3D printing for space: a titanium woov, and more

April 29, 2014

There have been several recent posts on the emerging technology of 3D printing, or additive manufacturing, as it is also called. A recent story caught my attention in this context. It's not a scientific journal article at all, but a feature web page from the European Space Agency (ESA), describing potential applications of the technology for the space program. The page is both fun and instructive.

The web page: Ten ways 3D printing could change space. (ESA, April 15, 2014.) There is a list of 10 points, with many pictures included. (My favorite picture is the one with point 4, but it has no obvious scientific value.) If you don't get 10 points, you may get a "Continue" button. If you still don't get 10, try another browser. Strange page.

Most recent post about 3D printing: 3D printing: simple inexpensive prosthetic arms (January 29, 2014).

More:
* 3D printing: Make yourself a model of the universe (December 19, 2016).
* Can you make a 777 by printing it? (May 9, 2015).

More titanium: The major source of positrons (antimatter) in our galaxy? (August 13, 2017).

Do elephants suffer long term harm if their social groups are disrupted by human intervention?

April 27, 2014

Elephants live in complex societies. How well do the animals themselves understand their society? What happens if the social structure is disrupted? A recent article offers some interesting insights into such questions. Caution... The experiments and the results are interesting. The interpretation is less clear. There is considerable news hype about this work; it is not clear it is all justified at this point.

The basis of the work in the new article is comparing two populations of elephants -- comparing how they respond to socialization tests administered by the scientists. Here is an example...

Why are the elephants at Pilanesberg less responsive to social cues? The authors interpret the work in terms of the history of the two elephant populations. Amboseli is considered a rather undisturbed park. In contrast, Pilanesberg was populated by orphan elephants during a cull of another park during the 1980s and 1990s. The authors suggest that the poor response of the Pilanesberg elephants is due to the severe social trauma that some of their members suffered 30 years ago.

The article used interesting methodology to probe elephant social structure, and the possible effect of social trauma caused by human intervention. Are there alternative ways to explain the results? What they claim is important if true, and it is "reasonable". However, I would be cautious about the interpretation; it's easy to think of other factors that might be involved. The scientists study two different populations of elephants, and assume that the key difference, the one responsible for the observed behavior, is the one they note. Perhaps, but that is an assumption. The authors do provide considerable discussion of other work that may be relevant, but it does not address this concern.

We need to distinguish how we might interpret this for immediate application to policy and how we understand it as science. There may well be enough here that we want to act with more caution in disturbing natural populations. That's fine. However, it is another matter to claim that we understand what is going on. This is a scientific paper; we should judge it by high scientific standards. We should distinguish whether an article provides conclusive proof of something, or whether it "merely" leads to an interesting hypothesis. We also have to accept that we make policy decisions on the basis of imperfect information.

News stories:
* Orphan Elephants Lack Social Knowledge Key for Survival -- Psychological impact from loss of family structure parallels PTSD in people. (Christy Ullrich Barcus, National Geographic Society, October 31, 2013.) Now archived.
* Mass Killings Can Haunt Elephants for Decades. (Science Now, November 1, 2013.)

The article, which is freely available: Effects of social disruption in elephants persist decades after culling. (G Shannon et al, Frontiers in Zoology 10:62, October 23, 2013.) A very readable article. I encourage you to look it over, especially the parts where they discuss the significance of the results.

Previous post about elephants... Was Linnaeus's original elephant African or Asian? (December 7, 2013).

Another psychology post: Can growing rice help keep you from becoming WEIRD? (July 22, 2014).

Another post about the effects of humans on other animals: Why male scientists may have trouble doing good science: the mice don't like how they smell (August 22, 2014).

The role of a government science adviser

April 22, 2014

I recently came across a delightful little "Comment" piece by the chief science adviser to the Prime Minister of New Zealand. What's it about? It's about what it means to be a science adviser to a government.

We have a science adviser to the President in the US. The role -- and the power -- of the adviser varies, depending on various circumstances, including the instincts of the President toward science. It was interesting to read the perspective of an equivalent in another country.

I encourage you to have a look.

The article, which is freely available: The art of science advice to government. (Peter Gluckman, Nature 507:163, March 13, 2014.) The subtitle: "Peter Gluckman, New Zealand's chief science adviser, offers his ten principles for building trust, influence, engagement and independence."

Another government science adviser: Science in the White House (June 11, 2009).

Also see: US Presidential candidates weigh in on science questions (October 18, 2016).

Development of insects resistant to Bt toxin from "genetically modified" corn

April 19, 2014

Bt toxin is an insecticidal protein, originally from the bacterium Bacillus thuringiensis (nicknamed "Bt"). Plants have been genetically modified to contain Bt toxin. Such plants are resistant to certain insects; the use of the plants means that it is not necessary to apply insecticides against those insects. (There are actually various types of Bt toxin, but we won't worry about that here.)

The question at hand is whether insects will develop resistance to Bt toxin after exposure to plants with Bt toxin.

The following figure illustrates the phenomenon, as reported in a new paper.

That insects are developing resistance to Bt corn is neither new nor surprising. (What is new here is that the resistance is expanding; worms developed as resistant to one form of Bt toxin are showing cross-resistance to another form.) In fact, there are precautions that are to be followed to reduce the chances of development of resistance. They aren't being followed. The problem was predictable; it's now in front of us. Perhaps it would be good to follow the precautions?

Lest we over-interpret that... There is no guarantee that we understand the problem completely or that the declared precautions are adequate. There certainly is room for further understanding, which will come with experience. The point is that we aren't fully using the understanding we do have.

News story: Pests worm their way into genetically modified maize. (Nature News, March 17, 2014.)

The article: Field-evolved resistance by western corn rootworm to multiple Bacillus thuringiensis toxins in transgenic maize. (A J Gassmann et al, PNAS 111:5141, April 8, 2014.)

Recent post about a genetically modified crop plant: Rotavirus: passive immunization via food (January 10, 2014).

More about resistance to Bt toxin:
* Alternative microbial sources of insecticidal proteins (December 9, 2016).
* Resistance to Bt toxin: What next? (July 15, 2016).

For more on GM crops, see my Biotechnology in the News (BITN) page Agricultural biotechnology (GM foods) and Gene therapy.

More about Bt toxin: How to administer Bt toxin to people? (May 16, 2016).

More about corn...
* What can we learn from a five thousand year old corn cob? (March 21, 2017).
* Atmospheric CO₂ and the origin of domesticated corn (February 14, 2014).

More about worms... Extending lifespan -- five-fold (January 12, 2014).

Can you see your hand in total darkness?

April 14, 2014

Try it. Go into an absolutely dark place (a closet, perhaps, with no light leaks). Close your eyes. Put on a perfect blindfold. Then move your hand in front of your face. Can you see it? The question is not whether you are aware of your hand in front of your face, but whether you think you see it. Some people say they can.

It's not easy to do that test just right. Perhaps there is a bit of light. One "control" is for two people to do this together. Move your hand in front of your face, then have your partner move his/her hand in front of your face. If you report that you can see your hand but not your partner's hand (even though it was in the same place doing the same thing), that is what we are talking about here.

What's going on? As noted, it is not a surprise that you know where your hand is. After all, it is your hand. What's a surprise is that you think you are seeing the hand. Your brain knows where the hand is; that's fine. However, for some reason it (your brain) reports to you that your eyes saw it. At least, that's what happens for some people.

Even with the control suggested above, this all seems quite subjective. Is it possible that someone could manipulate the results (consciously or otherwise)? A new article does further testing of the phenomenon, with that concern in mind.

In one set of experiments, two consecutive trials were done with the same people -- and with an attempt to trick them. In each trial, the participants were given a blindfold. However, they were told that one of the blindfolds would have small holes -- and that the other would give complete darkness. They were not told which was which. In fact, the two blindfolds were identical: both were light-tight. As a result, the experimental design might have created an expectation for Trial 2. For example, if the participants were somehow imagining hand motion in Trial 1, and thought that might be due to the light leak, they might report less in Trial 2.

Here are some of the results...

What about Experiment 4 (frame d)? It's the same basic experimental design as with Experiment 1, but this time there is a huge positive response. Most of the people report a 5 or 6; those scores were rare in the other experiments. What's different with Experiment 4? The subjects of this experiment have synesthesia. People with synesthesia report unusual connections between the senses. For example, some may report associating a particular color with a particular number. It's intriguing that people with one type of unusual cross connections, in synesthesia, are likely to report the type of cross connection of the current work. It's intriguing -- but we have no idea what it means.

The article contains one very different kind of experiment, which also helps to establish that the phenomenon reported here is real. The scientists do eye-tracking experiments. The simple answer is that people who report seeing their hand move in total darkness are more likely to show eye-tracking of the moving hand than those who do not report seeing the hand. Apparently, the brain not only attributes vision to the eyes, but tells the eyes where to look -- even in total darkness.

News story: 'Kinesthesia' Lets Us See, Perceive Our Own Actions In The Dark Without Even Noticing. (Medical Daily, October 31, 2013.)

Video. There is a promotional video from the University of Rochester. It's called What Synesthesia Can Tell Us About Connections in the Brain. It is available directly at YouTube. (4 minutes)

The article: Kinesthesis Can Make an Invisible Hand Visible. (K C Dieter et al, Psychological Science 25:66, January 2014.) (Put the title into Google Scholar, and you may find a copy from the authors at Univ Rochester. At last check, there were multiple links there, with various outcomes. Look around; one is the final published article.)

More about synesthesia:
* Can people learn to be synesthetic? (January 7, 2015).
* Synesthesia: the good side? (January 14, 2012).

More on the interrelationships of the senses: Connecting the senses (April 26, 2011).

More about eye tracking: Signs of autism in 2-month-old babies (February 7, 2014).

Google tracks the flu -- follow-up

April 11, 2014

Original post: Google tracks the flu (April 30, 2009).

In that post we noted that Google was using their records of what people searched for to predict the incidence of influenza. The idea is clear. The question is, how well have they done?

Here are some data...

At the heart of the problem is the underlying philosophy: that we can generate useful information by simply collecting lots of numbers. This is the "Big Data" issue, though it is fair to note that not everyone means the same thing by that term.

Among the points the authors make... What Google does is not transparent; thus it is not subject to the usual scrutiny of scientific analyses. Further, Google has said that they have tuned their method, and they will presumably continue to do so. Importantly, this includes tuning of both the Google Flu algorithms, but also Google search, which provides the raw data. In one sense, that's fine, but it also reminds us of their lack of transparency. What Google Flu does is to give an answer, but with little explanation or understanding. Is that good? It might be if it was correct. But we now know it may not be correct.

It's an interesting story. I encourage people to read it, whether they care much about tracking the flu or not. The article comes down rather hard on Google. Perhaps they overdo that, so let's not get distracted by trying to judge Google. The bigger issue is how we learn to use Big Data. Google is a pioneer there; that in itself makes them open to criticism.

News story: When big isn't better: How the flu bug bit Google. (Terra Daily, March 18, 2014.)

The article: The Parable of Google Flu: Traps in Big Data Analysis. (D Lazer et al, Science 343:1203, March 14, 2014.) A copy is freely available at the Harvard repository: pdf copy.

What about the other two curves in the graph? One, labeled "lagged CDC", is for making predictions based on the most recent CDC data available, which is typically about 2-3 weeks old. The curve labeled "Google Flu + CDC" is based on a combination of the lagged CDC numbers with the Google Flu numbers. The general pattern is that this combined indicator is better than the individual indicators. Using more information is good. See the lower graph in the article, where the data is plotted as errors.

* * * * *

* Previous post on the flu: Face masks and flu virus transmission on airplanes: an analysis of a flight (August 27, 2013).
* Next: Transparency of clinical trials -- Is the flu drug Tamiflu worthless? (May 4, 2014).

Many posts on various flu issues are listed on the supplementary page: Musings: Influenza.

More about Google:
* In what year was the word "slavery" most used in books? (February 23, 2011).
* elgooG (October 12, 2009).

Methane leaks -- relevance to use of natural gas as a fuel

April 7, 2014

Methane (natural gas, CH₄) is playing an interesting role in current discussions of fuels and greenhouse gases. Burning methane leads to much less greenhouse gas emission than does burning coal. That is because much of the fuel value of CH₄ comes from burning the hydrogen in it. Therefore, there is less CO₂ emitted for a given amount of energy released from the fuel. By this argument, switching from coal to natural gas is a good move. On the other hand, methane itself is a greenhouse gas -- a potent one, about 30 times more potent than CO₂. Even fairly small leakages of unburnt methane to the atmosphere could more than negate its advantage as a clean fuel.

Terminology confusion...We often hear the term carbon emission. Of course, not all C is equal. As noted above, CO₂ and CH₄ are both greenhouse gases, of quite different potencies. The term carbon emission in common usage typically means emission of CO₂. Emissions of other greenhouse gases are sometimes converted to the equivalent amount of CO₂.

Comment... Above I framed the issue in terms of a trade-off between coal and natural gas. You might wonder if that is the proper question. The point here is that it is one relevant question. We do use natural gas; we need to learn how to use it as cleanly as possible. There is a choice between coal and natural gas for some people; we need to address it as best we can. Climate change is complex. Looking at one piece at a time is one way to approach it. A corollary is that we need to be clear what the question is. Simply asking if natural gas is good is a poorly framed question; the question should be, good compared to what?

It would thus seem desirable to have a good understanding of the nature and magnitude of methane emissions into the atmosphere. A recent article in Science discusses this; the article attempts to take everything that has been reported about methane emission and integrate it into a coherent picture. Adam Brandt, the lead author, visited UC Berkeley in late March and gave a talk on the subject.

The main conclusion from the article is that we have a very poor understanding of methane emissions. In fact, the major role of the article may well be to help define the question rather than to reach a conclusion.

Nevertheless, the data that is available does suggest some conclusions. Even though they may be tentative, it is worth noting some of them...

Current estimates of methane emissions by the US Environmental Protection Agency (EPA) are likely to be low, perhaps by 50% or so. Among possible reasons for that are some procedural biases, and not taking into account some biological sources of methane, such as livestock and wetlands.

Despite the uncertainties, it is unlikely that the magnitude of methane emissions from natural gas operations negates its clean-fuel advantage over coal. (We should caution that some of the news media accounts of this report mis-represent this point.)

An issue of much current concern is production of natural gas by hydraulic fracturing (fracking). They find that methane leaks from this process are not large. This seems plausible. It's a more modern industry, largely developed during a time of greater consciousness about the problem of methane leakage. Further, methane is the product. Those whose business is natural gas have an economic incentive to minimize methane leakage. (In contrast, the petroleum producer may not have that incentive.)

An important finding that comes from analyses of individual units is that most emissions come from a fairly small number of very leaky units. For example, they note (p 734 middle), " ... one study measured ~75,000 components and found that 58% of emissions came from 0.06% of possible sources." This is good news, in a sense. It suggests that the industry can operate with a fairly low methane leakage rate. Programs to find and fix what they call "super-emitters" would be worthwhile; there is effort to develop such monitoring.

An interesting concern is the role of abandoned wells (for either natural gas or oil). In the old days, wells that were no longer productive were simply abandoned. In many cases there is little or no record of where they are, much less any monitoring for possible leakage. (The number of dead wells is several times the number of active wells. p 29 of the Supplement.)

The analysis is about methane in North America. (The 16 authors are all in the USA and Canada.) The question of global methane emissions came up at the talk. It was beyond the scope of this report, but the questions would be the same.

How does one study methane emissions? There are two general approaches. One is to study what individual units (such as wells or associated processing equipment) emit; this is referred to as "bottom up". The other is to measure the CH₄ in the atmosphere, and try to understand what affects it; this is "top down". Both of these are far more complex than they sound here. (Much of the talk was about the methodology.) For now, the two approaches do not agree well; the books don't balance!

This is an interesting and important topic. The new work is an admirable contribution. Getting the issues out on the table, with some preliminary suggestions, is good. But this needs more work. If you want more than my brief summary above, try the news story listed below. The article itself is rather dense, and is for those with a serious interest in either the policy or science sides.

News story: America's natural gas system is leaky and in need of a fix, new study finds. (Stanford University, February 13, 2014. Now archived.) From the lead institution. Good overview.

The article, which is presented as a Policy Forum: Methane Leaks from North American Natural Gas Systems. (A R Brandt et al, Science 343:733, February 14, 2014.) Check Google Scholar for a freely available copy. The Supplement is freely available at the journal web site.

Other posts on methane emissions include:
* Los Angeles leaked -- big time! (April 29, 2016).
* Boston is leaking (February 13, 2015).
* Space-based observation of atmospheric methane -- and the Four Corners methane hotspot (December 29, 2014).
* Quality of oil and gas wells -- fracking and conventional (August 18, 2014).
* Svalbard is leaking (March 7, 2014).
* Shale gas recovery using hydraulic fracturing (fracking) (October 7, 2013).

Related... Emissions from gas stoves, even when 'off' -- air pollution implications (February 21, 2023).

The following post addresses another aspect of the trade-off between CO₂ and CH₄: Climate change: Should we focus on methane? (March 24, 2012).

More on fracking... Fracking: Implications for energy usage and for greenhouse gases (October 26, 2014). This focuses on how less expensive gas might impact patterns of energy usage.

Also see:
* More about air pollution: The SF₆ story: an emerging greenhouse gas? (August 25, 2020).
* National contributions to global warming (June 25, 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.

YY in the mouth?

April 4, 2014

How appetite is controlled is the subject of much study. Appetite is one component of the broader topic of obesity. Understanding these is good basic science. Of course, there is also interest in the possible development of drugs, but let's emphasize the underlying science.

A hormone of interest is peptide YY (PYY). (The YY denotes that two consecutive amino acids are tyrosine; Y is the one-letter code for tyrosine.) PYY is a natural hormone; it's made in the gut, in response to digesting food, and circulates via the blood. It binds to receptors, inducing satiation -- the feeling of being full. That is, PYY suppresses appetite and leads to reduced food intake. It also induces what is called taste aversion; when given to humans systemically (by injection into the bloodstream), that manifests as a severe response politely called visceral sickness. Clinical trials of PYY as an appetite suppressant were short-lived.

A new article reports that giving PYY to mice directly in the mouth, as a spray, induces the desired appetite loss, without the taste aversion side effect. Of course, that has immediate implications for possible use as a drug, but it also raises the question of what is going on.

The scientists analyze what is going on by studying the receptors for PYY and what their effect is. Overall, what they find is a satisfying explanation for the observed results. The key point is that PYY receptors in the mouth selectively signal the region of the brain involved in satiety. In fact, it's now known that PYY is present in saliva as well as in the blood.

The article is quite detailed. But overall it offers some interesting results. We see that a hormone can have different effects depending on how it is administered, and we can understand that in terms of how the body is "wired". The article is part of our increasing understanding of what determines how much we eat -- a process not well controlled by many people.

News story: UF researchers use oral peptide spray to stimulate weight loss in animals. (University of Florida, December 19, 2013.) From the lead institution.

The article: Salivary Peptide Tyrosine-Tyrosine 3-36 Modulates Ingestive Behavior without Inducing Taste Aversion. (M D Hurtado et al, Journal of Neuroscience, 33:18368, November 20, 2013.)

More on appetite...
* What if one gave appetite-suppressing pills to mosquitoes? (March 15, 2019).
* Fructose and your brain (January 28, 2013).

Other parts of the obesity story...
* Could we treat obesity with probiotic bacteria? (August 5, 2014).
* Why exercise is good for you, BAIBA (March 10, 2014).

A post that is not relevant to the current topic... Y-Y: the first (May 5, 2019).

PYY is one of several hormones that affects, in one way or another, body weight. The long list of such hormones is confusing, but is perhaps to be expected. Body weight homeostasis is a big issue -- for your body; it shouldn't be surprising that multiple regulatory circuits are involved. Understanding them all opens the possibility of more specifically diagnosing why a particular person may not be controlling body weight satisfactorily. One of the very first of these hormones to be discovered was leptin, made by fat tissue. There is some information about leptin and some of the others in the section of my page Organic/Biochemistry Internet resources on Lipids.

Why chameleons change color (and get thin)

March 31, 2014

It may be common knowledge that chameleons change color as camouflage. However, that may be only part of the story. A new article provides evidence that one type of chameleon changes color to signal its status in a fight. The article is accompanied by a wonderful video; check it out regardless.

To set the stage -- literally...

What did the scientists do? They staged "contests" between pairs of chameleons, and made video recordings. Using the videos, they then analyzed the color patterns of the contestants over time, and correlated the colorations with the outcome. In doing the analysis, they took into account how the chameleon visual system works; that is, they tried to see what the chameleons saw. The analysis allowed the scientists to reach some conclusions about the role of chameleons changing color.

For example, brightness of body stripes was a good predictor of the willingness of a chameleon to fight. Interestingly, the animals turn sideways during the approach phase, as you can see in the video. On the other hand, brightness of the head was the best predictor of victory; the speed of changing head color was also predictive. Victory was generally recognized when the loser walked away; this usually occurred prior to much physical encounter. (The scientists intervened in one case, out of 45, where injury seemed likely.)

What do we learn from this? Animals -- including humans -- fight. Some aspects of the fighting have become ritualized, and fights are resolved during the preliminaries: the animal who knows he will lose walks away, with little or no physical damage. The current work gives some insight as to how these chameleons convey their status and resolve their disputes. We also learn that the color-changing ability of the chameleon is an active part of social communication, not simply about hiding.

Of course, many questions remain. For example.. What is the physiology of the signals to change color? Do some chameleons send deceptive signals? If this kind of color changing is so good at resolving fights, why isn't it more common in the animal kingdom?

Video. There is a short video available with the article (article web site; choose Supplementary Information). It is also available at YouTube. (2 minutes; no sound.) The video shows the activities of four chameleons, using the arena shown above. You can see color changes. Even more strikingly, look for the changes in thickness of an animal when you have an end-on view -- which is when they are displaying sideways. (Does this give new meaning to the term "flat panel display"?) You may want to focus on a single quadrant of the video; the upper left is a good place to start the first time you watch it. A must see!

News stories:
* Study shows male chameleons fighting prowess tied to color changing abilities. (Phys.org, December 11, 2013.)
* Chameleons Convey Different Info With Different Body Parts. (Ed Yong, Not Exactly Rocket Science (National Geographic blog), December 10, 2013.) Now archived.

The article, which is freely available: Chameleons communicate with complex colour changes during contests: different body regions convey different information. (R A Ligon & K J McGraw, Biology Letters 9(6):20130892, December 23, 2013.)

More about animals that change color... Deceiving a rival male (August 28, 2012).

More about lizards... When should the eggs hatch? (June 11, 2013).

Cooperation: a key to separating gases?

March 28, 2014

Separating chemicals that are very similar can be challenging. An example of industrial importance is separating the gases carbon monoxide, CO, and dinitrogen, N₂. A new article offers some progress on separating these two gases.

The key is that the scientists develop a material that CO binds to cooperatively. That is, the more CO binds, the easier it is for more to bind. That is an unusual behavior. More commonly, one molecule does not know that another has bound. Or, perhaps, if there is a limited number of binding sites, then one molecule binding makes it harder for the next to bind; it's harder to find a vacant binding site if most are occupied -- just as with parking spots for the car. With cooperative binding, one molecule makes it easier for the next to bind. It's as if one molecule binding opens up new binding sites. In fact, that is exactly what the scientists think is happening. Think about... how might parking one car make more parking spots available?

A classic example of cooperative binding is in your body: the binding of dioxygen, O₂, to hemoglobin in your blood cells. The first O₂ that binds changes the shape of the hemoglobin so that it is now easier for a second O₂ to bind. The cooperative binding of O₂ promotes delivery of the gas to tissues and its release there.

Let's look at some of their results for how CO binds to the new material.

What about N₂? They do the same kind of binding curve with N₂. The whole curve for N₂ looks like that first part for CO. Nothing special happens to the N₂ curve as more N₂ is added. That is, the binding curves for both CO and N₂ are similar at low pressures. However, at high pressures, CO shows cooperative binding, but N₂ does not.

The real test is what happens with mixtures. Here are their results...

Earlier I suggested you think about how parking one car might make more parking spots available. We might imagine that parking one car knocks out a garage wall, revealing a new area that is available for parking. If you prefer a gentler scenario, the car might actuate a switch that opens a door to a new area for cars; that's more likely to be a reversible system. What's going on with the CO may be like that. The material includes copper ions, Cu²⁺. The CO binds to the copper ions; when enough are bound, the material changes shape -- revealing more binding sites. N₂ does not bind to the copper ions, thus does not open up new spaces.

That explanation is not sufficient to explain why the separation works, but we'll stop here. The article has more about the nature of the cooperativity, and why it leads to separation.

The nanoporous polymer they develop here is an example of a metal-organic framework , or "MOF" material.

Back to the first figure for a moment... The right-hand scale, which we ignored earlier, is the ratio of CO bound to the Cu²⁺. You can see that the curve turns upward at a ratio of 0.76. For now, we simply note that this scale reflects the importance of the Cu²⁺ to the story.

Bottom line... A team of scientists has designed a new material to address a problem that is important to the chemical industry. In lab scale tests, it seems to work, and they have at least some understanding of why. Whether it is practical, either in its present form or as developed further, is open.

News story: Adaptable crystals allow quick, efficient separation of carbon monoxide from gas mixtures. (Nanowerk News, February 5, 2014.)

The article: Self-Accelerating CO Sorption in a Soft Nanoporous Crystal. (H Sato et al, Science 343:167, January 10, 2014.) Supplementary materials at the article web site include a short video (one minute; no sound; freely available), with a cartoon version of the separation process.

More about MOFs:
* Separating isotopes of hydrogen using a MOF (April 18, 2022).
* Capturing NO₂ from polluted exhausts (December 7, 2019).
* A novel device for measuring fluoride in water (March 1, 2019).
* Harvesting water from "dry" air (July 1, 2017).
* Doing X-ray "crystallography" without crystals (September 18, 2016).
* Zhemchuzhnikovite: a natural MOF (August 19, 2016).

More about porous materials:
* Liquids with holes (January 30, 2016).
* Upsalite: a novel porous material (September 6, 2013).

Other posts that mention carbon monoxide...
* A treatment for carbon monoxide poisoning? (January 13, 2017).
* Garlic or rotten eggs? (February 8, 2010).
* Seeing molecules under a microscope (September 19, 2009).

Recovery of live, infectious virus from 30,000 year old permafrost

March 25, 2014

This is a story that has gotten considerable news attention.

A team of scientists has taken a sample of 30,000 year old arctic permafrost, thawed it out in the lab, and inoculated a portion into a culture of amoebae. Viruses grew. That is, they claim to have resurrected a virus that had been frozen away in the permafrost for 30,000 years.

Claims of resurrecting material that old are not new; Musings has noted a couple before [links at the end]. Viruses, being small and chemically simple, should be simpler to resurrect than more complex organisms. Further, proving that what was found really was as old as claimed is difficult. Perhaps the important test is whether others can replicate this type of work. Nevertheless, the claim is made, and at least catches attention.

It is of some interest that it is an amoebavirus -- of the general type of giant amoebaviruses that has been getting quite a bit of attention lately, including a Musing post [link at the end]. Interestingly, the permafrost-derived virus looks very similar to one of the modern viruses reported earlier. However, upon closer examination, it has an unusual combination of genome and life cycle properties. The whole story of these giant viruses is rather new and obviously quite incomplete.

So we note the story. The significance will become clearer with further work.

News story: 30,000-year-old virus from permafrost is reborn. (Phys.org, March 3, 2014.)

The article: Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology. (M Legendre et al, PNAS 111:4274, March 18, 2014.)

Background posts...
* A 30,000 year-old plant, with an assist from a squirrel (March 10, 2012).
* Life at age 34,000? (October 8, 2011).

* The largest known virus (August 5, 2013). The new virus looks similar to the one shown in this post.

Other Musings posts that start with permafrost...
* Mercury pollution from Arctic melting (February 19, 2019).
* Inuk, a 4000 year old Saqqaq from Qeqertasussuk (March 1, 2010). This one yields genome information, but not a living organism.

More about the Arctic: What if your compass pointed south? (October 24, 2014).

There is more about the large viruses of amoebae on my page Unusual microbes in the section A huge virus.

More about amoebae: Trogocytosis -- How an amoeba chews its food (May 16, 2014).

A practical system for removing arsenic from water

March 21, 2014

A recent post featured the work of UC Berkeley professor Ashok Gadgil, who was honored for his invention of a system for disinfecting water [link at the end]. The day after posting that I came across a story about a new invention by Gadgil. This one is a system for removing arsenic (As) from water. It is intended for areas where there is an extremely high level of As in the groundwater, such as parts of South Asia; the As level there is as much as 50 times the common regulatory limit, and is of serious medical concern. As with his earlier inventions, it's not simply about developing a method in the lab, but about moving toward practical implementation.

There is a new article reporting a pilot test of the system in the field. Let's start with one of the results from that article.

How does the system work? The following cartoon figure outlines the process.

The process is called Electro-chemical Arsenic Remediation, or ECAR.

The process was developed in the lab. The test described above is a field test, intended to be close to real world conditions. The article contains an analysis of the cost of the treatment, which they think is acceptable. But success is ultimately measured by whether people make use of it. It's too early to judge that. However, the story that started me on this item was an announcement that a company in India has licensed the system, and plans to use it. That's a good sign.

News story: Indian Company Licenses Berkeley Lab Invention for Arsenic-free Water. (Lawrence Berkeley Lab, March 5, 2014.) This is how I learned of this topic. The story here is not about the article, but about the business development. It's a nice news story in how it emphasizes the implementation -- even if some of it reads as hype.

It's hype because it seems to assume that this is a successful project. That remains to be seen. But the message of this news story, as to how they plan a project and try to implement it, is good. In fact, this is a very good story about the project "big picture"; it is light on the details of the remediation process.

The news story also notes possible use of the method in some parts of California where there is a problem of As in the groundwater.

The article: Electro-chemical arsenic remediation: Field trials in West Bengal. (S E Amrose et al, Science of the Total Environment 488:539, August 1, 2014.)

Background post, about Gadgil... National Inventors Hall of Fame: 2014 inductees (March 11, 2014).

More about arsenic...
* Humans resistant to arsenic? (June 16, 2015).
* Rice and arsenic: rice syrup, baby food, and energy bars (April 23, 2012).

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

More about water in India... NASA weighs India, finds it deficient (October 2, 2009).

More about groundwater: Groundwater depletion in the nearby valley may be why California's mountains are rising (June 20, 2014).

Polio-like disease without polio virus?

March 17, 2014

Musings has noted the global effort to eradicate polio -- more specifically, the polio virus. A current news story reminds us that the relationship between disease and agent is more complex than we might routinely imply.

The immediate finding is that several cases of polio-like illnesses have been found in California. The cause is unknown.

It's important to emphasize "polio-like". It's not polio; more specifically, these cases are not due to any known strain of poliovirus.

The announcement that led to the current news story is based on an upcoming meeting talk. There is little to go on for now. On the other hand, this is not entirely a new story. We have known for some time that rare cases of polio-like paralysis occur without poliovirus. As the background of poliovirus-induced disease approaches zero, these other rare cases are being noticed.

The point for now is to be aware of the questions; there are no answers yet. The current eradication effort is aimed at poliovirus, an important infectious cause of paralysis. Whether the remaining types of paralysis are due to an infectious agent at all is an important question; the information in the news story should be taken as incomplete. If there is a new infectious agent, will it become more prevalent? Should we vaccinate against it? If there is not an infectious agent, what is happening? And so forth.

News story: Puzzling polio-like illness reported in 5 California children. (CIDRAP, February 24, 2014.) This is a good summary of the current situation, from a reputable source that focuses on infectious diseases.

Follow-up: Polio-like disease without polio virus? Follow-up (February 11, 2015).

* Previous Musings post on polio: Polio eradication: And then there were three (March 27, 2012).
* Next: WHO certifies "South-East Asia" free of polio (November 1, 2014).

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

Does this story indicate the emergence of a new disease? We don't know, but the question is on the table. More about emerging diseases is on my pages for Biotechnology in the News (BITN): Emerging diseases. That discusses some general issues, and also links to some specific diseases that have emerged in recent decades.

Self-powered micromotors for speeding up chemical reactions, such as destruction of chemical weapons

March 14, 2014

Degradation of toxic chemicals, such as pesticides or chemical weapons, must be done with great care; the degradation process itself might release toxic chemicals. A new article addresses one issue in such processes. The proposed solution is at least "cute"; we'll see whether anyone finds it useful.

The issue the scientists address is mixing the chemicals during the degradation process. Good mixing is important for complete timely degradation. Their solution builds on a phenomenon familiar to anyone who has taken a basic chemistry class: common hydrogen peroxide, H₂O₂, can break down to release oxygen gas, O₂ -- bubbles of oxygen gas. H₂O₂ is already part of the degradation process in some cases; what they have done is to harness the O₂ gas, and use it to provide effective mixing.

The following cartoon gives a sense of how they use the O₂ to provide mixing. It's not the clearest figure, so be patient with it.

Here is an example of using these little self-propelled mixing devices... In this test, the scientists measured the hydrolysis of the chemical methyl paraoxon (MP), a model for organophosphate agents. The MP has a para-nitrophenyl group; hydrolysis yields p-nitrophenol, which is yellow. That's what they measure; the yellow color of p-nitrophenol, as a measure of hydrolysis.

Thus we see that the micromotors speed up the reaction. They do so, we presume, by providing mixing from within the solution. That's good. Whether this is useful will depend on comparison with other ways of mixing; the analysis will include practicality, safety and cost. There is some comparison with magnetic stirring in the article, but it is hard to draw any conclusions from that at this point.

News story: Stirred from within: Micromotors mix for more effective oxidative degradation of chemical weapons. (Phys.org, October 31, 2013.)

The article: Micromotor-Based High-Yielding Fast Oxidative Detoxification of Chemical Threats. (J Orozco et al, Angewandte Chemie International Edition 52:13276, December 9, 2013.)

Another post on degradation of pesticides: Developing improved degradation of organophosphate pesticides (September 7, 2010).

Another use of the propulsion system: Colloidal microswimmers: 3D printing a micro-boat (December 13, 2020).

More on hydrogen peroxide...
* A simpler assay for detecting low levels of HIV, using gold nanoparticles (January 3, 2013).
* Why are the bees dying? (January 26, 2010).

More on platinum: Breaking C-F bonds? (October 26, 2018).

Why exercise is good for you, BAIBA

March 10, 2014

Exercise is good for you, and helps promote weight loss. Since exercise involves burning calories, one part of the explanation is clear enough: a direct loss of calories. However, the effects of exercise cannot be fully explained by simple loss of the calories expended. There are metabolic changes that provide further benefit.

A new article shows one part of how this happens, at least for mice. Interestingly, it involves brown fat, a tissue Musings has noted before. In brown fat, food is simply burned off; it gives off heat, with no other useful product to the animal. If we could stimulate brown fat, we could lose weight, because we would burn fat stores. According to the new article, exercise leads to a stimulation of brown fat. And the scientists think they have uncovered how that happens. One key part of the pathway is a small molecule called β-aminoisobutyric acid, or BAIBA.

Here are the results of one experiment...

This experiment is obviously not the entire story. This experiment does not start by comparing exercise vs no exercise. It starts with BAIBA -- and shows that giving BAIBA reduces body fat, without side effects. In other experiments, the scientists show that exercise itself stimulates the production of BAIBA.

That's with mice. The story is: exercise leads to production of BAIBA; BAIBA activates brown fat; brown fat burns calories. BAIBA is made in the exercising muscles, and acts in fat cells; it is a messenger between tissues. There are more pieces, but that's the idea: a connection between muscle and fat tissues, between exercise and burning calories. An interesting finding.

Any relevance to humans? There are no controlled studies, but there is some evidence consistent with similar effects in humans. For example, analysis of results from an earlier study of exercise showed that BAIBA levels were increased by exercise.

It's tantalizing. Perhaps we are closer to understanding why exercise is good for you. What are the implications, if further work supports this? It's easy to jump and suggest that BAIBA might be a useful drug, to promote weight loss. But let's not go there. Let's emphasize that it would represent improved understanding. If there is a connection between exercise and weight loss, mediated by BAIBA, then we would expect people to differ in how well this works. Do people who have trouble losing weight make less BAIBA? Do they respond less well to it? Better understanding of how exercise works should lead to better understanding of personal variation. In the long run, that should be good.

News story: Exercise Molecule Gives Metabolism a Workout. (GEN, January 8, 2014.)

* News story accompanying the article: Come on BAIBA Light My Fire. (H L Kammoun & M A Febbraio, Cell Metabolism 19:1, January 7, 2014.)
* The article: β-Aminoisobutyric Acid Induces Browning of White Fat and Hepatic β-Oxidation and Is Inversely Correlated with Cardiometabolic Risk Factors. (L D Roberts et al, Cell Metabolism 19:96, January 7, 2014.) Not an easy paper!

Previous post about brown fat: Brown fat: different kinds respond differently to cold (September 20, 2013). The type of brown fat discussed in the new article is the so-called beige fat, within white fat.

And more:
* Measuring the level of a non-existent hormone (April 10, 2015).
* Cachexia: is it BAT run amok? (September 22, 2014).

More about obesity...
* YY in the mouth? (April 4, 2014).
* Antibiotics and obesity: Is there a causal connection? (October 15, 2012).

More about exercise:
* Sparing glucose for athletic endurance (August 21, 2017).
* Hormone from bone boosts muscles (October 4, 2016).
* Would wild mice use an exercise wheel? (July 11, 2014).

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

There is now an extensive list of sports-related Musings posts on my page Internet resources: Miscellaneous under Sports. Added August 29, 2024.

Svalbard is leaking

March 7, 2014

Musings has recently reported leaks in various parts of the Solar System. But this one is close to home, and potentially very important to us. Svalbard, a part of Norway, is a group of islands north of the Norwegian mainland. And the leak there is methane.

Musings has noted that methane, CH₄, can form a complex with water called methane hydrate (or methane clathrate or methane ice). There are large quantities of methane hydrate below cold oceans. It's a potential energy source if we could figure out how to harvest it. On the other hand, there is fear that ocean warming could lead to release of methane from the hydrate. CH₄ is a greenhouse gas -- one far more potent than CO₂. Worst case, this could be a disaster. No one knows. [Links to background posts on both methane hydrate and solar system leaks are at the end.]

A few years ago, methane was found in the Arctic waters off Svalbard. What does this mean? Is this the first warning of a disaster?

In a new article, scientists have tried to analyze the methane emission from Svalbard. They show that this has probably been going on for thousands of years. They believe it is a stable situation, with intermittent gas due to seasonal variations. They caution, of course, that their conclusion can't be taken for granted for the future. An important part of their work is simply to establish a baseline.

It's an interesting article, addressing an interesting -- and important -- problem. Analyzing the methane record deep below the surface of the Arctic Ocean is a difficult problem. The discussion with the figure above gives you an idea that they develop interesting, but incomplete, arguments. I did not find the article very reassuring. It's good that they have done what they have done, but it seems a very small step. It is one thing to say that methane seepage has been going on for thousands of years; it's not at all clear that the rate is constant over that time. If methane leakage is currently sensitive to seasonal variations, as they claim, doesn't that suggest it might also be sensitive to even small changes in average temperature? Overall, then, this article is worth noting as a step toward addressing an important question.

News story: Methane hydrates and global warming. (Science Daily, January 2, 2014.)

The article: Temporal Constraints on Hydrate-Controlled Methane Seepage off Svalbard. (C Berndt et al, Science 343:284, January 17, 2014.) Check Google Scholar for a freely available pdf.

Background posts...
* Ceres is leaking (February 18, 2014).
* Europa is leaking (February 10, 2014).
* Fire from ice: is it practical? (May 13, 2013). A first effort to harvest methane from hydrate deposits.
* Ice on fire (August 28, 2009). More posts about methane hydrates are linked here.

Also see:
* Methane hydrate: a model for pingo eruption (August 4, 2017).
* Underwater "lost city" explained (July 25, 2016).
* Ancient forests of tropical Norway (April 19, 2016).
* Boston is leaking (February 13, 2015).
* Space-based observation of atmospheric methane -- and the Four Corners methane hotspot (December 29, 2014).
* Methane leaks -- relevance to use of natural gas as a fuel (April 7, 2014).

There is more about methane on my page Organic/Biochemistry Internet resources in the section on Alkanes.

More on the story of p

March 2, 2014

What does p = 0.05 mean? It's a question that recurs in science, because the statistical p value is used to evaluate how "good" the results are. However, few are clear what p means, and it often takes on a rigidity that is not helpful and was not originally intended.

A recent News Feature in Nature is a nice overview of the p story. It includes some of the history, which provides useful perspective. And it includes much humor. Well worth a browse for anyone who produces data or reads about it.

Bottom line... A p value cannot prove that a hypothesis is correct.

News feature, freely available: Scientific method: Statistical errors -- P values, the 'gold standard' of statistical validity, are not as reliable as many scientists assume. (R Nuzzo, Nature 506:150, February 12, 2014.)

A previous post on this topic is probably at: Mission Improbable (November 10, 2009).

More: What does a p value mean? Statisticians make a statement (August 6, 2016).

More about data presentation and analysis: How graphs can mislead (May 24, 2015).

More about mosquitoes: Malaria-infected mosquitoes have greater attraction for people (May 28, 2013). Read the current article, and you'll understand.

There is more about statistics on my page Internet resources: Miscellaneous in the section Mathematics; statistics. It includes a listing of related Musings posts.

Berkeley RadWatch: Radiation in the environment

February 24, 2014

RadWatch is a project that monitors radiation levels in the environment. Since radiation stories are often in the news, their posts can be relevant to current events.

Here are a couple of recent examples. I'll just introduce the topics and some key points briefly; see their posts for the stories.

1) Radiation in North America from Fukushima. RadWatch scientists have measured the level of several radioactive isotopes in salmon caught in Alaska, at various times since the Fukushima disaster (March 2011). A few months after the event, they detected low levels of a cesium isotope that was likely from Fukushima. None has been detected since then. Importantly, the level of that isotope, while detectable, was tiny compared to natural radiation levels (as well as to levels permitted by regulations). It is useful to be able to measure very low levels of radiation. In this case, they can track dispersal from Fukushima -- at levels far below what is of immediate concern.

A picture... I suppose it is from their "Materials and Methods". picture [link opens in new window]. (It's from the web page for this story, listed below. Larger version available there. Much larger.)

2) The Half Moon Bay monster. Recently, someone using an ordinary Geiger counter found high readings at a particular site on a beach a few miles south of San Francisco. Somehow, the story was interpreted as representing contamination from Fukushima, and it was associated with radiation-induced monsters. RadWatch investigated. Indeed the claimed measurement was correct: Geiger counter readings were relatively high where claimed. However, Geiger counter readings do little to help identify the type or source of the radiation. RadWatch, of course, used proper instrumentation, and found that it was due to normal variation in rock composition. The level, while measurably high, was not particularly dangerous and had nothing to do with Fukushima. The story is a good lesson about natural radioactivity, and about the limitations of Geiger counters.

RadWatch is from the Department of Nuclear Engineering at University of California Berkeley. The RadWatch web site is something like a blog. The posts contain data and discussion, but the site is not peer-reviewed. The RadWatch scientists do publish papers. I have an "in press" version of one such paper, which relates to Fukushima (and Chernobyl) radiation in the San Francisco Bay Area. I'll watch for the final published version.

Two radiation issues that are not discussed by RadWatch (at least on the pages I have seen)... One is radiation near Fukushima. RadWatch is a California activity, focused on local issues. In a sense, that makes it of wide general interest, since we are all potentially concerned about dispersal of radioactivity from occasional distant disasters. Second, they do not deal much with the biological effects, or with issues where the biology is quite different for different kinds of radiation.

What I have read at RadWatch is good science, well-presented for the general public. I encourage you to have a look -- and ask questions if you'd like.

Home page: Berkeley RadWatch. Among other things, check out their FAQ.

The two stories noted above can be reached directly at:
1) Results of Red Salmon from Alaska caught in 2011, 2012, and 2013 -- Gamma-ray analysis of 2011, 2012, and 2013 Red Salmon Samples. (K Thomas, January 30, 2014. Now archived.)
2) Half Moon Bay Measurements -- Measurements at Miramar Surf (Surfer's Beach). (R Pavlovsky, January 22, 2014. Now archived.)

Follow-up: Berkeley RadWatch: Radiation in the environment -- Follow-up (May 6, 2014).

Other Musings posts about radiation include...
* How radioactive is your avocado (and some other common exposures)? (November 16, 2016).
* Radioactivity released into ocean from Fukushima nuclear accident reaches North America (March 23, 2015).
* Effect of radiation near Fukushima on local monkeys (August 10, 2014).
* Are birds adapting to the radiation at Chernobyl? (August 3, 2014).
* Should physicists be allowed to use lead from ancient Roman shipwrecks? (December 2, 2013).
* Measuring radiation: The banana standard (April 17, 2011). This is actually relevant. The reason for the "banana standard" is that it contains a high level of potassium, thus of the radioactive isotope K-40. That isotope gets discussed in the current work. K-40 is one of our major natural sources of exposure to radiation.
* Does radiation treatment of cancer cause new cancers? (April 8, 2011).

More salmon...
* How the rain and cars in Seattle are killing the fish (January 26, 2021).
* Why robo-turtles may be useful (April 25, 2020).

My page of Introductory Chemistry Internet resources includes a section on Nucleosynthesis; astrochemistry; nuclear energy; radioactivity. That section contains some resources on the effects of radiation.

Color vision: The advantage of having twelve kinds of photoreceptors?

February 21, 2014

Humans have three kinds of photoreceptors for color vision: red, green and blue. We do rather well with that set; we can distinguish colors that differ by about 5 nanometers (nm) in wavelength. Some animals have four, including one that detects ultraviolet (UV) light.

Having more than four kinds of photoreceptors is uncommon. The champion is a group of organisms known as mantis shrimp. The species studied in a new article has 12 -- eight for what humans call visible light and four for UV; other species in the group may have as many as 21.

So how good is their color vision? Not very good, according to the article -- at least by the criterion mentioned above. They can distinguish colors only if they differ by about 25 nm -- five times worse than we do.

How do you test the color vision of mantis shrimp? The same way you test the color vision of people. You show them something where distinguishing colors is necessary, and see how they respond. Mantis shrimp aren't very good at saying numbers, but they are interested in food. The idea of the test, then, is that the animals are trained to associate food with a particular color. They are then tested to see how well they choose between that color and one that is close.

The following figure shows an example of such a test. (Both axes on the graph are poorly labeled. For now, follow my discussion of the graph. I'll note the labeling problems later.)

In the article, the scientists report that they did several such experiments, with training wavelengths across the spectrum. The same general result was obtained.

What does this mean? Humans can distinguish colors that differ by 5 nm, despite having only 3 kinds of photoreceptors. Why? Because the human brain does some rather sophisticated processing of those three inputs, integrating them into one perceived color. That takes brainpower -- and time. The first conclusion is that the mantis shrimp apparently does not do this with its 12 inputs. Perhaps that is not a surprise. It doesn't have much of a brain; it may be that the "simple" approach whereby one receptor means one thing is good for them. By this hypothesis, making more photoreceptors is not a path to better color vision, at least as we know it; it is an alternative to using a brain.

It's also possible that this system has an advantage for these animals. It's faster, since the slow steps of neural processing are reduced. This may be good for the mantis shrimp, noted for its fast physical responses.

We must wonder what scientists will discover next about this unusual visual system.

There is one more part to the story. You don't need it to understand the current work, but it is a key part of what makes mantis shrimp interesting. That is what they look like. Here is a picture of Haptosquilla trispinosa [link opens in new window], the species used here.

Notes about the animal...

Adult animals are as long as 44 mm (about 2 inches).

The eyes are on the two white stalks near the right end of the animal.

The picture is from: Mantis Shrimp: Haptosquilla trispinosa. This is part of a site, now archived, on arthropods by researcher Michael Bok, at the University of Lund. (Bok is quoted in some of the news stories on this work.) The page has more information on this organism.

The particular species of mantis shrimp studied here is rather drab. The news stories show other kinds of mantis shrimp. There is also more at Bok's site, noted above; in particular, look for his page on the peacock mantis shrimp.

News stories:
* Study finds mantis shrimp process vision differently than other organisms (w/ video). (Phys.org, January 24, 2014.) Includes some interesting videos of how mantis shrimp use their eye stalks. The videos are not about the species used in the current work. Check out at least the first one, for fun.
* The Mantis Shrimp Sees Like A Satellite. (Ed Yong, Not Exactly Rocket Science (National Geographic blog), January 23, 2014.) Now archived.

* News story accompanying the article: Physiology: Extraordinary Color Vision. (M F Land & D Osorio, Science 343:381, January 24, 2014.)
* The article: A Different Form of Color Vision in Mantis Shrimp. (H H Thoen et al, Science 343:411, January 24, 2014.)

More about the visual system of the mantis shrimp: How can the mantis shrimp see so many colors of UV? They use filters (August 30, 2014).

Among many posts on animal vision...
* Chromatic aberration: is it how cephalopods see color with only one kind of photoreceptor? (October 14, 2016).
* Color vision: an overview (December 1, 2014).
* What if you had eyes on your tail? (July 27, 2013).
* An unusual eye? (June 6, 2012). From an even simpler animal.
* Where are the eyes? (August 19, 2011).
* With 24 eyes, can they see the trees? (June 11, 2011). Another example of eye complexity compensating for brain deficit.

And human vision... The limits of the human visual system: can humans detect single photons? (October 7, 2016).

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

A plant virus that grows in bees: role in colony collapse?

February 17, 2014

It's a novel finding. Scientists looking at what they can find in bees have reported finding a plant virus.

What did they do? They analyzed the nucleic acids found in bees, and compared the results to the listings in genome databases. That is, using the latest in nucleic acid technologies, they looked at "everything". They found tobacco ringspot virus (TRSV), a well-known plant virus.

The scientists provide good evidence that the virus is actually growing in the bees. Bees visit plants -- and carry pollen; it's not surprising that they might have some plant material -- or plant virus material -- in them. Showing that the TRSV is not only present but actually growing in the bees is a significant step.

As a general biology point, finding a plant virus growing in an animal is interesting. The article is not entirely clear, but this may be the first documented example of a specific virus showing this trans-kingdom behavior. There is nothing "wrong" with this; there is no reason to be suspicious of the finding. (Of course, as a matter of principle, it needs to be confirmed.) Some viruses grow in diverse hosts. Some will grow in most any cell they can get into. In fact, getting in is often the key barrier. The inside of one cell is more or less like the inside of another. (Prokaryotic vs eukaryotic cells is a major exception.) It is not known at this point whether the virus growing in bees has genetic adaptations that promote its trans-kingdom behavior.

As noted, this may be the first documented example of a virus that grows in both plants and animals. But why would anyone notice? The scientists found this example by brute force. This kind of study would not have been practical even a few years ago. Before this type of work, it would have been something of an accident to find a virus growing in an unusual host -- unless it had a very clear effect on the host, or unless there was a reason to look for a specific virus. So perhaps this work opens a door. There will be more studies broadly looking for "anything". I wonder what they will find.

Colony collapse disorder (CCD) is a big issue for bees; inevitably, the scientists ask if this virus is associated with CCD. They show that the virus is more prevalent in unhealthy colonies than in healthy colonies. That's not evidence for a causal role. Lots of things are more prevalent in unhealthy colonies. There is no evidence here for any particular role of this virus in colony collapse; it simply joins the list of possibilities.

Bottom line... An interesting finding. Its implications remain to be worked out.

News story: Pathogenic plant virus jumps to honeybees. (Phys.org, January 21, 2014.)

The article, which is freely available: Systemic Spread and Propagation of a Plant-Pathogenic Virus in European Honeybees, Apis mellifera. (J L Li et al, mBio 5(1):e00898-13, January 2014.)

More about colony collapse disorder:
* Neonicotinoid pesticides and bee decline (July 12, 2014).
* A parasitic fly that causes hive abandonment in bees: Is this relevant to CCD? (January 27, 2012).

More about bees: Bees: Why pollen might be bad for them (November 4, 2013).

More about viruses: Bats and the origin of SARS (January 25, 2014). This, too, involves the issue of virus host range.

Atmospheric CO₂ and the origin of domesticated corn

February 14, 2014

Corn (maize), like most of our major foods, is a manmade creation. Over the last century, a strong case was developed that corn originated from a plant called teosinte, native to Mexico, the birthplace of corn. However, one part of the story seemed weak: teosinte, as we see it today, does not seem a very promising starting material. Why would ancient man choose teosinte for cultivation and subsequent breeding?

A new article offers an explanation, and they do it with a simple experiment making use of an idea that is current for other reasons. In the new work, the scientists grow teosinte under conditions likely to have been found ten thousand years ago. In particular, they use a lower concentration of carbon dioxide than found today; they use a level of CO₂ they think is the level of several thousand years ago. It turns out that teosinte looks different when grown under these "paleontological" conditions -- and it looks much more promising.

The key observation is that the teosinte grew quite differently under the two sets of conditions. You can see that in the picture above. More detailed analysis of plant features supported that, and showed that the teosinte looked more like corn under the old conditions than under modern conditions. Domesticating teosinte makes more sense if we look at what it was like at the time.

We often wonder hw global warming, with its increase of CO₂, will affect organisms in the future. Turns out we can run that clock backwards, too -- and see how organisms might have behaved long ago.

News story: Greenhouse 'time machine' sheds light on corn domestication. (Phys.org, February 3, 2014.)

The article: Teosinte before domestication: Experimental study of growth and phenotypic variability in Late Pleistocene and early Holocene environments. (D R Piperno et al, Quaternary International 363:65, March 30, 2015.)

Example of testing how organisms might behave with high levels of CO₂: Increased CO₂: effect on animals that make carbonate skeletons (January 11, 2010).

More on corn:
* How long have Americans been eating corn? (July 21, 2020).
* What can we learn from a five thousand year old corn cob? (March 21, 2017).
* Alternative microbial sources of insecticidal proteins (December 9, 2016).
* Development of insects resistant to Bt toxin from "genetically modified" corn (April 19, 2014).
* Pink corn or blue? How do the monkeys decide? (June 9, 2013).

More about domestication... It's a dog-eat-starch world (April 23, 2013).

A different kind of CO₂ study -- immediately above: An example of coral growing well in a naturally acidified ocean environment (February 16, 2014).

Why the lull in global warming?

February 11, 2014

The late twentieth century saw a rather clear trend of rising global temperature (T). The rise in T correlates with and is attributed to the increasing level of carbon dioxide in the atmosphere. However, the years since then have shown little or no increase. Why? Are there reasons why short term fluctuations over the past decade have masked the larger warming trend? Or is it possible that there is something fundamentally wrong with our understanding of the big trend?

Nature recently ran a "news feature" on the problem. It includes some data describing the temperature record. It discusses the alternative explanations that have been offered, with some emphasis on the role of the oceans as a short term effector. It's not easy reading, but if you find the topic of interest, at least give this a browse for an overview and update.

News story, which is freely available: The case of the missing heat -- Sixteen years into the mysterious 'global-warming hiatus', scientists are piecing together an explanation. (J Tollefson, Nature 505:276, January 16, 2014.)

One good place to start is the figure on the last page (p 278). The lower frame of that figure shows the global temperature over time. You can see the overall rising trend, plus some lulls -- including the current lull. The upper frame is a measure of the ocean effect that is the heart of the story here.

* * * * *

A previous Musings post on the lack of increased T in recent years: Why isn't the temperature rising? (September 12, 2011). This post, and the follow-up it refers to, focus on sulfur emissions as a short term effector. Both of these posts could be useful background for the current post.

And an update: Was there a significant slowdown in global warming in the previous decade? (May 30, 2017).

Other posts on global warming include...
* National contributions to global warming (June 25, 2014).
* When does global warming occur: day or night? (October 28, 2013).

The First Americans: the European connection

February 8, 2014

The conventional wisdom is that humans first reached the Americas by walking across a land bridge from Siberia to Alaska. These people were the ancestors of what we now call Native Americans (formerly, American Indians); they are also sometimes called the "First Americans." There is considerable evidence to support this view. However, bits and pieces of evidence for a European source have confused the picture in recent years. Some scientists have been quite skeptical of the reports, since the possibility of early peoples crossing the Atlantic seemed unlikely.

A new article -- one of the first scientific papers published in 2014 -- supports the contribution of European ancestry to Native Americans, and offers an intriguing explanation. What the scientists suggest is that Europeans migrated eastward -- to Asia, specifically to Siberia. There they mixed with the Asians of that era. It was these European-Asians who crossed into America, via that Siberia-Alaska land bridge often called Beringia. This offers an explanation for why western European characteristics are found in the Native Americans, without invoking the unlikely possibility of crossing the Atlantic.

What's the evidence? What's the new finding? Genetic analysis of a fossil human child from Siberia shows that his genes were largely "European". The fossil is about 24,000 years old; this puts it a few thousand years before the migration to America.

And that's about it. The rest is "story".

This is an exciting time for the study of human origins. It's made possible by the revolution in DNA sequencing -- not just the lowered costs, but the increasing ability to handle ancient DNA and get meaningful information about the genomes of our ancient ancestors. But be careful. Much of what we hear is based on the analysis of a single specimen. Scientists determine the genome of an ancient human, and then build a story around it. Each genome is a major accomplishment; the "story" offers some perspective. We've seen that in Musings posts, including the original report of Denisovan man; some of the interpretation in that first report was changed as more data became available. This is not a matter of errors in the work, but of over-interpretation. It is important here, as in all science, to try to understand what is fact, what is interpretation, and what is speculation. Many scientific papers contain all of those; that is fine, but we must make the distinction.

The new article presents the genome sequence of a new human ancestor specimen. The analysis suggests an alternative as to how European characteristics could have made their way to Native Americans. Is it right? Who knows. It's now a hypothesis on the table. Hopefully, more evidence will be brought to bear on the issue.

The new genome has implications beyond the story of the First Americans. It offers insight, more broadly, into early human migrations. There is some discussion of such further interpretations in the article and the surrounding news coverage. Again, that is mostly "story" for now -- very interesting story that we'll learn more about with more evidence.

News stories:
* Ancient Siberian genome reveals genetic origins of Native Americans. (Phys.org, November 20, 2013.) Excellent overview of a complex story; good pictures.
* DNA links Native Americans with Europeans. (ScienceNordic, November 22, 2013.) What's Nordic about the story? The lead institution is the University of Copenhagen -- the Centre for GeoGenetics there.

The article: Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. (M Raghavan et al, Nature 505:87, January 2, 2014.)

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. That list includes the work on Denisovan man, and other ancient humans.

The first of those posts on Denisovan man is: The Siberian finger: a new human species? (April 27, 2010).

The most recent post on ancient humans genomes is: DNA from a 400,000-year-old "human" (December 9, 2013).

More...
* Contributions of Neandertals and Denisovans to the genomes of modern humans (July 6, 2016).
* Genes that make us human: genes that affect what we eat (February 18, 2015).

More about the First Americans:
* How long ago did mankind arrive in the Americas? (March 18, 2016).
* Did the First Americans eat gomphothere? (July 29, 2014).

The idea of a "Centre for GeoGenetics" reminds me of the post: The Moon: might it be a child with only one parent? (April 13, 2012).

More about migrations: Magnetic turtles (July 5, 2015).

A story of ball lightning and burning earth

February 4, 2014

Many readers are familiar with ordinary lightning. During a thunderstorm, you can stand at the window and see it. Ball lightning is another matter. It's unpredictable and rare; as with ordinary lightning, individual events are short-lived. A new article offers what may be the first scientific report, with data from sophisticated instruments, of a natural ball lightning event. Quite by accident, a team of scientists just happened to have high speed cameras on at the right time. Have a look at their video... We'll "explain" it below, but first have a look if you can.

Video. ball lightning video at YouTube (10 seconds; no sound). It's also included with some of the news stories.

The video shows two things. One is roundish and whitish, at the left. The other is a rather brightly colored horizontal region, in the center. The ball lightning is the round thing at the left. Ball lightning indeed looks something like a ball. If you didn't focus on that the first time, go back and look at the video again. The other point to realize is the time scale. The video is 10 seconds. It's slowed down from real time. The video records 1.3 seconds of action; that is, the video is slowed down about 8x. Ball lightning appears rather mysteriously, and doesn't last very long. That's why pictures are rare, and scientific observations are unprecedented. It just happened that these observers were there when this event occurred, with their high speed cameras -- and spectrograph.

The spectrograph measures what wavelengths of light are given off. The bright region in the video is the spectrograph output. You can't tell much from it, but it can be analyzed in detail. The analysis shows that the light is coming from silicon, iron and calcium. It appears, according to the authors' interpretation of the spectrogram, that the ball consists of burning earth.

There are many proposals about the nature of ball lightning. One is that ordinary lightning hits the ground, and vaporizes some soil. The hot ball of soil-vapor reacts with oxygen; what we see is the glowing ball of burning earth. The spectrographic evidence recorded here, as well as the circumstances, support this interpretation, at least for this ball lightning event.

The glowing region was as much as 5 meters in diameter. It was about 0.9 km from the observers. The entire ball lightning event lasted 1.64 seconds.

News story:
* Burning soil fuels ball lightning. (Physics World, January 9, 2014.)
* Focus: First Spectrum of Ball Lightning. (Physics, January 17, 2014.) This item is written by, appropriately enough, Philip Ball.

The article: Observation of the Optical and Spectral Characteristics of Ball Lightning. (J Cen et al, Physical Review Letters 112:035001, January 24, 2014.) Put the title in Google Scholar; you might find a freely available pdf of the article.

More about lightning:
* What's the connection: ships and lightning? (October 14, 2017).
* When lightning strikes a tree... (April 8, 2014).

Improving the efficiency of making induced pluripotent stem cells (iPSC)

February 1, 2014

Briefly noted...

The procedure for making induced pluripotent stem cells (iPSC) involves starting with differentiated cells, such as skin cells, and adding a small group of "factors", which induce the cells to de-differentiate back to the pluripotent state. (Pluripotent cells are those that can give rise to most any type of body cell.) Use of iPSC has become one of the major approaches to stem cell work in recent years; the scientist who led the original development of iPSC, Shinya Yamanaka, received the Nobel Prize in 2012.

A problem with making iPSC is that it is quite inefficient. Commonly, fewer than 1% of the treated cells become iPSC.

A recent article offers some insight into why the procedure for making iPSC is inefficient. The authors show that the procedure induces not only de-differentiation, but also inhibitors of de-differentiation. That is, the procedure induces both helpful and unhelpful processes -- which "fight" each other. They show that a particular protein, called Mbd3, is largely responsible for the low efficiency of making iPSC. Mutating out Mbd3 makes the process nearly 100% efficient.

Problem solved? Not so fast. It is an interesting finding, but it raises questions of its own. Removing the problem protein is not really a practical solution; its complete removal may have its own deleterious effects. Further, some question some aspects of the result, as well as the importance of the problem. For now, this is not so much an answer but a clue. People will be following up on this report. How general is what they found? Is there a practical way to implement it? Importantly, simply studying the role of Mbd3 should lead to better understanding of the process of making pluripotent stem cells. As so often... stay tuned.

News stories:
* Inducing Pluripotency Every Time. (The Scientist, September 18, 2013.)
* Scientists produce induced pluripotent stem cells by removing one protein. (Nanowerk News, September 23, 2013.)

* News story accompanying the article: Stem cells: Close encounters with full potential. (K M Loh & B Lim, Nature 502:41, October 3, 2013.)
* The article: Deterministic direct reprogramming of somatic cells to pluripotency. (Y Rais et al, Nature 502:65, October 3, 2013.) For a pdf of a preprint: preprint pdf.

A recent post involving the use of iPSC: Down syndrome: Could we turn off the extra chromosome? (November 15, 2013).

More...
* A test of a stem cell therapy based on iPSC, in monkeys (August 29, 2014).
* Making stem cells using brain tissue from dead people (June 2, 2014).

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

3D printing: simple inexpensive prosthetic arms

January 29, 2014

Near the end of last year we had two posts on 3D printing [links at the end]. Both were on rather complex and exotic applications.

A few days ago there was a widely reported news story about an application of 3D printing. It immediately reminded me of those two recent posts. The contrast in the nature of the application was striking.

The news story stands on its own. Go read it. Here is one good version: How a 3D printer gave a teenage bomb victim a new arm - and a reason to live. (Guardian, January 19, 2014.)

The news story listed above links to the web site for the company behind this project. I found their web site to be complex and slow, and did not pursue it. There is a 4 minute video, which is also available at YouTube video. It gives an overview of the whole project. The video is too fast-paced to be effective, but you can see the final product, as well as evidence for the continuing effort.

Background posts on 3D printing:
* 3D printing: Sculplexity -- and a printed model of a forest fire (December 29, 2013).
* 3D printing: Neurosurgeons can practice on a printed model of a specific patient's head (December 16, 2013).

An earlier, simpler application: Print yourself new body parts (April 16, 2010).

More...
* 3D printing: Make yourself a model of the universe (December 19, 2016).
* 3D printing of human tissues: the ITOP (May 24, 2016).
* Can you make a 777 by printing it? (May 9, 2015).
* 3D printing for space: a titanium woov, and more (April 29, 2014).
* National Inventors Hall of Fame: 2014 inductees (March 11, 2014).

More on Prosthetic arms (September 16, 2009). Includes listing of related posts.

More about replacement body parts is on my page of Biotechnology in the News (BITN) for Cloning and stem cells. It includes an extensive list of related Musings posts.

The $1000 genome: we are there (maybe)

January 27, 2014

About three years ago we looked at the plummeting cost of DNA sequencing [link at the end]. That cost had declined by a factor of about 10,000 in less than a decade, since the original announcement of the human genome. Yet there was a goal, and it wasn't quite met. There was a declared goal of a "$1000 genome" -- being able to sequence a human genome for $1000. A round number of course, but it must have seemed a long way off when it was proposed in 2001.

We now have an announcement of the $1000 genome. It's a press release from a leading company that manufactures sequencing equipment. They are announcing a new piece of equipment -- scheduled for release some time this quarter. And there is some "fine print" -- see the "notes" below. So it's not quite real. Will the real world of peer-reviewed science support their claim? We'll see. Still, it seems worth noting.

The company announcement: Illumina Introduces the HiSeq X^TM Ten Sequencing System -- Breaks Barriers with World's First $1,000 Genome, Enables 'Factory' Scale Sequencing for Population and Disease Studies. (Illumina, January 14, 2014.) (Original URL: http://investor.illumina.com/phoenix.zhtml?c=121127&p=irol-newsArticle&ID=1890696 )
- Update September 2019... The page is no longer available, and it is not archived. In fact, the sequencing model referred to has been discontinued. Perhaps that is symbolic of the progress in the field.

News stories:
* Science enters $1,000 genome era. (BBC, January 15, 2014.)
* $1,000 Genome at Last? (Tracy Vence, The Scientist, January 15, 2014.) Now archived.

Notes...

The estimated cost of $1000 per genome includes amortization of the cost of the machines. Achieving the indicated cost requires using the machines to full capacity --which would be a lot of genomes!

The announced machine has not yet shipped, as noted above. In mid-2012 we noted the announcement of a revolutionary new machine for genome sequencing -- due to be shipped later that year [link at the end]. It hasn't been shipped yet. That's a reminder to be cautious about the current announcement. However, it's probably fair to note that the current announcement is about incremental improvements in an established product, and is less likely to suffer major delays.

* * * * *

Background post: The $1000 genome: Are we there yet? (March 14, 2011). This post focuses on the plummeting cost of sequencing. It also notes such issues as demands on computers and our limited knowledge of what to do with the genome information.

The 2012 post about the new machine -- that has not yet shipped: Nanopores -- another revolution in DNA sequencing? (June 22, 2012).

Also see: Pangenomes and reference genomes: insight into the nature of species (February 7, 2017).

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

Pop goes the hemozoin: the bubble test for malaria

January 24, 2014

If you are infected with the malaria parasite and we shine a laser at your finger tip, there will be a little explosion. That's the basis of a diagnostic test for malaria proposed in a new article. The authors think it could be a practical test; in any case, it is interesting.

What's exploding? Blood cells infected with malaria contain a little blob of pigment, called hemozoin. (The hemozoin is a by-product of the parasite degrading the host's hemoglobin.) The hemozoin pigment absorbs light -- a specific wavelength of light. Shine a lot of the correct light into the cell, with a laser, and the hemozoin absorbs so much energy that it literally blows up. An instrument can detect the hemozoin-induced bubbles, either acoustically or optically.

The following figure shows the idea. It's a simple lab version of the test, looking at individual cells -- infected or not.

How do you carry out this test? Stick a drop of blood in the machine? It's even easier than that. The test shown above was done with isolated blood cells, but that's not necessary. Just stick the finger (or the mouse ear) in the machine. This is a non-invasive test -- no needles, no handling of blood. The laser light penetrates just fine, reaching blood vessels just below the skin; the response, too, is detected through the skin.

Sounds high tech, doesn't it? Indeed it requires instrumentation. Interestingly, the authors think it would work well "in the field", under low-tech conditions and with non-specialized operators. The non-invasive nature of the test, noted above, is one aspect of its simplicity. The authors think the instrument would be robust in the field, and the cost per test would be low. Those claims will have to be tested. Trials with humans are planned for this year.

News story: Vapor nanobubbles rapidly detect malaria through the skin. (Nanowerk News, December 31, 2013.)

The article: Hemozoin-generated vapor nanobubbles for transdermal reagent- and needle-free detection of malaria. (E Y Lukianova-Hleb et al, PNAS 111:900, January 21, 2014.)

Other posts about malaria include ...
* Malaria and bone loss (September 10, 2017).
* A novel drug candidate that is active against all stages of the malaria parasite (October 10, 2015).
* A vaccine against malaria -- with 100% efficacy? (October 20, 2013).

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

More hemoglobin: A treatment for carbon monoxide poisoning? (January 13, 2017).

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

Preserving the Apollo landing sites

January 20, 2014

Interesting topic. Do you think that the landing sites for the Apollo spacecraft on the Moon should be preserved as historical sites for posterity? Do you think they should be made US national parks?

There is in fact a bill before the US Congress to protect those sites as US national parks. If nothing else, the bill is bringing attention to a topic that deserves attention.

The news story listed below is a good discussion of what the issues are.

News story: The Moon Belongs to No One, but What About Its Artifacts? (L Laursen (blog, Smithsonian), December 13, 2013.)

More about the Moon: The Moon: might it be a child with only one parent? (April 13, 2012).

Novel forms of sodium chloride, such as NaCl₃

January 17, 2014

What chemical reaction do you expect between common salt, NaCl, and molecular chlorine, Cl₂? How about... NaCl + Cl₂ --> NaCl₃?

A new article reports theoretical calculations suggesting that the above reaction should be favorable. The scientists then go on to test their prediction: they make the proposed compound, NaCl₃.

What's the catch? Pressure. The reaction occurs at a pressure of about 60 gigapascals (GPa); that's 600,000 atmospheres. The scientists carry out the reaction inside a high pressure device called a diamond anvil cell.

NaCl₃ can be thought of as an ionic compound consisting of Na⁺ and Cl₃^- ions. The trichloride ion, Cl₃^-, is analogous to the well known triiodide ion, I₃^-. (In fact, Cl₃^- is known, but no stable salts of it are known, to my knowledge.)

So they have predicted and made a novel sodium chloride. But what's above is just the beginning. Take the structure of two NaCl₃ units; that gives you Na₂Cl₆. Now replace one Na with another Cl; that would give NaCl₇. They predict that NaCl₇, too, will be stable -- at pressures above 142 GPa. Under such high pressure, Na and Cl are about the same size, allowing this replacement to occur without a significant change in the structure.

That's for reactions of NaCl with extra Cl₂. What about NaCl + extra Na? They predict novel compounds at high pressure there, too -- and make one of them: Na₃Cl. All in all, they predict five novel compounds of sodium and chlorine, and provide evidence that they have made two of them.

Here is a general outline of the work...

Is this all just for fun? Does anyone care what happens at these high pressures? Indeed they do. Such pressures -- even higher -- are found inside the Earth. The chemistry of the Earth's interior is understood poorly, partly because of our poor knowledge of how chemicals behave under what we might consider extreme conditions.

News story: Salty surprise: Ordinary table salt turns into 'forbidden' forms. (Phys.org, December 19, 2013.)

* News story accompanying the article: Geochemistry: Reformulating Table Salt Under Pressure. (J Ibáñez Insa, Science 342:1459, December 20, 2013.) Good overview of what was done -- and what its implications might be for planetary science. The author of this news item is apparently an Earth scientist.
* The article: Unexpected Stable Stoichiometries of Sodium Chlorides. (W Zhang et al, Science 342:1502, December 20, 2013.) (If you can't access the article, there is a draft posted at arXiv: pdf of draft.)

Notes...

Units for pressure. It's easy to get confused; the article and the news stories use different units. A good place to start is the "atmosphere" (atm). One atm is the pressure of the atmosphere on Earth, at sea level. That makes sense. The official SI unit for pressure is the pascal (Pa). One Pa is 1 newton per square meter (1 Pa = 1 N/m²). That's very logical within the SI, but probably leaves you cold. In fact, a pascal is a very small amount of pressure: there are about 100,000 (10⁵) Pa in 1 atm. (More precisely, 1 atm = 1.023x10⁵ Pa.) In the article, pressures are given in gigapascals: 1 GPa = 10⁹ Pa. Thus 1 GPa = 10,000 (10⁴) atm. 20 GPa, one of the "low" pressures in the work, is 200,000 atm.

Above we said that the scientists predict that a certain reaction should be favorable. That is, they predict that the product is more stable than the reactants. In other words, the product is the lowest energy form. If one has a mixture of 1 mole each of sodium chloride and chlorine at 60 Gpa pressure, calculations suggest that the lowest energy form of that mixture would be NaCl₃.

* * * * *

Other posts about the effects of high pressure include:
* Briefly noted... Novel Fe-O compounds in the Earth's inner core? (April 26, 2023).
* How many atoms can one nitrogen atom bond to? (January 17, 2017).
* What's the connection: rotten eggs and high-temperature superconductivity? (June 8, 2015).
* Metallic hydrogen? (March 16, 2012).
* Lakes that explode (October 13, 2009).

More about crystals of sodium chloride: Life at age 34,000? (October 8, 2011).

More sodium chemistry: The explosive reaction of sodium metal with water (April 20, 2015).

More on exotic chemicals: Iridium(IX): the highest oxidation state (December 14, 2014).

Multiplication tables, bamboo, 2300 years old

January 13, 2014

It's the oldest known copy of the multiplication tables -- for the decimal number system.

News story: Ancient times table hidden in Chinese bamboo strips. (Nature News, January 7, 2014.) It includes a picture -- and a translation. A fun story.

That's all we have. The news story says that the work is being published in a book, presumably in Chinese. Attempts to find other stories about this yielded only pages that referred to this one from Nature News.

Other posts on math skills include... Can plants calculate how long their food supply will last? (August 9, 2013).

More bamboo: Pandas: When did they become specialized to eat bamboo? (March 18, 2019).

There is more about math on my page Internet resources: Miscellaneous in the section Mathematics; statistics. It includes a listing of some related Musings posts.

Rotavirus: passive immunization via food

January 10, 2014

Rotavirus is a serious human pathogen. There are various approaches to dealing with rotavirus, including vaccines, which have proven to have their own problems.

One approach is to use a passive immunological treatment: treat with an antibody to the virus. (In contrast, a vaccine gives the recipient the antigen, which induces the person to make antibodies.) The current work uses rice that has been genetically modified to make an antibody to rotavirus.

A recent article reports testing the use of this rice that makes rotavirus antibody in treating a model system of rotavirus in mice. The following figure shows the results of one of the tests.

The experiment above shows that the antibody produced in rice is a useful treatment against the virus, even when administered after infection. Other results show that it is also effective prophylactically (administered in advance), that it works in immune-deficient mice, and that it survives heat treatment rather well. The authors also note work suggesting that the antibody used here is effective in humans; those results are not yet published.

This is an interesting result. Rotavirus infections are a serious cause of morbidity of children, especially in developing countries. Rice is a staple food in many areas where rotavirus is of concern. Delivery of a drug (in this case, an antibody) via food has some appeal -- but is not without concern. Merits include that the drug is easily and routinely delivered; no special handling and, apparently, no special cooking are needed.

Among the questions that need to be addressed... the merits of passive antibody treatment vs active immunization; the possible long term effects if the rice-with-antibody is a routine part of the diet; the ability to respond to changes in the nature of the virus.

Is the use of rice-with-antibody a good idea? That will require further testing, and comparison with alternatives. However, it would seem to deserve serious consideration. For now, that is the point.

News stories:
* Antibody-producing rice. (Technology.org, August 19, 2013.)
* New GMO Rice Protects Against Rotavirus Infection. (Science 2.0, August 8, 2013.)

The article, which is freely available: Rice-based oral antibody fragment prophylaxis and therapy against rotavirus infection. (D Tokuhara et al, Journal of Clinical Investigation 123:3829, September 2013.)

A post on another rice modified to have a health benefit: Golden rice as a source of vitamin A: a clinical trial and a controversy (November 2, 2012).

More about rice:
* How rice leads to global warming, and what we might do about it (September 2, 2015).
* Can growing rice help keep you from becoming WEIRD? (July 22, 2014).

Another story of GMOs... Development of insects resistant to Bt toxin from "genetically modified" corn (April 19, 2014).

For more on GM crops, see my Biotechnology in the News (BITN) page Agricultural biotechnology (GM foods) and Gene therapy.

My page Biotechnology in the News (BITN) -- Other topics has a section on Vaccines (general).

More about antibodies as drugs: SyAMs: Synthetic drugs that act like antibodies (May 31, 2015).

A simple way to make a supercapacitor with high energy storage?

January 6, 2014

Batteries are one well-known way to store electricity. In a battery, energy is stored in chemical compounds; a chemical reaction occurs resulting in a flow of electrons. An alternative is electrochemical capacitors (EC), sometimes called supercapacitors. These store energy by adsorption of ions on the electrode surface. Since no chemical reaction is involved, EC are fast and stable. However, they have a low energy capacity.

A new article offers a new approach to making such supercapacitors with high energy storage. The authors claim that the energy storage of their material is similar to that of the common lead-acid (automotive) battery.

Here's the idea... In the new work, the scientists make capacitors from graphene and a liquid electrolyte, such as sulfuric acid. The thin graphene provides lots of electrode surface area -- and mechanical strength. The liquid electrolyte not only plays its named role as an electrolyte, but serves as spacing between the graphene sheets. After making the basic graphene-electrolyte capacitor, they remove much of the electrolyte. How? By squeezing it. Simple. It works.

The following graph summarizes the basic finding, that collapse of the material by removal of excess liquid phase usefully increases the volumetric charge storage capacity of the device.

This represents a new development in making supercapacitors. The new work shows a major improvement in energy storage, on a volume basis. The authors suggest that their process for making these supercapacitors is practical. (It's very much like paper-making.)

An interesting issue here is the distinction between two ways of measuring the product; weight-based or volume-based. Which is most important? That depends on the application. Let's accept that this work represents progress toward better supercapacitors, as measured by one criterion.

News stories:
* Monash University team develops graphene-based supercapacitor with energy density of 60 Wh/L. (Green Car Congress, August 3, 2013.)
* New graphene-based supercapacitors rival lead-acid batteries. (Kurzweil, August 5, 2013.)

The article: Liquid-Mediated Dense Integration of Graphene Materials for Compact Capacitive Energy Storage. (X Yang et al, Science 341:534, August 2, 2013.)

A previous post on graphene: Loudspeakers: From gold-coated pig intestine to graphene (April 27, 2013).

More... How do you get silkworms to make stronger silk, reinforced with graphene? (October 24, 2016).

More about supercapacitors:
* Butt batteries (December 16, 2014).
* Supercapacitors in the form of stretchable fibers -- suitable for clothing (May 2, 2014).

And batteries...
* Flow battery (January 4, 2016).

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.

Another section of that page, Aromatic compounds, lists posts on graphene.

Killing persisters -- a new type of antibiotic

January 3, 2014

Antibiotics are a mainstay of our response to bacterial infections. However, they have limitations. One, which gets much attention, is the development of bacterial strains that are resistant to the antibiotics.

Another limitation is more subtle: bacteria that simply seem to ignore the antibiotics, even though they are not resistant. Here is the phenomenon... Treat a bacterial population with an antibiotic. Most die. Some survive. Some of the survivors are in fact resistant: grow them up, and their progeny are indeed resistant to the antibiotic. However, others that survived are, when grown up as a fresh culture, just as sensitive as the original bacteria.

What's the deal with these "persister" bacteria, as they are often called? And what might we do about them?

Persister bacteria are not well understood; it is quite likely that there are multiple phenomena. It's hard to study persisters; more or less by definition, once you isolate them, they don't have the property of interest any more. The general sense is that persisters are bacteria in some special physiological state. That is, they are physiologically resistant to the antibiotic -- not genetically resistant. Physiological resistance is lost as soon as the persisters are isolated. An example of how "persistence" might occur is based on the fact that many antibiotics act on bacteria during active growth; bacteria that, for whatever physiological reason, are inactive when the antibiotic arrives may survive the treatment -- and resume growth later.

A new article offers a possible approach to dealing with persisters. In addition to showing some promising results, the article explains how the approach works.

Here is an example of what the scientists found in this new work...

So what do we have? A candidate drug with significant action against non-growing bacteria. It works some alone. In combination with ordinary antibiotics, it seems to completely eliminate the bacterial population.

How does this new drug work? One activity of any type of cell is removing proteins that are no longer wanted. This is done by somehow recognizing the unwanted proteins, and then degrading them. What the new drug seems to do is to alter the protease (protein-degrading enzyme) that degrades unwanted proteins -- so that it is over-active. More specifically, the drug seems to widen the opening of the protease, so that it accepts normal proteins, not just those already partly unfolded and ready for degradation. Thus the protease now degrades the proteins of the cell -- unwanted or not. That kills the cells.

The article provides some promising data suggesting the effectiveness of their new candidate drug; some of this is shown above. Questions remain about how well this will work in the real world; certainly, many candidate antibiotics fail upon further testing. However, the fact that they understand the novel mechanism of this drug enhances the chance that further drugs of this type could be developed. All in all, this is a story that is intriguing and promising -- even as we remember that the results so far are only a start.

News stories:
* Thwarting Persistence -- Researchers show that activating an endogenous protease can eliminate bacterial persisters. (Abby Olena, The Scientist, November 13, 2013.) Now archived.
* Killing Sleeper Cells and Superbugs with Assassin Janitors. (Ed Yong, Not Exactly Rocket Science (National Geographic blog), November 13, 2013.) Now archived.

* News story accompanying the article: Antibiotics: Killing the survivors. (K Gerdes & H Ingmer, Nature 503:347, November 21, 2013.)
* The article: Activated ClpP kills persisters and eradicates a chronic biofilm infection. (B P Conlon et al, Nature 503:365, November 21, 2013.)

A post on the problem of antibiotic resistance: Restricting excessive use of antibiotics on the farm (September 25, 2010). With follow-up posts listed there.

A post that may also be about getting at persisters: Antibiotic action: effect of hydrogen sulfide (July 9, 2021).

More about "Staph" infections: Can the Staph solve the Staph problem? (July 12, 2010).

Another approach to antibiotics... Black silicon and dragonfly wings kill bacteria by punching holes in them (January 28, 2014).

More on biofilms... Salmonella and food contamination; the biofilm problem (April 28, 2014).

Also see: Inhibiting the TMPRSS in your nose to protect against respiratory viruses (COVID, flu) (July 11, 2022).

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