Blackstock & J C S Long, Science 327:527, 1/29/10.)
* Atmospheric science: A Test for Geoengineering? (A Robock et al, Science 327:530, 1/29/10.)

Also see:
* Geoengineering: the advantage of putting limestone in the atmosphere (January 20, 2017).
* How do you know if you have been in the sun too long? (August 5, 2016).
* Fish make their own sunscreen (September 29, 2015).
* Climate engineering: How should we proceed? (March 4, 2015).
* Fertilizing the ocean may lead to reducing atmospheric CO2 (August 24, 2012).
* Climate change: Should we focus on methane? (March 24, 2012).
* Why isn't the temperature rising? (September 12, 2011).
* Dust (February 19, 2011).

February 17, 2010

Pigs as organ donors for humans

February 16, 2010

Borislav sent the following news story: Pig lungs in human transplants move step closer. (Telegraph, February 3, 2010.) Along with that, I also suggest the following coverage of the same story: Pig lungs could soon be transplanted into humans after astonishing medical breakthrough. (Daily Mail, February 4, 2010.)

Pig His lung could be your lung.

The figure is from the first news story listed above.

At the start, let's emphasize that the information here is quite incomplete. As the stories above note, they will be presenting the work in August -- and are not talking much until then. So, we have few details.

What they seem to have done is to set up a pig lung in the lab; they flow human blood through it, and show that the blood becomes oxygenated. Ok, sounds good; the lung works. They have overcome one major barrier: incompatibility of the human blood with the pig tissue. They have done this by genetic modification of the pig; details not clear. (A few years ago, one group reported that they had finally bred a pig line genetically modified to lack one major antigen of concern. I do not know the relationship of the work here to that earlier work.)

What they did is a preliminary step towards trying to transplant a lung from a pig to serve as a replacement lung in a human. The work here is progress, but by no means guarantees success of the transplantation.

Some issues...
* Heart valves from pigs have been used in humans; they work well.
* Why pigs? The general view is that pigs are the animals most similar to humans "all things considered" -- ignoring the primates, for which availability would be a major barrier. In particular, pigs are about the right size, and have similar physiology (including diet). However, there is a major immunological barrier.
* Disease. A complex story, which I can only introduce here; I do not pretend to have an answer. Transmission of ordinary infectious disease would be controlled by maintaining disease-free pigs. Of greater concern is PERV: porcine endogenous retroviruses. These are viruses in the pig genome. Are these viruses active? Can they be transmitted to humans? Can they be controlled? This is a field of active work. I think it is a fair summary that there is no evidence that PERV is a major problem -- and no certainty it is not. (In some ways, these are issues common to all transplantation. We noted earlier that several percent of the human genome consists of retroviruses. We also know that diseases have been transmitted from one human to another by transplantation.)
* Some may recall that one xenotransplantation (transplantation of a foreign organ) was done some years back with a baboon heart to humans. It worked, but not for very long.
* Xenotransplantation now competes with regenerative medicine: the use of stem cells to make new organs, possibly even from cells from the recipient. Stem cell use would have the advantage of avoiding the immunity barrier. Beyond that, both methods are at such an early stage of work that there is little value to trying to compare them.
* The stories quote one bioethicist, who apparently is opposed to xenotransplantation (though that is not particularly clear in one of the stories). His view should not be taken as "the answer". Bioethicists -- just like other people -- will vary on this. Debate by the public, including the bioethicists, is good. New developments often raise ethical questions. Over time, we tend to accept new things, as we understand them. For now, the important point is that getting new organs by either xenotransplantation or stem cells is quite a ways off, simply due to technical work that needs to be done.

Science published a short news story a few months ago about the use of pigs as xenotransplant donors. It was not about the current work, but about the possible use of pig pancreas cells for the treatment of diabetes. Some of the general issues in the article are relevant here. Cell therapies: Clean Pigs Offer Alternative to Stem Cell Transplants. (Science 326:1049, 11/20/09.)

* * * * *

There is a follow-up post: Pigs as organ donors for humans -- follow-up (February 23, 2010).

More... Organ transplantation: from pig to human -- a status report (November 23, 2015).

Also see:
* Can human lungs that are too damaged to be transplanted be fixed? (August 22, 2020).
* A prosthetic heart valve that can "grow" as a child grows (April 13, 2020).
* DNA testing -- for rejection of a transplanted heart (May 24, 2011).

For more about pigs, in a different context... Cooking pork (June 4, 2011).

A post about endogenous retroviruses: Is a "dead" virus in the human genome contributing to the neurological disease ALS? (January 11, 2016).

There is more about regeneration and stem cells on my page Biotechnology in the News (BITN) for Cloning and stem cells. It includes an extensive list of related Musings posts.

A book to enjoy (online)

February 16, 2010

book, at Project Gutenberg. Good for reading aloud, maybe with a small group of people.

The chart. The map (or "chart"). From the book, in the Second Fit. (Reduced.)

"And the crew were much pleased when they found it to be
A map they could all understand.

You may wonder about what appear to be blurred lines running across the map. They are not part of the map. The figure is a photo of a page in the original book, and lines of text are showing through the paper.

Why? Well, it actually is relevant to two different private discussions I have been having recently. And it is a lot of fun.

A virus that is or is not associated with chronic fatigue syndrome

February 12, 2010

A few months ago, there was a report linking the xenotropic murine leukaemia virus-related virus (XMRV) to the mysterious human illness chronic fatigue syndrome (CFS). Now, we have a new report showing there is no connection between XMRV and CFS.

The initial report of a link was less than a smoking gun. They found the virus XMRV in about 70% of CFS patients, but only 4% of healthy people. That suggests something, but it is just a first step. Certainly, it does not show causation. The new report finds the virus in zero of 186 CFS patients. That certainly seems to contradict the earlier finding.

What gives? Whom do we believe? Well, contradictory reports are common enough. There are many possible reasons. CFS is a complex and poorly defined disease. Perhaps XMRV initiates disease, but then may disappear. Perhaps XMRV is linked to some forms of CFS and not to others. Perhaps XMRV grows better in CFS patients, thus accounting for its association with the disease; if its prevalence varies for other reasons, its apparent association with CFS would vary. Perhaps one of the research groups did something wrong, and thus reached an incorrect conclusion. Sometimes, such an error involves a subtle methodological problem that was not obvious in advance. Perhaps. Perhaps. Over time, these various ideas will get examined more closely. For now, we don't know.

News story: New Virus Is Not Linked to Chronic Fatigue Syndrome, Suggests New Research. (Science Daily, 1/6/10.)

As I was about ready to post this, I came across a short news item in Science covering the story. It discusses the background, and gives an overview of some of the possible ways this story might get resolved. Virology: An Indefatigable Debate Over Chronic Fatigue Syndrome. (Science 327:254, 1/15/10.)

The article is freely available from PLoS: Failure to Detect the Novel Retrovirus XMRV in Chronic Fatigue Syndrome. (O Erlwein et al, PLoS ONE 5:e8519. 1/6/10.) There is also a link to it at the bottom of the Science Daily story listed above.

XMRV has also been linked to prostate cancer. Once again, subsequent studies have found no linkage.

The virus name is something of a tongue twister. Xenotropic murine leukaemia virus-related virus. That hyphen is important. There is a well-known virus called murine leukaemia virus (MLV). This virus is related to that virus, but is distinct. And it grows not in mice, but in "foreign" hosts, thus is xenotropic. So we have: Xenotropic MLV-related virus, or Xenotropic murine leukaemia virus-related virus.

* * * * *

Updates on this story:
* A virus that is or is not associated with chronic fatigue syndrome -- an update (July 26, 2010).
* Does XMRV cause CFS? We have a verdict. Maybe. (July 11, 2011).
* Does XMRV cause CFS? Wrap-up. (December 10, 2011). Overall, the XMRV-CFS story is a good case study in how a scientific dispute is handled. A "newsfocus" in Science, listed with this post, is an excellent overview of the whole story.

For a post on another controversial association of a virus with a human condition: A virus associated with obesity? (October 4, 2010).

More on CFS: Chronic fatigue syndrome: a clue about the role of inflammation? (October 27, 2017).

Another controversy... Measuring the level of a non-existent hormone (April 10, 2015).

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

Truth and reconciliation

February 12, 2010

The idea of truth and reconciliation came up in a private discussion, and I was surprised that the other person did not know about it. It got the most attention in South Africa after apartheid. A divided society faced the conflicting desires to move forward and yet to also deal with major societal crimes of their recent past. They tackled the problem through a Truth and Reconciliation Commission (TRC). The South African TRC was generally regarded as successful, and has served as a model for others.

A Wikipedia page presents the basic idea, and links to many specific examples. Truth and Reconciliation Commission.

Think about it. What are the pros and cons of using something like a TRC rather than the traditional criminal justice system? What values are reflected by each choice?

More about justice: Police training (July 19, 2020).

Methuselah's secret: methionine?

February 12, 2010

One of the intriguing finds of recent years is that a severe restriction of food intake leads to an increased lifespan. It works for a wide range of organisms, including yeast, worms, fruit flies, and mammals. Many people suspect that it would also work for humans, though it is almost impossible to test with scientific rigor.

The increased lifespan comes at a cost. Not only is the dietary restriction (DR) so severe that few humans would want to endure it, it also leads to impaired reproduction. So, for many studying the field, DR is a clue to something rather than an answer in itself. (DR is sometimes called caloric restriction.)

Now we have some new work that offers a glimpse into how DR works. The basic system is simple: They took Drosophila (fruit flies), and fed them a severe DR diet. The DR diet caused increased lifespan and reduced fecundity (egg-laying), as expected. That is the baseline. As an experiment, they added back certain nutrients for the flies. For example, some flies received the basic DR diet plus extra vitamins or extra carbohydrate. Most of these additions had no effect. However, adding back essential amino acids (EAA) did have an effect. ("Essential" amino acids are those the body cannot make for itself. That is, they are essential in the diet.)

Well, if the group of EAA has a special effect, the logical next step is to look at them individually. And when they did that, they found some fascinating results...
* First, simply adding back the amino acid methionine to the DR diet causes an interesting result. The flies had the increased lifespan typical of the DR diet, but normal fecundity. That is, a specific chemical (methionine) seems to have reversed the fecundity problem. The simple notion that increased lifespan and reduced fecundity are inextricably linked no long holds.
* Second, they repeated the experiments with mutant flies that were defective in a particular hormone signaling pathway; the methionine effect was not observed with the mutant flies. So, we not only have a clue about a specific chemical but about where it is acting.

Figure S9, showing effect of methionine. An example of their data...

The two parts of this Figure show two sets of measurements made from a single experiment.

There are three conditions, which are color coded. The baseline conditions are fully fed (red) and dietary restriction (DR; blue). The experimental condition is DR + methionine (gray).

The upper frame shows a measure of reproduction or fecundity: egg-laying. You can see that the DR flies (blue bar) have low fecundity compared to the fully fed flies (red bar). You can also see that adding methionine to the DR diet (gray bar) restores fecundity to the fully-fed level. (The figure shows error bars; the accompanying legend gives p values.)

The lower frame shows the lifespan results. The y-axis is probability of survival: the fraction of flies alive at a given time. All are alive at day 0 (p = 1), and none are alive at the end (p = 0). The curve, vs time, declines as the flies die. You can see that the curve for DR flies (blue) is shifted to the right -- to longer times -- compared to the curve for fully fed flies (red). You can also see that adding methionine (gray) to the DR diet has essentially no effect. (This is a common way to show survival data. For example, data showing that a drug treatment prolongs life may be presented with a graph like this.)

This is Figure S9, from the supplement to the paper. It was actually done with an alternative DR diet -- to see if the result would hold with a different diet. I chose this Figure to present here because it shows their two major types of measurements, and is one of the simpler experiments to explain.

Other work has also focused attention on methionine as a key player. Quite possibly, the ratio of amino acids -- methionine vs some other specific amino acid that has not yet been identified -- is important. The big message is that we now have an effect that is much more specific than simply "calories". The details will continue to be studied -- in flies and rodents, and eventually in primates.

News story: Balancing Protein Intake, Not Cutting Calories, May Be Key to Long Life. (Science Daily, December 6, 2009.)

* News story accompanying the article in Nature: Ageing: Diet and longevity in the balance. (T Flatt, Nature 462:989, 12/24/09.)
* The article: Amino-acid imbalance explains extension of lifespan by dietary restriction in Drosophila. (R C Grandison, Nature 462:1061, 12/24/09.)

More about CR: A drug that delays neurodegeneration? (June 14, 2013).

More about aging: Would young blood be good for your brain? (October 21, 2011).

My page for Biotechnology in the News (BITN) -- Other topics includes a section on Aging. It includes a list of related Musings posts.

February 10, 2010

You are part Borna: follow-up

February 9, 2010

Original post: You are part Borna (January 31, 2010). See the end of it.

Microbes -- some thoughts

February 9, 2010

Microbes (e.g., bacteria) are the dominant type of life on earth. Yet, they are largely invisible, and remained largely unknown to us until a century or so ago. We now recognize that they comprise about half of the biomass on earth. Further, they comprised all of the biomass on earth for a couple billion years -- and are the life type most likely to be found "elsewhere".

The December issue of Microbe featured an "essay" by Moselio Schaechter, one of microbiology's senior figures. He reviews some of the ideas that have developed over the time span of his -- and my -- career. Some are major, what might be called paradigm shifts. An example is the increasing recognition of the importance of microbial interactions.

It is a delightful two page essay, which many will enjoy, regardless of background in microbiology.

Paradigm Shifts, Paradigm Drifts. (M Schaechter, Microbe 4:538, December 2009.)

I know others of you here also read Microbe magazine -- the news magazine of the American Society of Microbiology (ASM). (We have here two of the youngest members of ASM.) Update... Microbe is no longer being published. The web site for the old issues is something of a mess. It's sad. But the article noted here is still there.

* * * * *

More about the role of microbes: The ultimate census: the distribution of life on Earth (June 22, 2018).

HHMI Bulletin

February 9, 2010

The Howard Hughes Medical Institute (HHMI) is a world leader in funding biomedical research. Jitesh notes that their quarterly news bulletin might be of interest to some of you, either in the field or thinking of it for your future. Check it out: HHMI Bulletin.

Update November 15, 2018... The HHMI Bulletin is no longer published. The last issue was Fall 2015. Back issues remain freely available at the web site.

* * * * *

Musings posts that refer to HHMI news stories include:
* CSI: Microbe (March 22, 2010).
* Finding cancer genes (September 19, 2010).

An HHMI educational resource, called BioInteractive, is listed on my page Internet resources -- Biology: other.

Garlic or rotten eggs?

February 8, 2010

Well, that's not exactly what they tested. The title of the news story is "Freshly Crushed Garlic Better For The Heart Than Processed". What they did was straightforward, as suggested by the title. They did it with rats. Then, in discussing the significance of the work, they describe the special biochemistry of garlic. They suggest that the effect they observe is due to hydrogen sulfide, H2S. Of course, the most famous source of H2S is rotten eggs. So it is easy to suggest that if fresh garlic is better than processed garlic because it releases more H2S, then some nice fresh rotten eggs in the diet should be even better for heart health.

Joking aside, the H2S story is interesting. Not too many years ago, biologists identified nitric oxide, NO, as a signaling molecule in animals. A gas. It wasn't really the first gaseous hormone found in biology; that honor probably belongs to ethylene, the plant ripening hormone. But it was the first for animals, and was something of a surprise. It also explained why nitroglycerin works as a heart drug. Then, evidence developed that two additional gases -- both commonly considered highly poisonous -- may play signaling roles in animals, including humans. These are carbon monoxide, CO, and hydrogen sulfide, H2S. I'm not sure that either of those is completely accepted yet as a human hormone, but the stories are developing. Now, we have evidence that garlic, a favorite of many, may act in part by providing us with H2S.

A caution... That some chemical has an effect does not mean it is a normal part of our signaling mechanisms. I think there is agreement that H2S can affect blood vessels. What is less clear is whether this is a normal process in our bodies. This requires showing that there are natural sources in our body, and that the amount responds to something or other. That is, we need to show some signaling process, not just an effect of the chemical.

Freshly Crushed Garlic Better For The Heart Than Processed. (Science Daily, 7/29/09.)

Freshly Crushed Garlic is a Superior Cardioprotective Agent than Processed Garlic. (S Mukherjee et al, J Agric Food Chem 57:7137, 8/12/09.)

I first learned of this work through a column in the February 2010 issue of the Journal of Chemical Education. The column, called Research Advances, by Angela King, also includes an item on the effect of curcumin -- the active ingredient of turmeric -- on biological membranes. Whether anything in the work explains the reputed effects of curry is not clear. See Curry and Alzheimer's disease (June 15, 2009) for an item on curry.

More about carbon monoxide... Cooperation: a key to separating gases? (March 28, 2014).

More about hydrogen sulfide...
* Antibiotic action: effect of hydrogen sulfide (July 9, 2021).
* What's the connection: rotten eggs and high-temperature superconductivity? (June 8, 2015).
* Huntington's disease: Is it an amino acid deficiency? (October 4, 2014).

More about nitric oxide... SNO and the higher prevalence of Alzheimer's disease in women (January 14, 2023).


February 5, 2010


For follow-up, see GEBA: B -- revisited. Horizontal gene transfer: the web of life? a challenge to evolutionary theory? (March 26, 2010).


February 5, 2010

Need to protect yourself from prying parents or bosses? From crabs who think you would be a nice dinner? From the all-knowing Google? How about a 3-layer armor consisting of a layer of calcium carbonate, followed by a thick flexible organic layer, followed by iron sulfide? It works for Crysomallon squamiferum, a snail found near hydrothermal vents in the Indian Ocean. (No, they don't report all the specifics I suggested, and the Google problem may be truly hopeless.)

Armored snail It.

The snail is about 4 cm across. (According to Figure 1A of the paper.)

Larger version [link opens in new window]. Recommended.

Multi-layered skeletons are not novel, but this particular combination is.

Studying how biology has solved various problems offers engineers new models. There is an emerging field of bio-mimetic, or, better, bio-inspired engineering. For more, see my Biotechnology in the News (BITN) topic Bio-inspiration (biomimetics).

News stories:
* Unusual Snail Shell Could Be a Model for Better Armor. (Science Daily, January 19, 2010.)
* The Fantastic Armor of a Wonder Snail -- Exoskeleton of newly discovered gastropod mollusk could improve load-bearing materials. (National Science Foundation, January 18, 2010.) The figures above are from this page. (This is a press release from a funding agency.)

The paper is freely available: Protection mechanisms of the iron-plated armor of a deep-sea hydrothermal vent gastropod. (H Yao et al, PNAS 107:987, January 19, 2010.) I encourage you to read the abstract and maybe the first page or two for good perspective on why bio-skeletons are interesting.

The paper is from MIT, Raytheon, and Asylum Research. Asylum Research?

Next post about snails: Why is there an advantage in being left-handed -- if you are a snail? (January 18, 2011).

More about the strength of mollusk skeletons: A new way to make impact-resistant glass (August 9, 2019).

More about exoskeletons:
* Ants with skeletons hardened by calcite (January 30, 2021).
* How do you breathe while changing your skeleton? (October 31, 2014).

More about calcium carbonate shells... A see-shell story (February 21, 2016).

February 3, 2010

Book review: Kepler

February 3, 2010

From time to time Nature runs a column called "In retrospect", in which they feature a book of yesteryear that seems of interest. It is something of a new review of an old book, putting the book in a modern context. In this case, the book is Astronomia Nova (New Astronomy), published in 1609 by Johannes Kepler. The one page review is certainly worth reading; maybe the book is, too.

In Retrospect: Kepler's Astronomia Nova. (J J Lissauer, Nature 462:725, 12/10/09.)

From the same Nature series about books of yesteryear... Book review: Galileo (October 6, 2010).

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

This post is also noted on my page Book suggestions: Kepler, Astronomia Nova (New Astronomy).

The panda genome: update

February 2, 2010

Original post: The panda genome (1/11/10).

I have added the news story that accompanied the article in Nature. This may be of particular interest to those of who you are curious about DNA sequencing technologies. The panda sequencing was done entirely with so-called next-generation sequencing.

Another disease has been eradicated. GREP.

February 2, 2010

In 1980, the end of smallpox was officially declared. An intensive worldwide effort, over many years, had led to the total elimination of a disease.

Now, we have news that another disease has probably been eradicated, though the final steps of monitoring will continue for another 18 months before an official announcement. The disease is rinderpest (cattle plague) -- a viral disease of cattle, related to (and perhaps the origin of) human measles. It is not well known in the US, but worldwide over time has been a serious killer, with major economic consequences.

Here is the news story in Nature that made me aware of this development: Cattle disease faces total wipeout -- Rinderpest goes the way of smallpox. (Nature 462:709, 12/10/09.)

Here is a page from the FAO (Food and Agriculture Organization, of the United Nations). It is not very technical, but includes some interesting information, in Q&A format. Maintaining Global Freedom from Rinderpest: Questions & Answers. (Now archived.)

The idea of eradicating a disease raises a number of issues, both scientific and social. What makes a disease "easy" to eradicate? How much does it cost to eradicate a disease? Here is a "Commentary" article from a few years back which addresses these issues. It includes an interesting historical perspective, discussing some failed attempts to eradicate diseases, and some plans for the future. The PubMed listing gives the abstract, and links to a freely available copy of the article: When Is a Disease Eradicable? 100 Years of Lessons Learned. (B Aylward et al, American Journal of Public Health 90:1515, 10/00.)

What's next? The big eradication project in progress is for polio. The project has made great strides, but is behind schedule, with four key countries proving to be difficult. Science did a very nice news story on the polio situation last winter, with a discussion of the unique issues with each of the four countries. Polio: Looking for a Little Luck (Science 323:702, 2/6/09.) I encourage you to look over this article, perhaps with the one above. The combination will give you an overview of disease eradication, with some focus on the specific human disease currently near eradication. The polio story is frustrating -- yet somehow we must remain hopeful. As you read the polio story, a few things to remember... There are actually two viruses here (polio types 1 and 3); both need to be eradicated. If you compare the polio data in the 2009 article with the polio data in the 2000 article, you will see that much progress has been made. In fact, the situation of having four difficult countries has held for several years. (Sometimes you will hear of more than four; most likely, that is due to spillover from Nigeria into neighboring countries.)

Also see:
* WHO certifies "South-East Asia" free of polio (November 1, 2014).
* Polio eradication: And then there were three (March 27, 2012). A polio milestone for India.
* Poliovirus eradication: an update, with some good news and some bad news (May 22, 2011).
* Polio: progress toward eradication (November 5, 2010).

Picture? Do you really want a picture of a dead cow?

Here is A cow dying of rinderpest [link opens in new window]. (It is from an older FAO page: Cleaning out rinderpest's last reserves. (11/20/02. Now archived.))

The Nature story listed above has a nice picture of cattle getting their rinderpest shots.

There is also a dead cow in the post Lakes that explode (October 13, 2009).

More about cows dying: If cows had eyes on the rump, would they be less subject to ambush attack by lions? (September 22, 2020).

My page on Biotechnology in the News (BITN) -- Other topics includes a section on Smallpox (the first disease to be eradicated). It also includes a section on Measles.

* * * * *

More, January 29, 2012... Here is a news story following the official announcement. It is full of interesting historical information, as well as information about the eradication. Rinderpest eradicated. (JAVMA News, June 15, 2011. JAVMA = Journal of the American Veterinary Medical Association.)

Spinning gears -- driven by bacteria

February 1, 2010

Actually, the title I wanted to use is: A lesson in violating the laws of thermodynamics. Or maybe: A Maxwell's demon for the New Year. But that might be too complex for some, so I decided to use the simpler title. Nevertheless, I do hope that this item has some of you scratching your head.

Since people here are interested in energy issues, I should add that this item is really relevant to anyone who needs a femtowatt energy source. (That is 10-15 watt -- a millionth of a billionth of a watt.)

Thien sent me the following item: Bacteria taught to spin microscopic gears right round, could make for better solar panels. (12/21/09.) Nice pictures, showing the result, but it is not clear what is behind this.

Gears, driven by bacteria
A gear, being spun by bacteria (which are not visible here). The arrow points to a mark on the gear, for reference. This is part of Figure 2 of the paper; it was also included in both news stories listed here.

Since the above item noted that the work was done at Argonne National Laboratory (ANL), I checked for more information at the ANL site. That led to: Argonne scientists use bacteria to power simple machines -- Organisms turn microgears in suspended solution by swimming. (12/16/09. Now archived.) This has more explanation -- and more modest claims. And it has a movie -- try it. It also led to the paper, which is listed below -- with more movies.

An intriguing aspect of this finding is that the random motion of the bacteria leads to the gears spinning in one direction. I'm not sure that they really explain how this rectifying occurs, although it may be in earlier papers. One key point is that the gears are asymmetric; apparently, they cannot easily spin in the opposite direction. They also talk about how the "collective motion" of the bacteria is responsible. Indeed, many bacteria are needed to spin the gears at a noticeable rate. However, I find their evidence that the effect is non-linear to be unconvincing (see Fig 4 of their paper, and look at the error bars). Nevertheless, the gears spin -- in one direction; clearer explanation can come later.

* The paper is Swimming bacteria power microscopic gears. (A Sokolov et al, PNAS 107:969, 1/19/10.) Caution: not easy reading.
* The paper is accompanied by a set of movies. You can get to them by clicking on "Supporting information" at that site, or you can go directly to: Supporting information (Movies). This page links to the movies. (It also links to a pdf file, which contains a brief description of the movies; the pdf is not really very helpful.) Note that this page of supplementary materials for the paper is freely available -- regardless of whether you have access to the paper or not.

More about bacteria swimming: How bacteria swim and why -- a physics view (October 2, 2009).

More on gears... Quiz: What are they? (September 27, 2013).

More things spinning... A new record: spinning speed (October 12, 2018).

You are part Borna

January 31, 2010
(with addition February 9, 2010)

Borna? It's a type of virus, one that causes disease in some animals. Bornaviruses are known in humans, but with no clear association to any human disease. Borna is an RNA virus, with no known DNA stage. (Some RNA viruses make a DNA copy during their normal life cycle; these are known as retroviruses. HIV is perhaps the best known retrovirus.)

So we are part Borna? What does that mean? The new discovery is that a gene, rather clearly identified as a Bornavirus gene, is found in the human genome -- and in the genomes of (some) other animals studied.

Why are scientists excited about that? It is the first example of finding a gene in our genome that seems to derive from a virus with no DNA stage.

Does it matter? Who knows. They just found it, and have no idea what role, if any, it might have. Several percent of the human genome is derived from retroviruses, and some of the retrovirus genes in our genome are functional. At least one of the Borna genes found in humans seems to make a protein. The Feschotte article listed below highlights that the discovery is "leading to speculation about the role of these viruses in causing mutations with evolutionary and medical consequences."

News story: Evolutionary Surprise: Eight Percent of Human Genetic Material Comes from a Virus. (Science Daily, January 8, 2010.)

* News story accompanying the article in Nature: Virology: Bornavirus enters the genome. (C Feschotte, Nature 463:39, January 7, 2010.)
* The article: Endogenous non-retroviral RNA virus elements in mammalian genomes. (M Horie et al, Nature 463:84, January 7, 2010.)

* * * * *

Another post about viral genes in animal genomes: Ebola virus: ancient origins? (November 4, 2014).

* * * * *

A reader reply, and my comment. Posted February 9, 2010...

Reader reply...

Fun trivia: Borna is a common Croatian name. We had a king of that name.

Borna of Croatia.

My comment...

Gee, some of you take these things so personally.

The Borna virus was named after the town of Borna, in Germany.

Preparation of posters

January 30, 2010

Posters are now an important way of presenting material at scientific meetings. Some of you have done it (and one has already won a couple of awards for good posters!). But not all posters are good.

Here are a couple of sites with "advice" on making posters. I think you will find them useful guides.
* The Poster Session: A Guide for Preparation. An article by Carol Waite Connor (U.S. Geological Survey, 1988).
* Creating Effective Poster Presentations. From G Hess et al, North Carolina State University.

If you have suggestions to add to this list, let me know.

January 27, 2010

Why are the bees dying?

January 26, 2010

Bees are dying. Whole colonies are dying. The phenomenon is called colony collapse disorder (CCD). But a name is not an explanation, and attempts to find the cause have not been productive. In fact, there is not even a clear understanding of what describes the phenomenon. Bee populations vary. Nevertheless, there is a sense that something is wrong, especially in North American bees. The problem is of economic importance; in some places there is a shortage of bees needed for pollinating crops.

Now we have a new report which offers a new explanation. They suggest that the bees suffer from poor diet. More specifically, cultivated bees often are fed only one food (the crop they are pollinating), thus lack the dietary diversity found in natural populations. Why does this matter? They suggest that bees with narrow diets are less able to resist disease, thus succumb more to a range of diseases. This shifts the emphasis from any particular infection to the generalized susceptibility to infection. Ideas like that have been suggested, but the current work makes the idea much more specific, and testable.

The paper does indeed show some improvements in disease resistance when bees are fed a more varied diet (five types of pollen, rather than just one). I must say that I am not overwhelmed by the data. On the other hand, their idea does make some sense, and is testable.

Bees: effect of diet on glucose oxidase activity. Here is an example of their results.

In this test, they fed the bees with various diets, shown along the bottom. They then tested the level of the enzyme glucose oxidase; this enzyme makes hydrogen peroxide, which helps to sterilize the hive. The black bars show the results at 10 days.

You can see that the two groups of bees fed "polyfloral" diets (five kinds of pollen) had higher levels of the glucose oxidase enzyme than those fed "monofloral" diets (only one kind of pollen). (There is a group at the left, labeled 0%; these bees were fed no pollen at all, only "candy" -- sugar. The numbers given as % show the amount of protein in the diet.)

The figure is part of Figure 1 of the paper.

I use the term "disease resistance" above. You'll find that the paper talks about the immune system of the bees. We're talking about the same thing, and any distinction between our terms is not important here. I prefer the more general term for a couple of reasons. The immune system of bees is not much like ours, so the use of that term does not help you much. Further, their biggest effect -- shown above -- is actually for an aspect of disease resistance that does not seem to be "immune" at all. The production of hydrogen peroxide is more a matter of housekeeping than of immunity in the usual sense. Nevertheless, it is an aspect of disease resistance.

A news story: Bee decline linked to falling biodiversity. (1/20/10.)

The paper, which is freely available: Diet effects on honeybee immunocompetence. (C Alaux et al, Biology Letters 6:562, Aug 23, 2010.)

I have posted on CCD before, but it has been a while. None of the older items are currently on the Musings pages. There have been other items on bees, such as Origin of gas warfare (September 11, 2009). There has even been another item on "CCD" -- having nothing to do with bees. If you are curious, search the Musings page for 2009.

Here is a more recent item on CCD: US Army attacks colony collapse problem -- and an ethics story (October 25, 2010).

More about bees and pollen and defense:
* Bees: Why pollen might be bad for them (November 4, 2013).
* Should bees eat honey? (July 12, 2013).

Another case of using glucose oxidase to make H2O2 for killing: Engineering a worm to treat cancer (July 23, 2022).

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

More on glucose oxidase: A smart insulin patch that rapidly responds to glucose level (October 26, 2015).

Synthetic brains

January 25, 2010

Jitesh sends the following site, with "This is fantastic": Building synthetic brains capable of human level discovery and invention... -- Creative Brains for Robots. (URL given here is an archived copy.)

Caution... This is a company web site, promoting its developments. So expect some hype. In fact, the presentation is rather overdone. Nevertheless, the ideas stand -- not as worked out practical accomplishments, but as fascinating challenges. Look around. Under "products", you can even get a Creative Robots screen saver from them.

A previous Musings item on robots: Failbot (10/5/09).

The next Musings item on robots: Folding towels (4/10/10).

Did Neandertals use cosmetics?

January 24, 2010

A group of scientists studying the remains of Neandertal sites claim they have evidence that the Neandertals used cosmetics. How do they conclude this? And why do we care?

The heart of the evidence: They find shells that contain non-natural pigments, which could have only been made by some intentional process. Why do we care? If their interpretation is right, it is evidence that the Neandertals shared a characteristic of modern humans; the type of evidence they have is similar to that used to infer "symbolism" in early human populations.

What do we make of this? Well, it is fun; that is a good enough reason for looking at it. The underlying scientific issues are all quite technical, and hard for us to evaluate. They involve the identification of the materials, the dating of them, and the inferences made. I suspect that experts will argue on some of these points. Let them do so; that is how science proceeds. The work here has no immediate implications for any of us, even if it potentially offers insight into the human story. Enjoy the story, and let it proceed.

News story: Neanderthal 'make-up' containers discovered -- Scientists claim to have the first persuasive evidence that Neanderthals wore "body paint" 50,000 years ago. (BBC, 1/9/10.)

The paper: Symbolic use of marine shells and mineral pigments by Iberian Neandertals. (J Zilhao et al, PNAS 107:1023, 1/19/10.)

More about cosmetics: Is lipstick toxic? (July 2, 2013).

Other posts about Neandertals include...
* Head injuries in Neandertals: comparison with "modern" humans of the same era (February 22, 2019).
* Did Neandertal children hate broccoli? (November 22, 2009).
* What happened to the Neandertals? (October 8, 2010).

On being ambidextrous

January 24, 2010

The bodies of higher animals are bilaterally symmetric: the left and right halves are mirror images of each other. Of course, as we look more closely, we note that is not entirely true, but clearly a simple bilateral state was the basis of simpler animals. The brain reflects this pattern. It has two very similar -- but not identical -- halves. Simple animals may have symmetric brains, but higher animals have some degree of cerebral lateralization -- specialization of the two sides of the brain. This allows an effective increase in brain function without an actual physical increase.

Animals often show a dominance of one side of the body for key tasks. In humans, we recognize that most people are right-handed, and a significant percentage are left-handed. Most people have a natural tendency to be one or the other. A few people are ambidextrous: use either side about as well. Analogous side-preference can be found for use of feet or eyes. It seems likely that these preferences for one side are related to cerebral lateralization; we do not understand the underlying reasons..

What now? New work shows that parrots with a strong side preference do better at certain tasks than those that are ambidextrous. Interestingly, in parrots species vary in their side preferences. The preference shows up as a dominance of the foot and eye on one side. Some species are entirely right-"handed", some entirely left-handed, and some more ambidextrous.

It is an intriguing result, consistent with an emerging view that cerebral lateralization, reflected in side preferences, is important. It's a fun story, but be cautious in interpreting it. First, as the news story notes, they have shown a correlation, not a causation. Second, they are comparing distinct parrot species with different lateralizations, not members of the same species. Thus there are more uncontrolled factors than one would prefer. Finally, this is for parrots, not humans. On the other hand, there have been similar results with primates.

I think we are inclined to think of someone who is ambidextrous as having a special strength. This work makes us wonder whether such a person actually has a weakness: a less developed cerebral lateralization. Or perhaps, there are various ways for humans to become ambidextrous. The big caution, for now, may be to keep an open mind on this. It is generally well understood that it is best to allow children to develop their natural handedness -- the handedness that comes from their own brain. That should include any tendency toward being ambidextrous. It is not something that should be forced, one way or the other.

A news story: Biased parrots pass tests with flying colours. (9/2/09.)

The article, which is freely available: Laterality enhances cognition in Australian parrots. (M Magat & C Brown, Proc. R. Soc. B 276:4155, 12/09.)

More about handedness...
* Handedness in kangaroos: significance? (July 31, 2015).
* On handedness in humans (September 30, 2013).
* Analysis of teeth confirms that Regourdou was right-handed (September 7, 2012).

More about parrots... Bird brains -- better than mammalian brains? (June 24, 2016).


January 22, 2010

A reader asked me to post an item. I know nothing of the source or author, but the topic is certainly of profound importance. I post it, then, without endorsement or further comment.

There Are More Slaves Today Than at Any Time in Human History. (8/24/09. Now archived.)

Major follow-up: Slavery - II (November 5, 2013).

More on slavery: In what year was the word "slavery" most used in books? (February 23, 2011).

Words of wisdom; Newton's Law

January 22, 2010

Some Haphazard Aphorisms for Epidemiology and Life. (J M Cowden, Emerging Infectious Diseases, January 2010. Link here is to the article at PubMed Central.)

Such collections are inevitably mixed, but some items are fun. Some seem relevant at certain moments. Remember, as he notes at points... For every aphorism (wise saying), there is another that says exactly the opposite. I don't recall where I first heard that, but I refer to it as Newton's Law of Aphorisms.

The journal, commonly known as EID, is a publication of the US Centers for Disease Control (CDC). It is freely available online, and you can sign up for e-mail notification. Caution: This item is not typical of the contents. Browse the listing for an issue before signing up.

January 20, 2010

Genes that protect against malaria

January 19, 2010

It is a well-known story: Having one copy of the sickle cell hemoglobin (HbS) allele (form of the gene) provides protection against malaria, but having two copies causes a serious blood disorder. If malaria is common, the cost to the population of the two-copy disease is more than outweighed by the benefit from the one-copy protection. On the other hand, if malaria is rare, the sickle cell allele is simply bad.

Historically, the story of HbS was one of the first cases where we understood a disease resistance at the genetic and molecular levels.

Mosquito. After dinner. One of the central figures of the story.

After-dinner view.

There is much more to the story than that brief summary. Two recent reports have added a couple of interesting new pieces. The big theme is that there are various genes that can protect against malaria.

The first study clarifies the role of another malaria-protective mutation. It is a mutation in the gene for G6PD. (That is glucose-6-phosphate dehydrogenase, if you care.) The mutation is well known to cause a disease: favism, a genetic condition in which eating fava beans causes illness. Thus we already knew the "bad" side of this mutation; this work clarifies its "good" side -- the side that results in the mutation being maintained in the population at a high level. There had long been suspicion that the mutation provides protection against malaria, but the evidence was confusing. Here they show that the mutation protects not against the best known malaria parasite, Plasmodium falciparum, but against malaria due to P vivax.

The second study addresses an interesting story about the geography of malaria protection in different human populations. The major protective mutation against malaria in some places (e.g., southern Africa) is HbS, noted above. The major protective mutations against malaria in other places (e.g., Mediterranean) are of a type known as thalassemias. Interestingly, it is rare to find a population where both HbS and certain thalassemia mutations are common together. Why? Because those two types of protection are "incompatible" with each other. Each alone has its good and bad sides, as noted above for HbS. Combine them, and the benefit is reduced.

For the story of G6PD, favism, and vivax malaria...
* The press release from the Pasteur Institute, where (part of) the work was done: Malaria: a beneficial genetic mutation in South-East Asia. (December 11, 2009.) The figure above is from this page.
* The paper: Positively Selected G6PD-Mahidol Mutation Reduces Plasmodium vivax Density in Southeast Asians. (C Louicharoen et al, Science 326:1546, December 11, 2009.)

The second paper is freely available at the PNAS web site: Epistatic interactions between genetic disorders of hemoglobin can explain why the sickle-cell gene is uncommon in the Mediterranean. (B S Penman et al, PNAS 106:21242, December 15, 2009.) The word epistatic in the title refers to interaction between genes. I did not find a good news story for this item; if you want a bit more than my brief note above, try reading the first page of this article.

For another study of how a single gene can have both good and bad effects, see Why African-Americans have a high rate of kidney disease: another gene that is both good and bad (August 17, 2010).

For a post on controlling mosquitoes, see Mosquitoes that can't fly (May 3, 2010).

Also see...
* Diagnosing diabetes in people of African ancestry: a race-dependent variable (January 3, 2018).
* An easier way to get infected with malaria (January 18, 2013).
* What does "Anopheles" mean? (August 27, 2012).

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

Is Arthromitus a key bug in your gut?

January 16, 2010

By now, we all realize that each of us is inhabited by many trillions of bacterial cells (many more of them than human cells) -- our microbiota. Some 90% of them, representing a few hundred types of bacteria, are in our gastrointestinal (GI) track -- our gut. We presume they help with digestion of food.

It is becoming clear that our gut bacteria are also involved in our immune system. Germ-free mice (lacking all gut bacteria) have defective immune systems. Adding back the usual mix of bacteria leads to restoration of the immune functions.

What's new? A rather simple finding -- remarkably simple: a single type of bacteria provides a key immune system stimulation. The bacteria, with the proposed name of Arthromitus, have long been known as segmented filamentous bacteria, or simply SFB. They are considered related to the Clostridia, but are poorly characterized because they are "unculturable" -- they have never been grown outside the host animal. What do these bacteria do? They stimulate production of Th17 cells in your immune system -- cells needed for proper immune response to infection, and likely also involved in some auto-immune diseases, such as inflammatory bowel disease.

EM images of gut lumen, for two mice: one with and one without the bacteria Electron microscope images of cells on the gut surface.

Top pair of images: Two mice. One without (left) and one with (right) the SFB.
Higher resolution image, showing the segmented filamentous bacteria. Lower image: A higher resolution image showing the nature of the segmented filamentous bacteria.

Unfortunately, they do not show the scale. I suspect that the width of the bacterial filaments is about 1 micrometer, or a little less.

Images are parts of Figure 2 of the Ivanov et al paper listed below.

The work here is all with mice, though similar bacteria are known for humans. I'm sure many will be following up this work to see how it plays out in humans. Importantly, do changes in the amount or nature of the Arthromitus (or SFB) correlate with good or bad manifestations of the immune system? Ultimately, the question may be whether treatment designed to promote or inhibit these bacteria would be appropriate for specific conditions.

What is most important here? I think the big story is identifying that a single specific gut bacterium has a specific effect. This can be followed up, with possible implications for disease and treatment. It also serves as an example; perhaps other specific gut bacteria will be associated with specific effects. At the more philosophical level, it would support the emerging view that the human organism cannot be considered alone; in some sense, the human plus its associated microbiota is a single superorganism.

A news story, with a good overview of both papers listed below: Gut Bacteria Linked to Immune Response. (10/16/09. Now archived.)

Here are the two papers, from two groups working independently, but coming up with largely similar results. There is also a news story accompanying one of the articles in the same issue. I caution that these are all difficult articles, perhaps even for those fluent with the ins and outs of the immune system. So, if you do want more than the news story above, proceed with caution.
* Gut Immune Balance Is as Easy as S-F-B. (S K Mazmanian, Immunity 31:536, 10/16/09.) A "preview" news story of the following article.
* The Key Role of Segmented Filamentous Bacteria in the Coordinated Maturation of Gut Helper T Cell Responses. (V Gaboriau-Routhiau et al, Immunity 31:677, 10/16/09.)
* Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria. (I I Ivanov et al, Cell 139:485, 10/30/09.)

Subsequent posts involving the function of the gut bacteria...
* Sushi, seaweed, and the bacteria in the gut of the Japanese (April 20, 2010).
* Obesity, gut bacteria, and the immune system (May 24, 2010).
* How probiotics work: a clue? (October 11, 2010).

Also see...
* A phage treatment for inflammatory bowel disease (August 13, 2022).
* Appendix. Yours. (12/11/09) Are these items related? I wonder.
* Are childhood infections bad for brain development? (February 5, 2011).

Thanks to a couple of people here for stimulating my interest in the immune system.

Genomic information: What not to do.

January 16, 2010

The scenario: a person enters the UK, asking for asylum because of the war scene at home in Somalia. But the authorities are suspicious. Alter all, people want to enter the UK for various reasons, including economic opportunity. Certainly, claiming to be from Somalia might enhance the prospects of being accepted. So, how do you tell whether the asylum seeker really is from Somalia -- rather than perhaps from neighboring Kenya?

It's a perfectly legitimate question. But DNA testing is not a legitimate answer.

The UK government recently began a program to do DNA testing to determine where asylum seekers are from. I first came across this issue in a short news item in Science, which addressed the scientific issues. By now, the government has set aside the program -- perhaps because of the scientific objections. Still, it's worth looking at this; it is a good science story.

What would we need for the testing to work -- to achieve the intended goal? Well, first we would need to show that there are reproducible measurable differences in the genomes of Somalis and Kenyans (to stick with that particular case). Is that so? No one knows! It might be. But apparently the program was instituted without finding out whether there were known differences, or developing a plan to identify such differences. Further, even if such a test was validated (and we assume that Somalis and Kenyans do not inter-marry), this is a test for ancestry. That's not even the right question. The question is where the people came from, not who their ancestors were. The testing, assuming it otherwise worked, would not distinguish between a Somali living in war-torn Somalia and a Somali whose family had lived for generations in Kenya.

Here is the story from Science: Forensic science: Scientists Decry Isotope, DNA Testing of 'Nationality'. (Science 326:30, 10/2/09.)

Although I have discussed DNA testing above, there was also a second test. It involves isotope measurements. I've chosen not to deal with that here, but it is discussed in the Science article. The short answer is, once again, that there might be something to it in principle, but that they have not shown it works.

* * * * *

Recent related posts include:
Personalized medicine: cancer therapy (November 9, 2009).
Personalized medicine: Getting your genes checked (October 27, 2009).
In both cases, there is concern that use of the information is getting ahead of what is really known. That theme continues with this post. Whether the use is by government officials, businesses, or scientists, we need to emphasize the importance of developing the background information behind any application of genomic information.

More about asylum seekers: Immigration and asylum-seeking (December 14, 2016).

Dancing birds - more

January 16, 2010

Dancing birds.

For context, see Dancing birds page. I have added this item right near the end.

January 13, 2010

Do cell phones prevent Alzheimer's disease?

January 13, 2010

We did not have to go far into 2010 to get a bizarre science story in the popular media.

There have long been stories suggesting that cell phones cause brain cancer; somehow the media like those stories. Proper testing has failed to support such an effect.

Last week, a big story was that cell phones might prevent or even reverse Alzheimer's disease (AD). At least the story said the work was in mice.

What's this about? Does it make any sense? Before getting into some of the details, it may be good to start with a "bottom line"... They indeed show an effect -- one that seems to have surprised them as much as anyone. However, the experiments are quite preliminary -- as always with something brand new. The work is rather clean (well-defined experiments), and easy enough to follow up. I'm sure we will be hearing about attempts to reproduce this work, and to better define key parameters (such as how much irradiation). Importantly, even if this all holds for mice, it is not certain that it will carry over to humans. And testing in humans is much more difficult -- and time-consuming. So... treat this as an interesting -- and fun -- finding; whether it holds up, for mice or for humans, remains to be seen.

What they did is fairly straightforward. They took special mice that serve as a model system for human AD. (How good a model system is not entirely clear.) They split them into two groups, and exposed one group to the type of irradiation that is associated with cell phone usage. (No, the mice did not actually use the cell phones. Have you ever looked at the thumb of a mouse?) The treated mice showed improvement in certain specific memory tests; they also showed some interesting changes in the status of the Aβ protein that may be related to the AD disease process.

AD mice: effect of EMF An example of data showing an effect of cell phone irradiation on AD.

The mice are "Tg" -- transgenic, carrying an AD gene. They are tested at two times, about two months apart. The graph shows the number of errors they made during testing, vs time. The upper curve shows that the Tg mice make more errors over time, as their AD develops. The lower curve, for the mice treated with EMF (electromagnetic field; cell phone irradiation), shows that the increase in errors is prevented.

The Figure is part of Figure 1B of the paper listed below.

Interestingly, normal (non-AD) mice also showed certain test improvements with irradiation. That is, in addition to providing evidence that irradiation might be good for AD-mice, they suggest that the irradiation might provide cognitive improvements for normal mice!

Is it possible that they have uncovered an important benefit of cell phone irradiation that eluded previous workers? They argue that they have done two novel things. One is that they designed an improved memory test, and the other is that they used a long-term treatment. The validity of their arguments -- and of their basic findings -- will get tested.

This news story provides a good overview of what they did, as well as the mixed reaction the work has received: Alzheimer's Mice Improved by Cell Phone Radiation. (1/6/10.)

The paper: Electromagnetic Field Treatment Protects Against and Reverses Cognitive Impairment in Alzheimer's Disease Mice. (G W Arendash et al, Journal of Alzheimer's Disease 19:191, 1/10.) Check Google Scholar for a freely available copy.

Also see:
* GSAP -- a clue to treating Alzheimer disease? (October 2, 2010).
* Curry and Alzheimer's disease (June 15, 2009).

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.

For more on possible biological effects of cell phone use, see... Effect of cell phone on your brain (April 11, 2011).

The panda genome

January 11, 2010

The first complete genome sequence (beyond viruses) was reported in 1985. Now, they are reported regularly. But anything having to do with the giant panda is news -- and that includes the genome sequence. Panda
At right: the gal whose genome is reported.

Genome papers can be rather maddening. The main experimental result is, well, the genome sequence -- which is much too big to show, and would not be intelligible anyway. So genome papers usually contain summaries of what they learned, and make some effort to address some interesting biological questions.

An interesting question for the panda is about its diet. The panda is famous for mainly eating bamboo -- yet it is most closely related to carnivores (meat-eaters). The genome analysis supports its closeness to other carnivores; the genome is most closely related to the dog genome (but remember that not many mammalian genomes are available for comparison). The panda genome does not seem to have key genes needed to digest bamboo (there must be a fairly major typo!), so they conclude that it needs microbes in its gut for that. Ok, that is true for all other cellulose-eating animals, so is not a surprise. Perhaps a bit more interesting: the panda seems to lack a taste receptor needed to taste meat. [The panda diet was briefly mentioned in an earlier post: Bet hedging (December 5, 2009).]

News stories:
* Giant Panda Genome Reveals New Insights Into the Bear's Bamboo Diet. (Science Daily, March 6, 2010.)
* Genome reveals panda's carnivorous side. (Nature News, 12/13/09.)

* The news story that accompanied the article: Genetics: Decoding a national treasure. (K C Worley & R A Gibbs, Nature, 463:303, January 21, 2010.) An important aspect of the work is that this sequencing project was done entirely with so-called "next-generation" sequencing, which promises a major cost reduction of sequencing. This article provides a good introduction to the sequencing methodology issues.
* The paper: The sequence and de novo assembly of the giant panda genome. (R Li et al, Nature, 463:311, January 21, 2010.) Only the hard core biologists will want to tackle the paper.

A subsequent post on genome sequencing: Inuk, a 4000 year old Saqqaq from Qeqertasussuk (March 1, 2010).

Also see:
* Pandas: When did they become specialized to eat bamboo? (March 18, 2019).
* How the giant panda survives on a poor diet (August 2, 2015).
* Loss of ability to taste "sweet" in carnivores (April 6, 2012).
* What is it? (December 14, 2010).

There is more about genomes on my page Biotechnology in the News (BITN) - DNA and the genome.

Increased CO2: effect on animals that make carbonate skeletons

January 11, 2010

Increasing levels of carbon dioxide, CO2, in the atmosphere leads to greater acidity in the oceans. This effect is straightforward chemistry: CO2 dissolves in water to make carbonic acid, H2CO3. As the name suggests, H2CO3 is indeed an acid -- a weak acid. It releases hydrogen ions, H+, thus lowering the pH of the oceans. In fact, a lowering of the pH of the ocean by about 0.1 pH unit has already been attributed to rising CO2.

So, what are the biological effects of this? One type of effect is on organisms that make their skeleton from carbonate, specifically calcium carbonate, CaCO3. CaCO3 dissolves in acid -- as many of you have probably shown yourself, simply by adding some ordinary chalk to some acid, such as vinegar or lemon juice.

Of immediate interest is a new paper, in which they measured the rate of calcification -- of depositing CaCO3 -- with various amounts of CO2 in the air for 18 quite diverse organisms. The main conclusion is that the organisms respond to the higher level of CO2 (the greater acidity) in various ways.

As an example...

At the right are two (of 18) parts of Figure 1, the main data figure from the paper.

Let's look at these graphs. Some aspects are simple, some are not.

In simple terms, the graphs show the rate of calcification (Y-axis) vs the CO2 level (X-axis). But be careful; more about the X-axis below.

Each graph shows the data points, a black line that is calculated to be the "best fit" to the data, and a gray band showing the 95% confidence interval for that line.
Data for response to CO2, for shrimp and purple urchin.

A striking observation is that the two graphs are different. Whatever other complications we introduce, the organisms in these two graphs responded to the increased CO2 differently. Very differently. And indeed, that is the major conclusion.

However, to understand this further, we need to look more carefully at how they plot the data -- in particular, how they plot CO2 on the X-axis. I cut off the labeling here, but if you look at the paper, you will see that the X-axis is labeled Ωaragonite (say "omega aragonite"). The key point is that this scale runs "backward" -- if you are thinking in terms of increasing CO2. That is, increasing levels of CO2 are to the left -- lower Ωaragonite. Thus, when you look at the graphs above, and see that the shrimp do best at the left, that is at high CO2. The shrimp seem to respond favorably to high levels of CO2, with its increased acidity.

Ωaragonite is a measure of how much calcium and carbonate are available, compared to the solubility of one common form of calcium carbonate. A value of 1 is the edge of solubility. Values below 1 -- to the left, with more CO2 and more acidity -- mean that an aragonite shell should be soluble.

A news story -- a reasonable overview, despite the hyped headline: Lobsters to Be Supersized by Climate Change? (National Geographic, 12/7/09. Now archived.)

The paper: Marine calcifiers exhibit mixed responses to CO2-induced ocean acidification. (J B Ries et al, Geology 37:1131, 12/09.)

This work has gotten a lot of attention. Some of you sent me messages about it. I was a little surprised that the paper got all the attention, since, in some sense, the main points here are not new. Varying responses of calcifying organisms to increased CO2 have been shown before. I think that what might be nice here is the range of organisms that are studied in parallel.

Besides the diverse nature of the responses of different organisms, it is also important to note the caution given in both the article and the news story. The tests here are simple tests. The biological world is complex. There is no simple way to get from these results to predicting what will happen in the real world.

More on the effect of CO2 and ocean acidity on CaCO3 skeletons:
* An example of coral growing well in a naturally acidified ocean environment (February 16, 2014).
* Can a coral adapt to a more acidic ocean? (September 29, 2013).

More about carbonate skeletons: Ants with skeletons hardened by calcite (January 30, 2021).

Other posts on global warming, CO2, and the oceans:
* CO2 emissions threaten clowns (Sept 20, 2010).
* Global warming, boric acid, and a noisier ocean (Aug 9, 2010).
* The effect of defecation by whales on global warming (Aug 2, 2010).

More about sea urchins: Where are the eyes? (August 19, 2011).

How about looking at the effects of lower levels of CO2? Atmospheric CO2 and the origin of domesticated corn (February 14, 2014).

More about carbonic acid: The real carbonic acid, at last? (January 10, 2015).


January 11, 2010

Punctuation. (5 minutes.)

Previous posts on English include:
* Spleling (June 11, 2009).
* Possessives (December 23, 2008).

January 6, 2010

What is the difference between a neutrino and a whale?

January 5, 2010

A simple story... Physicists set up a neutrino detector in the deep sea -- and find whales.

The neutrino and the whale. (Nature 462:560, 12/3/09.)

It's fun -- with some good science, including a good story of scientific collaboration between people in different fields.

More about whales... Tracking new songs as they cross the Pacific (June 21, 2011).

More about neutrinos: IceCube finds 28 neutrinos -- from beyond the solar system (June 8, 2014).

Science: breakthrough of the year

January 4, 2010

It is now something of a tradition: Each December, Science magazine chooses one scientific development as the Breakthrough of the Year. Actually, there is more to it. They also choose nine runners-up, and they comment on other happenings -- past and future. It is no more objective than most lists of the greatest this-or-that, but it is fun. The set of short articles provides a brief glimpse into some key developments over a wide range of science.

The #1 science story for 2009, according to Science magazine, is the report of Ardipithecus ramidus.

Ardipithecus ramidus: three views. Ardipithecus ramidus. Two views of the reconstructed skeleton, plus an artist's conception of what she might have looked like.

"Ardi" -- as she is known among friends -- is based on 4.4-million-year-old fossils from Ethiopia. Is she a human ancestor? Well, she has an interesting collection of features that is consistent with that. Many in the field suspect that she is, as a working hypothesis. In any case, she is the best characterized representative of animals this far back that may be part of our human ancestry, and thus offers an insight as to what was around at the time. (Ardi is about a million years prior to "Lucy".) Data, data, data. We need more data. Over time, the picture will get clearer.

One of the distinctive features that should be obvious to the casual reader is the opposable big toe.

The BBC offers a short summary: Human-like fossil find is breakthrough of the year. (12/17/09.) The figure above is from this story.

The feature in Science, with links to all the individual stories: Special Online Collection: Breakthrough of the Year 2009. (December 18 issue.)

Science started the annual recognition of the Breakthrough of the Year in 1989. (It was originally called Molecule of the Year.) The first award was for the polymerase chain reaction (PCR) -- and the heat-stable "Taq" DNA polymerase that made that process practical. PCR was developed at Cetus Corporation, where I was a Senior Scientist for nearly two decades. The key inventor of PCR, Kary Mullis, shared the 1993 Nobel prize for chemistry.

Added March 14, 2023. PCR developments: Ultra-fast PCR (March 14, 2023).

The next Breakthrough of the Year feature, expanded to include Insights of the Decade: Science: highlights of the decade (January 25, 2011).

A new year

January 1, 2010

Happy new year everyone.

Borislav wants you to know that the New Scientist calendar for 2010 features a nude Croatian female for January. Calendar competition: the winners.

(Parents... relax.)

I wonder what else the new year will bring.

Also see... The spider with the mostest ... (and such) (January 2, 2018).

Older items are on the page Musings: 2009 (archive).

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