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Musings: May-August 2015 (archive)

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

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Archive items may be edited, to condense them a bit or to update links. Some links may require a subscription for full access, but I try to provide at least one useful open source for most items.

Please let me know of any broken links you find -- on my Musings pages or any of my regular web pages. Personal reports are often the first way I find out about such a problem.

August 31, 2015

What do chimpanzees think about cooking food?

August 30, 2015

They like the idea, according to a recent article.

Why would we study what chimps think about cooking food? Well, cooking is an important part of human culture. It may be an important part of our biology; cooking typically releases more nutrients from food. So, we might want to know how we got started cooking. We know very little about that. Can we learn something about how humans might have started cooking by studying a related animal that does not cook? What traits do we see in them that might lead toward cooking? What traits do they lack?

In Experiment 1 of the current article, the scientists tested whether the chimps preferred a food raw or cooked. The chimps were offered the usual raw food and a version that was cooked. They got to choose, either after a taste test or by odor. The chimps preferred the cooked food -- overwhelmingly. Each chimp tested preferred it to some extent.

That experiment lays the groundwork for the other experiments. Since the chimps prefer the food cooked, the scientists explored various aspects of the preference. For example, how much effort are the chimps willing to spend to get their food cooked?

Here is another of the experiments. The general purpose here is to see if the chimps understood what to cook. The two parts are similar, but the way the results are presented is a bit different, so be careful.

In part a, the chimps were given various things. The scientists observed whether the chimps cooked it or ate it. The darker bar at the left of each set shows the frequency of cooking the item; the lighter bar (right) shows the frequency of eating it. You can see that the chimps usually cooked the raw potatoes, cooked carrots about half the time, and usually did not cook the potatoes if they were already cooked.

In part b, the basic experimental design was the same. In this case, the graph shows only the frequency of cooking. High for potato, low for wood. What it means to say that the chimps cooked the food is explained in the article, but not important here. Note that the labeling on the graph refers to a cooking device. In part a, the two bars are for alternative responses to the same situation. One might expect the two bars in a pair to total 100%. They are close; apparently, a few chimps didn't yield a result. In part b, the two bars are for the same response to different situations.    This is Figure 3 from the article.

There is a risk of over-interpreting here, so I won't try to explain the results further. I'll just suggest that the results "make sense".

There is much more, a total of nine experiments, each focused on one question. It's an intriguing article. The list of questions the scientists developed is interesting. And the results are intriguing. Does the work begin to provide some insight about the origin of cooking food?

News stories:
* The naked chef? Chimpanzees can 'cook' and prefer cooked food - study. Findings suggest chimpanzees have the intellectual abilities required for cooking, which could have an impact on our view of human evolution. (H Devlin, Guardian, June 2, 2015.)
* Cooking up cognition: Study suggests chimps have cognitive capacity for cooking. (Phys.org, June 3, 2015.)

The article: Cognitive capacities for cooking in chimpanzees. (F Warneken & A G Rosati, Proceedings of the Royal Society B 282:20150229, June 2015.) I strongly encourage you to at least read the abstract, and I hope some readers will go on and read more.

Recent post about chimpanzees... Can chimpanzees learn a foreign language? (March 10, 2015).

A post about why we cook food (at least, one reason): Killer chickens (December 2, 2009). Also see posts linked there.

More about carrots: Carrot allergy (October 25, 2020).

More apes... Do apes say "hello"? (September 14, 2021).

How rice recognizes a Xoo infection

August 28, 2015

The figure shows three rice plants, all of which have been infected with bacteria. The middle plant shows extensive signs of the infection. The ones on the left and right show signs of the infection only near the tip. They have been largely protected from the infection by the immune system of the rice plant. The infection was with the bacterium Xanthomonas oryzae pv. oryzae, or "Xoo". (pv? It stands for pathovar, or pathogenic variety. Something like sub-species.) Xoo is an important pathogen of rice.    This is Figure 1C from the article.

A new article explains how the immune response works. More specifically, it identifies the part of the bacterium that the rice plant is sensing.

What's going on with those three rice plants in the figure? The key variable was that the scientists infected them with various strains of Xoo.
* The left-hand plant is for an ordinary infection. It's labeled PXO99; that's their strain name for the bacterium.
* The middle plant was infected with PXO99ΔraxX. That means the original strain, but with a deletion (Δ) of the gene raxX.
* The right-hand plant was infected with PXO99ΔraxX(praxX). That's like the middle one, but with praxX. That means there is a plasmid (p) that carries the raxX gene.

The pattern is simple... If the Xoo bacteria carry the raxX gene, the rice are protected (left and right). If that gene is missing, the rice suffers (middle). Somehow, the rice senses and responds to the protein from the raxX gene, and that protects them from the infection. But if the bacteria infect without sending that signal, then the rice suffers.

The infection at the right is a control. In the middle, the scientists removed a gene; at the right they added it back. It is possible that something went wrong in the middle test; maybe the strain caused an active infection for some other reason. Adding back the gene we thought was involved is a test to see if things were as we thought.

What does the RaxX protein do? It interacts with a rice protein, and that activates the rice defense system. This part of the story had been worked out previously. What's new here is identifying the bacterial signal.

Various species of Xanthomonas are important pathogens for a wide range of plant crops. The authors found that the raxX gene is common among these bacteria. The broader implications of the finding remain to be investigated.

I referred to this as an immune response of the rice. Is that a proper usage? Presumably we would agree it is part of a defense system, but is it part of an immune system? Well, we now understand that the human immune system has two distinct (but interacting) parts. One is the adaptive immune system, which makes antibodies to match a particular invader. The other, more recently understood, is the innate immune system. The innate immune system works by recognizing general features of pathogens, and responding with a generic defense. It's very much like what the rice does here.

News stories:
* Unlocking the Rice Immune System -- Joint BioEnergy Institute Study Identifies Bacterial Protein that is Key to Protecting Rice against Bacterial Blight. (L Yarris, Lawrence Berkeley National Laboratory, July 24, 2015.) From one of the institutions involved in the work.
* Research in Focus: Recognizing pathogens, and recognizing errors. (M Williams, Plant Science Today (blog at American Society of Plant Biologists), August 19, 2015.) More depth on some interesting questions. The two-part title of this item refers to a back-story. The lab reporting this discovery reported that they had found the signal once before. That report proved wrong, and they retracted it. The scientific community has generally given them good marks for how they handled the error. In any case, it is a reminder that a single report should not be taken as "the answer".

The article, which is freely available: The rice immune receptor XA21 recognizes a tyrosine-sulfated protein from a Gram-negative bacterium. (R N Pruitt et al, Science Advances 1:e1500245, July 24, 2015.)

A post about a toll-like receptor, or TLR, which recognizes general pathogen signals in the mammalian innate immune system: Why vaccine effectiveness may vary: role of gut microbiome? (February 27, 2015).

And the similar phenomenon in plants... How the tomato plant resists the Cuscuta (November 4, 2016).

Posts about rice include...
* A perennial rice (March 4, 2023).
* How rice leads to global warming, and what we might do about it (September 2, 2015).
* Rice and arsenic: rice syrup, baby food, and energy bars (April 23, 2012).
* What to do if you are about to drown (September 23, 2009).

A post about CRISPR, which is something of an adaptive immune system in bacteria: CRISPR: an overview (February 15, 2015).

Another example of the control test discussed above, where the gene of interest is added back to make sure one has the right gene... CRISPR: What's it doing to help bacteria carry out infections? (September 8, 2013). This kind of test is called complementation. Note that the post linked here is somewhat analogous to the current post, and it also involves CRISPR.

More about sulfated tyrosine: Modifying bacteria, with help from a bird, so they can make and use an unusual amino acid (October 8, 2022).

August 26, 2015

In the shadow of Ebola: The story of Lassa virus

August 26, 2015

Ebola has caught our attention over the past two years. However, arguably, Lassa virus is more important. It causes a hemorrhagic fever with a high fatality rate, somewhat like Ebola. And it kills 5000 or so each year, far exceeding the death toll from Ebola for every year except for the current, waning, Ebola outbreak. It occurs in a region of west Africa that overlaps that of the current Ebola outbreak.

A new article begins to give Lassa virus the attention it deserves. We'll note it briefly.

The scientists obtained an extensive collection of Lassa samples, from around the region where Lassa is common. They sequenced the viral genomes. Then they did what modern biologists do with a collection of genomes: they tried to make a family tree. And, using estimates for how fast things change, they estimated how far back the Lassa tree goes.

The current work involved sequencing 194 samples of Lassa virus. (These were mostly from infected people, but also included 11 samples from the rats that are the major reservoir for the virus.) That is 15 times more than all previous Lassa work. The viral genome itself is tiny, even by virus standards. It's only about ten kilobases, coding for four proteins. (That's on the order of 1/1000 a common bacterial genome.) However, the sequencing is not easy. They started not with clean virus samples, but crude clinical samples. Only a small fraction of the sequencing "reads" were Lassa virus. This is an example where high-throughput "next-generation" sequencing is so important.

The conclusion? The family tree suggests that Lassa originated in the Nigeria area, about a thousand years ago.

The scientists inferred something else from the collection, something that enhances our understanding of how Lassa is transmitted... If the virus were transmitted between humans, one would expect viruses in cases at about the same time and place to be similar. They aren't. Therefore, it is likely that most cases of Lassa originate from independent infections "from the wild", with very little human-to-human transmission. This contrasts with Ebola, where an outbreak is presumably caused by a single infection from the wild, but then is maintained by transmission between humans.

The sequence information for a collection of Lassa strains may help guide development of diagnostics and therapeutics. For example, the authors suggest that the Lassa in Sierra Leone has diverged enough that it might need distinct tools. This is only suggestive at this point; the current work provides some information, but it does not lead to definitive conclusions.

News stories:
* Study establishes genomic data set on Lassa virus. (Science Daily, August 13, 2015.)
* International Team Discovers the Ancient Origins of Deadly Lassa Virus. (Scripps Research Institute, August 13, 2015. Archive copy.) From one of the institutions involved in the work.

Video. (YouTube, 6 minutes.) This is a "video abstract" of the article, produced by two of the participating institutions, and provided by the journal. Two of the authors narrate the story. There are lots of pictures, but no real explanation of them. So it's something of an audio presentation of the highlights of the work, but does not really take advantage of the video medium. Try it if you want, but don't expect too much, beyond meeting the scientists and seeing some pictures.

The article, which may be freely available: Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus. (K G Andersen et al, Cell 162:738, August 13, 2015.)

Recent post about Ebola: An Ebola vaccine: 100% effective? (August 7, 2015). There has been experimental work on a Lassa vaccine, but there is no approved vaccine. The current article may help with getting a Lassa vaccine by providing a better sense of the variability of the virus. Perhaps more importantly, the recent Ebola experience may help us get over the barrier of inertia and complacency for other diseases.

Also see: After Ebola, what next? and how will we react? (September 5, 2015).

There is a section on my page Biotechnology in the News (BITN) -- Other topics for Ebola and Marburg (and Lassa). That's my old section on Ebola, now expanded to include Lassa. (I may re-think how that is organized.) That section links to related Musings posts, and to good sources of information and news.

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.

What's the connection: blue cheese, rotten coconuts, and the odorous house ant?

August 24, 2015

Caution... If you are eating some blue cheese, you might not want to read this right now. In fact, if you like blue cheese, you might not want to read this at all. Unless you are interested in chemistry.

There is an interesting kind of ant known as the odorous house ant, Tapinoma sessile. Squish one, and it smells. Smells like... Well, people say various things.

A new article reports analyses of the odor of these ants, along with some of the things it is compared to. This leads to an amusing side story.

Here are the main analyses reported. In each case, the analysis was done on the headspace: the gas around the object. The results are shown here as chromatograms; the x-axis is the time at which each compound comes through the analysis. The main compounds of interest are shaded and labeled.

The first conclusion is that the ant odor seems due to the same type of compound as found in blue cheese or rotten coconut. Not the same specific compound, but the same type. Since these compounds may have similar, though different, odors, this result can help to explain why some people make the connection. (It would be interesting to have analyses for some of the other things the ant is compared to.)

The second finding is that the rotten coconut analysis is similar to that of the blue cheese. How did they get this rotten coconut? The scientists buried some coconut in the ground. When they dug it up, it was covered with mold -- perhaps similar to the Penicillium mold used to make blue cheese.

The type of chemical discussed here, 2-ketones, is easily made from fats (lipids). Such chemicals are common enough, and have been found in ants before. What's novel here is that this ant makes an unusually large amount of the chemical, thus leading to a strong odor, one that even humans can detect.

The article starts with a little discussion of how people perceive the odor. The authors note that most web sites they found refer to these ants as smelling like rotten coconut. However, in a test at a local bug event, they found that more people identified the odor as blue cheese.

News story: The Ants That Smell Like Blue Cheese -- Or Is That Pine-Sol? (G Pearson, Wired, June 8, 2015.) This actually has most of the content of the article.

The article: The True Odor of the Odorous House Ant. (C A Penick & A A Smith, American Entomologist 61(2):85, Summer 2015.) (A 21 MB pdf, for a three page article -- perhaps because of the high resolution half page picture of an ant.)

Previous post about ants: The advantage of washing with formic acid (August 8, 2014).

Next... Who cleans up the forest floor? (November 3, 2017).

Previous post about coconut: The octopus and the coconut (December 28, 2009).

Previous post about cheese: The oldest known piece of cheese (April 25, 2014).

More cheese (and fungi): Cheese-making and horizontal gene transfer in domesticated fungi (January 19, 2016).

More ascomycetes... Penidiella and dysprosium (September 11, 2015).

* Previous "What's the connection" post: What's the connection: rotten eggs and high-temperature superconductivity? (June 8, 2015).
* Next... What's the connection: Narcolepsy and the flu vaccine (or getting the flu)? (October 3, 2015).

More about odors: Copper ions in your nose: a key to smelling sulfur compounds (October 10, 2016).

There are sections of my page Organic/Biochemistry Internet resources on Aldehydes and ketones and on Lipids. They list related Musings posts.

Do human genes function in yeast? Yeast-human hybrids.

August 21, 2015

A new article provides an interesting update on an old story.

What goes on in cells is similar in many ways in all organisms. For example, cells generally need the same amino acids, and use the same basic pathways to make them. And all cells undergo cell division. The question is whether the proteins that carry out these tasks can function in another organism. Same task, different organisms.

People have been testing this for decades -- for individual genes. What's new is the scale of the current experiment, a systematic test of hundreds of genes. Human genes in yeast. Two organisms that diverged a billion years ago.

Here is the basic plan for the experiments... Take a mutant yeast with a defect in an essential gene. By essential gene, we mean that when the gene is defective the yeast cannot grow. Now add the human version of the same gene. If the strain now grows, it shows that the human version of the gene can substitute for the yeast version.

The test is often called complementation. The question is whether the added gene can complement, or compensate for, the defect of the host strain.

There are various technical points that make these experiments practical. It is no accident that yeast is the host organism. It is a eukaryote, but one that is simple and fast growing. There are good genetic tools to make the manipulations practical. For example, there is already a library of mutants with defects in individual genes. Further, it helps to be able to turn genes on and off under the control of the experimenter. It is hard to grow mutants that can't grow, so scientists use a little technical trick: it's called a conditional lethal. What that means is that the experimenter can turn the gene on and off as needed. One, classic, type of conditional lethal is a temperature sensitive mutation. At low temperature, the gene behaves fine and the organism can grow. Raise the T and the gene (more typically, the gene product) becomes inactive, and the strain can't grow if the gene is essential.

Is the test about genes or about proteins? It's about both -- as a practical matter. The main intent is to see whether the proteins can substitute. However, it is much easier to do the test with genes. A successful complementation requires that the gene function and that the resulting protein function. The technical design of the experiment helps to emphasize the role of the protein rather than gene issues, but the latter cannot be completely eliminated.

As noted, some such tests have been done over the years. Sometimes it works, sometimes it doesn't. In the new work, the scientists systematically test a collection of 414 yeast strains, each mutant in one essential gene. In each case, they add the corresponding human gene, and see whether the yeast can grow.

The human gene works in about half the cases they test. After a billion years of divergence, half of our genes still function reasonably in one of the simplest eukaryotes. (That "half" is a little misleading. It's not really half of our genes. It's half of those tested. And the ones tested were those where human and yeast had corresponding genes. Both organisms have genes that are unique to that organism. They are not an issue here.)

The authors go beyond that and ask why some genes work and some don't. Are there common features of genes that can be successfully transferred from human to yeast?

The following figure summarizes one of their analyses...

The authors group the genes by type of function. (This is a standard classification of genes.) For example, the first group (upper left) is "metabolism of cofactors and vitamins". The pie chart shows that 92% of the genes tested from this group were "replaceable" (yellow). Only 8% were "not replaceable" (blue).

The results for six groups of genes are shown here. (It's just a sample of all the groups they looked at.) They are in order, from highest % replaceable (upper left) to lowest (lower right). There is a pattern, an interesting pattern... The three groups in the top row, with high % replacement, are for basic biochemical functions involving small molecules, such as the amino acids and vitamins. The three groups in the bottom row, with low % replacement, are for more complex processes, typically involving proteins interacting with each other. The full set of groups, shown in the article, fits with the pattern I have suggested here.    This is part of Figure 3C from the article. The full figure shows results for 12 groups of genes.

The pattern makes some sense. In the first group, the proteins act independently and carry out individual biochemical steps. The first protein might make chemical "A"; the second converts A to B. So long as the first one can make A and the second one can make B, they are likely to work together. For the second group, let's take the ribosome as an example. It includes many proteins that form a complex. The proteins interact with each other. If one protein is a bit different, it may be unable to interact with its neighbor.

The pattern they found is not surprising. What's new here is having data that tests what we expected. But it is striking that about 90% of genes for basic biochemical functions are sufficiently conserved that they can be successfully transferred from human to yeast.

An interesting follow-up would be to learn why individual failures occur. Also of interest will be exploring why some proteins in complexes can be transferred; the article presents some analysis of one such case.

News story: Human Genes Can Save Yeast -- Replacing yeast genes with their human equivalents reveals functional conservation despite a billion years of divergent evolution. (R Williams, The Scientist, May 21, 2015.)

The article: Systematic humanization of yeast genes reveals conserved functions and genetic modularity. (A H Kachroo et al, Science 348:921, May 22, 2015.) Check Google Scholar for a copy.

An example of complementation: CRISPR: What's it doing to help bacteria carry out infections? (September 8, 2013).

An example of using temperature sensitive mutants: "Moonwalkers" -- flies that walk backwards (May 28, 2014).

On making other organisms more human...
* Developing a monkey with a gene for a human brain protein (July 6, 2019).
* As we add human cells to the mouse brain, at what point ... (August 3, 2015).

More about yeast: On genome duplications (September 10, 2015).

Also see:
* Cataloging gene knockouts in humans (July 10, 2017).
* Ribosomes with subunits that are tethered together (October 5, 2015).

August 19, 2015

Quiz: What is it?

August 17, 2015

There is an important follow-up post, listed at the end.

That's "it". What kind of animal do you think this fossilized skeleton is from? Caution... If you decide to count the vertebrae, you should realize that only a small part of the vertebral column is shown. There is a scale bar at the lower right, but size per se is not helpful here.    This is Figure 4C from the article listed below. The answer is below. But first, what do you think, and why?

Answer and discussion...

Well, that wasn't hard, was it? Especially after I gave a big hint. It's a snake with "hands". Or with limbs, to be more general. You can't tell from this excerpt from the animal, but it's a four-legged snake -- and there are 272 vertebrae (160 before the tail).

Modern snakes don't have legs. Fossil snakes with two hind-limbs have been found. The current fossil is the first known four-legged snake. We presume that snakes developed from something like lizards, by elongation and loss of legs. The snake reported here is perhaps a transitional state. We caution, however, that we do not know where this snake fits in. As so often with fossil finds, there is insufficient evidence to make a strong case how it fits in. We look forward to more specimens.

It's about 110 million years old, and is a beautifully preserved specimen. It's apparently a very young snake. It's called Tetrapodophis, which means four-legged snake.

Interestingly, the limbs here appear to be quite functional, not degenerate. The authors suggest that they were more likely used for grasping than for walking.

News story: Four-legged snake fossil found. (Science Daily, July 23, 2015.)

Video. (YouTube, 3 minutes.) It's a nice introduction to the story, narrated by the lead author. He is good at pointing out features in the skeleton. Highly recommended.

* News story accompanying the article: Paleontology: Four legs too many? -- A long-bodied fossil snake retains fore- and hindlimbs. (S Evans, Science 349:374, July 24, 2015.)
* The article: A four-legged snake from the Early Cretaceous of Gondwana. (D M Martill et al, Science 349:416, July 24, 2015.)

There is an important follow-up post: A dispute about an issue in a Musings post: the four-legged snake (December 5, 2016).

More snakes:
* Poisonous snakes and their mimics (August 15, 2016).
* How to climb a pile of sand (November 7, 2014). Elizabeth.

* Previous quiz... Quiz: What is it, and ... ? (July 7, 2015).
* Next: Quiz: what is it? (April 5, 2017).

Gondwana? See How were the Gamburtsevs formed? (December 7, 2011).

Using your phone to find Loa loa

August 14, 2015

This post is about using phone-based cameras for medical applications, such as diagnosing parasites; this was introduced in an earlier post on the CellScope [link at the end]. We now have a field trial of a device for a specific application.

Some background... Two important diseases in parts of central Africa are onchocerciasis (river blindness) and lymphatic filariasis (leading to elephantiasis). These worm infections can be treated, using the drug ivermectin. However, there is a problem. The use of ivermectin is good -- unless the person also carries Loa loa, in which case the drug becomes quite toxic.

Loa loa is a tiny worm, which causes loiasis. By itself, it is often a minor infection. What is important here is that it interferes with the use of ivermectin for the other diseases. Therefore, it is important to screen those being given the drug for Loa.

The common screening for Loa is slow. It requires a trained observer to examine a blood sample. A new article offers a smartphone-based test, which is quick and easy -- and highly automated. The article reports a field trial of the device.

Here is the device, called CellScope Loa...

The top part of the figure shows the device; the bottom part shows the innards. The phone is used for its camera and computer. Blood is taken from the person directly into the capillary (v, in the lower frame). The capillary is inserted into the slot on the right side of the device. The user presses a button on the phone screen. The rest is automatic. The device takes pictures, analyzes them, and reports the count of "little things that move" -- the Loa loa. No treatment or staining of the blood is needed. You can see it in operation in the video files listed below.    This is Figure 2A from the article.

Here is a summary of the results from a recent field trial, in Cameroon...

The graph shows a scatter plot comparing the results for the two methods. The y-axis shows the results from the new device; the x-axis shows the results by the traditional procedure, using a sample of blood that has been stained and read by a trained observer. The axes are labeled with the units mf/ml. The mf stands for microfilariae, that is, the worms of interest. You can see that the results for the two methods generally agree well. Let's look more closely; it gets more interesting.

The graph is divided into four quadrants. The dashed lines show the cutoffs: 26. That's 26,000 worms per mL of blood. If a person is below that level, they get the drug; if they are above it, they don't. Many of the points are in the white lower left quadrant. This means that the assay is below the cutoff by both methods. A couple of points are in the white upper right quadrant. This means they are above the cutoff by both methods. So far, so good. There are two points in the blue quadrant (upper left). This means that the new phone-based assay says they are above the cutoff, whereas the traditional test says they are not. The new assay is reporting something that is not true by the traditional test, considered the "gold standard". These are false positives. There are no points in the pink quadrant (lower right); these would be false negatives.    This is Figure 4B from the article.

It's good to follow that discussion of the graph; it is typical of how one compares two analysis methods.

However, there is perhaps more to it. In pointing out more, I'm not trying to criticize the new method or the authors, but to point to some complexities that, at some point, need some attention. The current study is small; it's not surprising it leaves some questions.

For example, we might note that of the values above the cutoff by the new method, half (two of four) seem to be false positives. In fairness, the false positives are just barely across the line. But the big point is that there are very few samples here with high values.

In doing the comparison, the traditional method is considered the "gold standard"; it is taken as correct. But we don't really know that for sure -- especially when the discrepancies are small.

Why is there a simple cutoff? A single number, applicable to all people: below it you're ok, above it, you're not. Our state of knowledge may be that simple, but real biology usually isn't.

Questions, questions. Typical of real world medical issues. If the new method ends up proving to be simpler to use, perhaps it will allow better analysis of some of those questions.

In the article, the authors discuss some of the development that has gone into getting to the current device. They note the challenges of getting a device that is "correct" and also easy to use and inexpensive. The current test was "in the field", under conditions they consider close to the real intended application.

News stories:
* New smartphone microscope able to detect blood parasites quickly. (J McIntosh, Medical News Today, May 7, 2015.)
* Smartphone video microscope automates detection of parasites in blood. (S Yang, UC Berkeley, May 6, 2015.) From the lead institution.

Video. (YouTube, 30 seconds, narrated.) Brief overview of how the device works. This video is included in the UC Berkeley news story, listed above.

There are also three videos posted with the article at the journal web site, as Supplementary Materials. Of particular interest...
* Movie S1 shows you Loa in the blood. They are the little wriggling things. (5 seconds.)
* Movie S2 is a longer version of the narrated description of how the device works (2 minutes.)

The article: Point-of-care quantification of blood-borne filarial parasites with a mobile phone microscope. (M V D'Ambrosio et al, Science Translational Medicine 7:286re4, May 6, 2015.)

Background post about the CellScope: Connecting a cell phone and a microscope (September 2, 2009).

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

More you can do with your phone:
* Can you detect the SARS-2 virus with your phone? (March 2, 2021).
* Testing for lead in drinking water: a quick and inexpensive test using a smartphone (October 20, 2018).
* Using your smartphone to detect cosmic rays (April 7, 2015). Note that the current device, for parasites, requires both hardware and software beyond the phone. The cosmic ray device requires only software; it can be done with your phone without further equipment.

More from Cameroon: Lakes that explode (October 13, 2009).

More worms... Could a tapeworm with cancer transmit the cancer to its human host? (November 16, 2015).

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

August 12, 2015

Monitoring the wildlife: How do you tell black leopards apart?

August 10, 2015

In general, telling leopards apart is easy enough. You look at the pattern of spots.

However, in Malaysia there is a problem, as shown in the following figure:

An ordinary color photo of a leopard.    This is Figure 1a from the article.

In some areas of Malaysia, most of the leopards are melanistic. In plain English, black. You can't see the spots.

A new article reports a trick. Click here [link opens in new window]. The top part is the same photo as above. The bottom part is a photo taken with an infrared (IR) flash. You can see the spots. (The linked figure is the full Figure 1 from the article. These are two different animals and scenes. I wonder why they didn't publish two shots of the same animal, with the two types of lighting.)

Scientists have been aware that that the black leopards actually have spots; sometimes one can see them, depending on the angle of the lighting. The new work provides a practical way to see the spots during routine daytime photography.

Their system for monitoring leopards in the wild uses automated camera trap stations. Apparently, the traps routinely take color pictures in daylight, and IR pictures at night. What the scientists did here was to cover the light sensor, forcing the station to take IR pictures at all times.

The scientists were able to identify the individual leopard in 94% of the photos, with two observers agreeing. This is higher identification than achieved by any previous method for black leopards.

It is important that conservation biologists be able to track individual animals. Now, they can study the leopards in Malaysia. In fact, the article presents an estimate of the density of leopards in the area, probably the first such measurement.

News story: Mysterious black leopards finally reveal their spots. (Science Daily, July 13, 2015.)

The article: Melanistic Leopards Reveal Their Spots: Infrared Camera Traps Provide a Population Density Estimate of Leopards in Malaysia. (L Hedges et al, Journal of Wildlife Management 79:846, July 2015.)

More on cat coats: Big cat, little cat: Taqpep determines coat pattern (December 27, 2012). Links to more about cats.

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

More from Malaysia: Who cleans up the forest floor? (November 3, 2017).

Also see:
* Using drones to count wildlife (May 15, 2018).
* Re-introducing captive animals into the wild: an orang-utan mix-up (June 27, 2016).
* Leopard horses (December 2, 2011).

August 5, 2015

Do babbler birds construct words?

August 4, 2015

Consider the words "at" and "cat". The second word includes the sound of the first word, but there is no relationship between the meanings of the two words. That is, the sound of "at" is an abstraction of language that means completely different things depending on its language context.

A new article reports that a common Australian bird known as the chestnut-crowned babbler (Pomatostomus ruficeps) uses sounds in a way that is very much like that. That is, the bird constructs different "words", with different meanings, from the same sounds.

The work started with analyzing the sounds made by the birds. Later, the scientists did playback experiments. The birds responded to playing artificially constructed sounds the way the scientists expected.

The authors claim that this is the first example of finding such word construction in non-human animals. It is tempting to look at it as a step toward language. Is there any connection between what these birds are doing and what the first humans might have done in acquiring language?

An article such as this teases us. If offers something new, something surprising. Be cautious. Nothing is served by trying to reach a conclusion at this point. We have a new finding about vocalization and communication by these birds. It leads to suggestions (ideas, hypotheses) and further work. Let's try to understand what the birds can -- and can't -- do. What can other animals do, now that the idea has been raised? The role of an article such as this should be to expand the exploration of how non-human animals communicate.

News story: Key element of human language discovered in bird babble. (Science Daily, June 29, 2015.)

The article, which is freely available: Experimental Evidence for Phonemic Contrasts in a Nonhuman Vocal System. (S Engesser et al, PLoS Biology 13(6):e1002171, June 29, 2015.) It's a long article, but generally readable. You might find it interesting to look over the introductory parts, even if you don't want to get into the more technical parts.

More on language... Can chimpanzees learn a foreign language? (March 10, 2015).

How the giant panda survives on a poor diet

August 2, 2015

The giant panda is famous for its diet: bamboo. That's certainly unusual -- especially for a carnivore. A panda is a type of bear, and bears are carnivores. The specialist panda has specialized in a way that is inconsistent with its family.

If you have been paying attention to recent science, you might suggest that the panda has a gut microbiota specialized for digesting bamboo. The microbiota clearly plays a role in digesting food, and it is plausible that it might adapt relatively quickly. Perhaps the panda switched from carnivory to bamboovory (don't look that up in your dictionary, but I bet you know what it means) largely by developing a new gut microbiota. Perhaps, but recent evidence suggests it isn't true. The story is incomplete, but a first analysis of the panda microbiota suggests it isn't helping with the bamboo.

A new article offers a different analysis. The scientists measure the metabolism of the panda: it's slow. Very slow.

The following figure shows one manifestation of the slow metabolism. It shows the surface temperature of various animals.

Let's start with the bottom part of the figure, labeled T = 10 °C (with brown bars). Several large animals were kept at this T, and the T of the body surface was measured (x-axis). For simplicity, you might just look at the little red bars, which mark the average T of the animals. The striking finding is that the pandas are several degrees cooler than the dogs and cows. The top part of the figure is the same kind of work, but now with the animals kept at -4 °C (blue bars). Again, the pandas are cooler than the other animals tested. This is part of Figure 2 from the article. I have added the temperature labels within the figure. These are for the ambient T.

The lower surface T of the pandas, compared to other large animals kept under the same conditions, reflects that the pandas have a slower metabolism, and are thus producing less heat. That is how, apparently, they survive on a poor diet. They have reduced their energy needs to match their diet.

The authors uncover one explanation for the slow metabolism. They find that pandas carry a mutation that leads to a low level of thyroid hormone, which plays a key role in regulating metabolism. It may be that this mutation was a key step in adapting to a diet of bamboo.

Quantitative measurements of the metabolism show that the panda spends about half as much energy as a human of the same weight. Its metabolism is more like that of a sloth, an animal noted for its low metabolism. But that last point also shows that the panda metabolism is within the range known for mammals, just near the lower end.

News stories:
* Stay Cool And Eat Bamboo. (Asian Scientist, July 22, 2015.) Includes a thermal image of a panda; interesting picture! The article includes some such pictures, but they are hard to interpret.
* Pandas spend less energy to afford bamboo diet. (Science Daily, July 9, 2015.)

The article: Exceptionally low daily energy expenditure in the bamboo-eating giant panda. (Y Nie et al, Science 349:171, July 10, 2015.)

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

More...
* Pandas: When did they become specialized to eat bamboo? (March 18, 2019).
* Rewritable W-based paper and a disappearing panda (January 30, 2017).

More on thyroid issues...
* Failure to regenerate heart tissue: role of thyroid hormone (May 14, 2019).
* Did the Fukushima nuclear accident lead to a burst of thyroid cancer? (July 17, 2016).
* BPA: Effect on thyroid hormones in pregnant women and babies (December 8, 2012).

Also see:
* Low-carb diets: Long-term effects? (September 4, 2018).
* The opah: a big comical fish with a warm heart (July 13, 2015).

Handedness in kangaroos: significance?

July 31, 2015

A red-necked wallaby, Macropus (Notamacropus) rufogriseus, in a bipedal position, using the left forelimb for eating.    This is Figure 1A from the article.

A team of scientists has made systematic observations of several marsupial species to see which "hand" (forelimb) they used for various tasks, such as feeding and grooming.

Here is a summary of their results...

The graph shows the overall handedness they found for seven marsupials. Each bar is for one type of marsupial; the "height" of the bar shows the handedness they found. The y-axis is a handedness score, which they call the mean handedness index. Positive scores mean a bias toward use of the left hand; negative scores are for a right-hand bias. The bars are shown extending from zero (no bias) to whatever mean score was found for the species. Note the vertical divider in the graph. And note that the results seem different on the two sides of that divider. What does that mean? The four (darker) bars to the right all have values near +0.5, and all are marked as significantly different from zero. These four species are left-handed. The three (lighter) bars to the left are all smaller, and are "NS" -- not significantly different from zero. These three species do not show a significant handedness bias. The two sets of bars? One set is for quadrupedal marsupials, the other set is for bipedal marsupials. The bipedal marsupials show a handedness effect -- and they are left-handed. The quadrupedal marsupials do not show a handedness effect.    This is Figure 3 from the article.

So what do we learn from all this, assuming that the results seen here are representative and are being properly interpreted?

First, we learn that some marsupials are left-handed. This appears to be the first example of species where left-handedness is the more common bias. For now, we have no idea what the significance of this is.

The second finding is intriguing: that handedness is found in bipedal species, but not in quadrupedal species. Does this really mean that handedness develops along with the bipedal posture? It is true that the species we most commonly note for its handedness bias is indeed bipedal.

The handedness score for humans, using similar tests, is about -0.6. (This is shown in Figure 4 of the article.) Except for the opposite sign, the results are not very different from those for the red kangaroo.

News stories:
* Most kangaroos are 'left-handed'. (BBC, June 18, 2015.)
* Lefties are all right with kangaroos. (Science Daily, June 18, 2015.)

The article: Parallel Emergence of True Handedness in the Evolution of Marsupials and Placentals. (A Giljov et al, Current Biology 25:1878, July 20, 2015.) Check Google Scholar for a freely available copy of the preprint.

Other posts about handedness include...
* On handedness in humans (September 30, 2013).
* Analysis of teeth confirms that Regourdou was right-handed (September 7, 2012).
* On being ambidextrous (January 24, 2010).

More about kangaroos: An animal that walks on five legs (February 3, 2015).

and maybe... Kangaroo mother care for premature babies: start immediately (June 27, 2021).

July 29, 2015

Close-up view of an unwashed human

July 29, 2015

Briefly noted...

Here he is...

The figure shows the distribution of sodium lauryl ether sulfate (SLES) on his body. The results are shown as a heat map, with redder colors indicating higher concentrations and bluer colors indicating lower concentrations. There is a key at the lower left, but it is only qualitative.    This is one part of Figure 2 from the article.

What's the point? The methodology for making such a "skin atlas". The authors of a new article have developed methods to allow extensive examination of the skin, for many many things. The analyses reported in the article include a variety of substances, including metabolic products from the person as well as environmental chemicals. The particular chemical above is a detergent found in shampoos.

Much of the analysis was done by sampling the skin at 400 sites with swabs, and analyzing them by mass spectrometry. They also analyze for microbes, based on ribosomal RNA sequences. In fact, one goal is to be able to correlate skin chemicals with skin microbes.

One observation from the limited work so far is that much of what is on our skin is from things we apply, such as hygienic or cosmetic products. The detergent shown above is an example. Interestingly, a good fraction of the chemicals found on the skin could not be identified.

Two individuals were sampled for this study, one male and one female. Their preparation included not bathing for three days prior to the sampling. Again, we emphasize that the primary purpose of the study was methods development, and not conclusions about what is on the skin.

News story: 3-D human skin maps aid study of relationships between molecules, microbes and environment. (Science Daily, March 30, 2015.)

* Commentary accompanying the article: Skin molecule maps using mass spectrometry. (R G Cooks et al, PNAS 112:5261, April 28, 2015.)
* The article, which is freely available: Molecular cartography of the human skin surface in 3D. (A Bouslimani et al, PNAS 112:E2120, April 28, 2015.)

More mass spectrometry...
* Hydride-in-a-cage: the H₂₅^- ion (January 22, 2017).
* Coupling the surgeon's knife to a mass spectrometer (August 13, 2013). Mass spec analysis as surgery proceeds guides the surgeon as to how much cancerous tissue to remove.
* US Army attacks colony collapse problem -- and an ethics story (October 25, 2010). Large scale mass spec analysis of bees helped to identify an infectious agent.

A post on the skin microbiota: Sharing microbes within the family: kids and dogs (May 14, 2013).

More shampoo: Nanotechnology leads to the development of a superoleophobic polypropylene -- and a better shampoo bottle (November 6, 2016).

Making a new species in the lab

July 26, 2015

Can Man design a new species of organism?

Two organisms are considered to be different species if they are reproductively isolated, that is, if they cannot interbreed. There are complications to defining species, but that rather traditional view is useful for organisms with sexual reproduction.

It follows then... if we could engineer an organism so that it forms a new breeding population, unable to breed with the first, then we have created a new species.

A team of scientists now claims to have done just that.

The organism here is Schizosaccharomyces pombe, a yeast. It has a system of true sexual reproduction. There are two sexes, or "mating types"; they are called M and P. A cell of the M type makes a protein factor called the M-factor. The M-factor is secreted, and binds to a receptor on a P-cell. The binding of M-factor to the P-receptor is the basis of forming a mating pair. The mutual recognition of M-factor and P-receptor is the basis of species identity.

The following figure outlines the work...

The top part of the figure shows what happens with wild type (WT) yeast. The figure shows a WT M-cell at the left, and a WT P-cell at the right. You can see that the M-cell makes M-factor, which binds to the P-receptor, called Map3, on the P-cell. Pictorially, the square factor fits into the receptor with a square slot for it. That binding is what starts a mating event. At the bottom, we have an M'-cell, which makes a mutant M-factor, which binds to a mutant P-receptor (mutant Map3) on the mutant P'-cell. Pictorially, the mutant factor is round (not square) and fits into a round spot on the receptor.

The top pair of cells is labeled as a wild type mating pair. The lower pair of cells is labeled as a novel mating type pair. Importantly, the two types cannot cross-mate; this is shown by the dashed lines in the middle, which are blocked. The two types are reproductively isolated. That is, the two types of mating pairs shown here are for different species. What's important here is that the novel mating type was created in the lab, by goal-directed engineering.    This is Figure 1A from the article.

How did the scientists do this? There are two steps. In outline... In the first step, they isolated mutant yeast that are unable to mate. They screened a collection of these, and found one that is unable to mate because it makes a mutant M-factor.

In step 2, they isolated mutants that can successfully mate with the M-factor mutants from step 1. These carry "suppressor" mutations in the gene for the P-receptor (Map3 gene), so that the mutant M-factor can now bind to the mutant P-receptor. It works. The mutant M cells from step 1 now mate with the mutant P cells from step 2. And the two types cannot cross-mate.

Here are some examples of the results showing the behavior of the two species (old and new). In these experiments two parental strains were crossed. The two parents had genetic "markers" that made it easy to follow them. In fact, in this case, the conditions were such that the two parents could not grow, but progeny from a successful mating could grow. Let's look...

That's the plan, and there are some results. Pretty good! A new species. An "artificial" species, made in the lab.

News story: How to Make a New Species. (R Williams, The Scientist, July 1, 2015.)

The article: Molecular coevolution of a sex pheromone and its receptor triggers reproductive isolation in Schizosaccharomyces pombe. (T Seike et al, PNAS 112:4405, April 7, 2015.)

The title of the article refers to a "sex pheromone". That's the M-factor. The general notion that one mating type makes something that attracts the other was described before the details were understood.

The abstract for the article concludes... "In conclusion, we have succeeded in creating an artificial reproductive group that is isolated from the WT group. In keeping with the biological concept of species, the artificial reproductive group is a new species."

* * * * *

Posts about the nature of species include...
* What if yeast had only one chromosome? (August 26, 2018).
* Nuclear-mitochondrial interactions -- and the definition of a biological species (June 18, 2017).
* Finding a gene behind the beak diversity of Darwin's finches (July 14, 2015).
* What if two of the world's most destructive pests spent the evening together in Fort Lauderdale? (April 4, 2015).
* Development of a new species of lizard in the lab (May 20, 2011).

Effect of low dose radiation on humans: some real data, at long last

July 24, 2015

Radiation causes cancer. And the more radiation, the more cancer; the effect is proportional to the dose. That's all easy enough.

But there is a limit to what we can measure. At low doses of radiation, the effect -- if any -- is so small that it is almost impossible to measure. Yet, we are all exposed to low dose radiation, from various sources. (The accompanying post, immediately above, is about this.) We honestly don't know what the effect is; worse, there is active debate about it, because there are a variety of reasonable models.

Here are two models for what we might expect from low dose radiation. These are simple models, and are perhaps the major models that get discussed.
1) The linear relationship holds for all doses.
2) At low doses there is less effect than expected from the linear relationship, because we can adapt to it, or can repair some level of damage. That is, this model says that biology intervenes and protects us from some level of radiation; at higher doses, our protection is overwhelmed and we get the "real" effect.

What now? Some data. A new article measures low dose radiation exposure of 300,000 people over many years -- over 8 million person-years of exposure, and also looks at the incidence of cancer (leukemia) in the group.

Where does one get such a remarkable data set? From workers in the nuclear energy field, who wear radiation badges (dosimeters) that record their exposure. It has long been recognized that such workers may have an increased exposure to radiation. Thus they have long been monitored (and they are subject to restrictions). The article collects records for such workers in the US, UK and France.

Here is a summary of the findings...

The graph shows the risk of death from leukemia as a function of radiation dose to the bone marrow. The risk is shown as relative risk (y-axis), with the risk at zero dose taken as 1. Zero dose here means zero as recorded by the dosimeters when the people are at work. They are still exposed to the normal background radiation.

There are three curves. Each shows the best-fit line based on a particular dose range, along with the 90% confidence limits. For example, the short red line at the left is for exposure of less than 100 milligrays (mGy). The general observation is that the three lines are, statistically, all the same. The effect (risk of getting leukemia) seems to be linearly proportional to dose over the entire dose range. Further, the slope of the line here is about the same as has previously determined with higher doses. This supports model 1; there is no evidence for anything special going on at low doses.    This is the figure from the article.

For perspective... The average dose for these workers was 1.1 milligray per year. If a person received that dose for an entire lifetime, say 100 years, they would get about 100 mGy exposure. That would give them about a 30% increased risk of getting leukemia over the lifetime.

More specifically... In the population studied here, a population with a high exposure to radiation, 531 people died of leukemia. The authors estimate that 30 of those leukemia deaths, about 6%, could be statistically attributed to the occupational radiation exposure.

In both cases, we see that the increased risk of leukemia is small. But it is real. It can be hard for the public to digest what those statements mean. There is no inconsistency between saying that a risk is real but small. There is no inconsistency between saying "don't worry" while at the same time considering how we might reduce the exposure. However, if the risk is small, then we might ask if it is worth spending much effort reducing it. One answer to that is that the risk is not spread evenly. Understanding the risk, trying to minimize it, including trying to minimize accidents, can help reduce exposures in the long run.

Do we need to re-think our safety standards for radiation? The short answer is probably not. Standards are currently set using the linear dose response assumption (model 1), which is the more conservative model. The results here support that model.

Is this the last word? There is no last word in science. But this article is the best evidence we have so far about the effects of low dose radiation in humans.

A couple other studies, of similar scope, are in progress. We'll see if they all agree.

There are various questions one can raise about the details of this study. For example, the data suggest that the effect may be different for different cancers. In one case, they even found a negative effect -- with radiation dose reducing cancer. It is likely that some of these differences are simply due to the smaller sample size when looking at more specific types of disease. In any case, the big picture for now is to treat this as one answer: risk is proportional to dose, as far as we can measure it.

News story: Medical research: Researchers pin down risks of low-dose radiation -- Large study of nuclear workers shows that even tiny doses slightly boost risk of leukaemia. (A Abbott, Nature News, June 30, 2015 (Corrected July 8, 2015). In print... Nature 523:17, July 2, 2015) This news story is also the basis of the preceding post.

* "Comment" story accompanying the article; it is freely available: The merits and limits of pooling data from nuclear power worker studies. (M Blettner, Lancet Haematology 2:e268, Published Online, June 22, 2015.) If you want to get serious about the study, read this.
* The article, which is freely available: Ionising radiation and risk of death from leukaemia and lymphoma in radiation-monitored workers (INWORKS): an international cohort study. (K Leuraud et al, Lancet Haematology 2:e276, Published Online, June 22, 2015.)

The post immediately above is related: Major sources of radiation exposure (July 24, 2015).

Measuring radiation: The banana standard (April 17, 2011). This post introduces the confusing issue of how radiation is measured. You will note that the current work uses two units: the gray and the sievert. The gray is a real measurement; it is what the dosimeter measures. The sievert is an attempt to estimate the effective dose. Don't get lost in all that. The authors note that in this work they take 1 Gy as equivalent to 1 Sv.

Does radiation treatment of cancer cause new cancers? (April 8, 2011). An example of dealing with the trade-off of medical radiation.

More leukemia... Why some viruses may be less virulent in women (March 1, 2017).

More cancer... The role of combinations of chemicals in causing cancer? (September 21, 2015).

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

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. It also includes a list of related Musings posts.

July 22, 2015

Can the naked human eye measure distance to nanometer accuracy?

July 20, 2015

The human eye can typically see things as small as about 0.1 millimeter (1 mm = 10^-3 m). A good light microscope lets us see things about a thousand-fold smaller, down to about 0.1 micrometer (1 µm = 10^-6 m). A bacterial cell about 1 µm across is clearly visible with the microscope, though one can see little detail.

A new article reports getting humans to measure things much smaller than such bacteria, and without even using a microscope. The human observers are measuring distances to the nearest nanometer (1 nm = 10^-9 m).

At first glance, that may seem remarkable. But perhaps what is as remarkable as anything is that it isn't really very remarkable. The scientists did not discover any new laws of physics or biology, or develop any fancy apparatus. The principle behind the new work is well known, and skilled users have been making use of it. What the new work does is to press the limits; the key tool they used was extreme care.

The new work involved measuring the thickness of some small pieces of film made out of titanium dioxide, TiO₂. (The choice of material isn't important, except that it is easy to make well-defined thin films from it.)

This figure shows the seven thin films used. Photographs of the actual films are shown in the bottom row. The top row shows examples of the computer screen images that have been adjusted to match.    This is Figure 1 from the article.

Let's play for a moment... Can you tell the difference in the colors of the seven disks in the figure above? (By the way, this test -- and what they did in the article -- requires normal color vision.) With possibly one exception, I suspect you can. The thicknesses of the disks are given in the table (below, but it is not clear which disk is which in the figure). One pair of disks differs by only about 10 nm. Another pair differs by about 20 nm. Other pairs differ by about 40 nm. So, if you can tell the differences in most of these colors, you could tell the thickness of such a disk to within 20-40 nm. That's already rather good.

The actual test is a formalized version of that. Here is what the panel of observers in the article found...

The table lists the seven films, with two types of measurements. For each, there is d, the average thickness reported, and σ, the standard deviation. All values shown are in nm. One type of measurement is what the observers recorded "by eye". The other is an instrument measurement; for convenience, we'll consider that to be the "correct" value. The column headers for the two types of measurements are shown with subscripts b and e, respectively.

An example, to make that clearer... The first row, sample #1... The observers reported a mean thickness db of 46.6 nm (with standard deviation σb 2.6 nm). The instrument reported a mean thickness de of 47.9 nm (with standard deviation σe 0.1 nm). You can see that the mean for the observers was 1.3 nm less than the instrument value. Look at the other rows, and the big message is the same. The observers are usually within about 1 nm of the instrument value. (The worst case is sample 6.) This is part of Table 1 from the article. (The additional columns, omitted here, contain a couple other measurements; they are interesting, but do not change the basic story. Perhaps most interesting is that the electron microscope did poorly in this test; in fact, it had trouble seeing the samples at all.)

The results above show that the observers were able to estimate the thickness of each disk to within about 1 nm. Impressive.

What did they actually do? They matched the colors. But how? Here is a brief version... The thin film itself was placed on the computer monitor. The observer then adjusted the color of a nearby circular disk on the screen to match. For example, one pair of buttons allowed the observer to adjust the red-greenness to match the sample. Having the object being measured right on the screen helped to ensure consistency of lighting. The settings the observer used to match the color were compared to a standard curve -- thus giving the observer's measurement of the thickness. The measurements were fairly easy to make. An observer typically took less than two minutes to measure a thickness, which is in the same ball park as the instrument procedure.

The scientists are not suggesting that this is the proper way to make such measurements. For one thing, the relationship between color and thickness depends on the material. As much as anything, they were curious to see how well the human observers could do. Not bad, it seems.

Have you ever noticed the colors in a soap bubble? The colors are due, in part, to the thickness of the soap film making the bubble. That's the idea underlying these measurements. For a specific material, the relationship between color and thickness is well-defined and reproducible.

Are you concerned that the observers aren't really measuring distance; they are measuring color, and figuring out the distance from the relationship? That's true, but it's fine to measure something indirectly. We use the time of an echo to measure distance. Same idea. But it is true that the trick here to measuring distance to 1 nanometer is to make direct observations of some other property -- one that we can relate back to distance.

News stories:
* Thanks To Color Vision, The Human Eye Can Distinguish Between Most Subtle Nanoscale Differences. (L Bushak, Medical Daily, July 9, 2015.)
* How to visually determine thickness at one-nanometer resolution by eye. (Kurzweil, July 10, 2015.)

The article, which is freely available: Human color vision provides nanoscale accuracy in thin-film thickness characterization. (S Peterhänsel et al, Optica 2:627, July 2015.)

More about high resolution distance measurements...
* Expansion microscopy: making an object bigger can make it easier to see (February 23, 2015).
* Characterization of carbon nanotubes (December 3, 2013).

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

Posts on color vision include:
* Color vision: an overview (December 1, 2014).

There is a section of my page Internet resources: Biology - Miscellaneous on Medicine: color vision and color blindness. It includes a list of related Musings posts.

Increased risk of congenital heart defects in offspring from older mothers: Why? and can we do anything about it?

July 18, 2015

The incidence of congenital heart defects increases with the age of the mother. It is not understood why.

A new article reports a clever experiment that reveals part of the story -- and offers some hope for dealing with the problem.

The question the scientists asked here was whether the effect was due to the age of the mother per se or to the age of the egg cells (the oocytes). They addressed this in a model system with mice; the mice carried a mutation that increases the risk of heart defects. The scientists transplanted ovaries between young and old mice. Thus they had young mothers with old ovaries, and vice versa. They then looked at the incidence of the defects in the offspring of these mice.

The following figure summarizes the results...

The graph shows the incidence of heart defects (y-axis) for the two hybrid conditions. The scientists are scoring a particular type of defect, called ventricular septal defect (VSD). Careful... The graph shows three sets of bars, but there is only one set of data here. The middle pair of bars, labeled "Observed", shows the results. The dark bar is for old mother with young ovaries; the light bar is for young mother with old ovaries. (See the key at the right of the graph.)

The dark bar, for old mother with young ovaries, gives the highest incidence of heart defects. That is, it is the age of the mother that matters, not the age of the ovaries (or eggs). What about those other two sets of bars? They are the predictions, for one or the other model. You can see that the actual results (middle set) substantially match the expectations based on maternal effect (left-hand set).    This is the lower part of Figure 1 from the article.

So, the results show, rather clearly, that the age of the mother is the important factor here, not the age of the eggs. That's interesting, and perhaps unexpected.

Age of the mother? Physiology of the mother, perhaps? The result raises the question of whether anything can be done to reduce a mother's chances of having a child with a heart defect. One thing the scientists tried was having the mouse mothers exercise, prior to conception. Turns out this reduced the rate of heart defects in the offspring by half. That's a big effect.

Caution... This is mouse work. Mouse work using a specific mutation that increases the rate of heart defects. (It is similar to a mutation found in humans.) The findings here may or may not apply to humans, may or may not apply to other causes of heart defects. How does the exercise effect carry over to humans? Who knows? Mouse work gives us leads that can be tested in humans; sometimes that is fruitful, sometimes not.

News story: Exercise for older mouse mothers lowers risk of heart defects in babies. (Science Daily, April 1, 2015.)

The article: The maternal-age-associated risk of congenital heart disease is modifiable. (C E Schulkey et al, Nature 520:230, April 9, 2015.) Check Google Scholar for a freely available copy of the preprint.

Other heart posts include...
* A drug for heart hypertrophy? (March 4, 2016).
* The opah: a big comical fish with a warm heart (July 13, 2015).
* Can we pinpoint a specific molecular explanation for tissue damage following a heart attack? (March 24, 2015).
* Mutations that lead to reduced risk for heart disease (November 21, 2014).
* Fixing the heart with some glue and light (July 27, 2014).

A recent post on a maternal effect on the outcome of pregnancy: A gene that reduces the chance of successful pregnancy: is it advantageous? (May 18, 2015).

And...
* How oocytes limit oxygen-induced aging (August 20, 2022).
* Why human egg cells become increasingly defective as the mother ages (June 21, 2016).

A DNA test that can distinguish identical twins

July 17, 2015

It's now routine to identify individual people by their DNA. In fact, there are enough differences between people that sampling small portions of the genome is sufficient to distinguish them.

A limitation of DNA testing is that monozygotic twins, commonly called identical twins, cannot be distinguished by the common tests.

It now seems likely that even identical twins differ in a "tagging" of their DNA, called methylation. However, routine analysis of genomes for such methylation is expensive.

A new article reports a new way to uncover these methylation differences.

Ordinary DNA consists of two strands wrapped around each other. Upon heating a DNA sample, the two strands separate. That process is commonly called melting the DNA; the temperature at which it occurs is called the melting temperature (T_m) of the DNA. The exact temperature at which the strands separate depends on the nature of the DNA. The new work shows it depends on the methylation -- and can be used to distinguish the DNA of identical twins.

The effect of methylation on the melting temperature is indirect. The scientists do not measure the TM of the original DNA. Instead, they do a chemical treatment of the DNA, which itself is affected by the methylation. It is that treated DNA that they measure.

The following figure shows an example...

A cautious interpretation is that the results show that the method might work, sometimes. That is, the results shown here are encouraging, but hardly overwhelming.

The scientists also tested the melting of another gene. Those results are similar -- in fact, a little better. Two pairs of twins got two stars, and the other three got one star. (I chose to show the results that were less good.)

The method developed here is relatively easy to carry out. Not easy, but easier than other methods offered to distinguish the DNA of identical twins. It seems to have promise. The current article establishes that it can work. It's not clear how well or how often; that will require further work. Remember, we said there is currently no good way to distinguish the DNA of identical twins. This is a useful lead.

News story: Crime scene discovery: Scientist separates the DNA of identical twins. (Science Daily, April 23, 2015.)

The article: Differentiating between monozygotic twins through DNA methylation-specific high-resolution melt curve analysis. (L Stewart et al, Analytical Biochemistry 476:36, May 1, 2015.)

More about twins...
* Identical twins: an epigenetic marker, which may allow people to tell if they are an identical twin (October 16, 2021).
* Unusual twins: neither monozygotic nor dizygotic, but... (March 11, 2019).
* Twins? A ducky? Spacecraft may soon be able to tell (August 4, 2014).
* Malnutrition: is more (or better) food the answer? (March 8, 2013).
* Twins (April 30, 2009).

Methylation of DNA is an example of an epigenetic modification: a change in the DNA that does not affect its common base-pairing properties. The role of epigenetics is a hot -- and murky -- subject. Here is another post that notes an epigenetic modification: Why the facial tumor of the Tasmanian devil is transmissible: a new clue (April 5, 2013).

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

July 15, 2015

The opah: a big comical fish with a warm heart

July 13, 2015

We'll focus here mainly on the warm heart (and some related issues).

Fish are typically ectotherms; the common term is cold-blooded. Their body temperature is substantially that of their surroundings. In contrast, birds and mammals are endotherms (warm-blooded); they produce excess heat and maintain their body at a temperature higher than that of the surroundings.

Things need not be that simple. There is no requirement that any particular type of animal fit into one of two distinct categories. And there is no requirement that any particular species has all the common characteristics of its group. We have noted these points before, in discussions of whether dinosaurs were warm- or cold-blooded. One view is that they were perhaps intermediate -- like some fishes [link at the end].

A recent article is about a little-studied strange-looking fish, the opah, Lampris guttatus; it is also known as the moonfish. The scientists present data showing that this fish is not cold-blooded.

Here is an example of their results...

The graph reports measurements for a fish swimming in the ocean. The x-axis shows the time. Start with the black curve -- the lowest one for much of the figure. This shows the depth of the fish in the ocean; see the y-axis scale at the right.

Then look at the blue curve, just above the depth curve. This shows the water temperature (T); see the y-axis scale at the left. You can see that the water T closely follows the water depth. And now, the important part... look at the red curve. It is for the fish body T. More specifically, it is the T of the pectoral muscle; the fish had been fitted with a thermocouple, and allowed to swim freely (though on a leash). You can see that the fish T is substantially constant, about 14 °C, throughout the time measured. The fish spends substantial time at two different depths, with different water T, but the body T remains 14 °C. This is Figure 1B from the article. I have added the label for the right-hand y-axis, which is, oddly, missing in the article.

In summary, the figure above shows that the fish maintains a pectoral muscle T very near 14 °C, regardless of the water T. That's about 5 degrees above the cold water T experienced for an extended time. That's what warm-bloodedness (endothermy) means. At least within the limits of this experiment, the opah appears to be an endothermic fish.

In another experiment, the scientists measure the T over the entire body of a freshly killed specimen. That whole body T profile shows that the whole body is warm. One thing that stands out is the region of the heart, which is unusually warm. Keeping the heart warm allows the animal to swim better in the cold water.

How does the fish do it? Well, the scientists do some anatomical work. A fish, like any animal, is exposed to the environment, at the surface and where the environment intrudes. For a fish, that is the gills. The opah has an unusual arrangement of blood vessels. Blood that gets cooled in the gills is quickly reheated by being passed near warm blood. Engineers would call such a process "counter-current heat exchange." This heat exchange is done right in the gills; the cold blood is not allowed to cool the animal body. The opah not only keeps its body warm, and its heart extra-warm, but we can begin to see how it adapts to achieve its own form of warm-bloodedness.

It's an interesting study. Limited endothermy in fish has been noted before, with some parts of the body kept warm; this is called "regional" endothermy. But the opah is perhaps the most endothermic fish yet found, with its whole body kept warm. The warm heart is striking and novel. As typical of new observations, there is much more we would like to know. For example... Is the fish still able to maintain the same body T in even colder water? Does its ability to maintain T limit its range?

News story: First fully warm-blooded fish: The opah or moonfish. (Science Daily, May 14, 2015.) Includes a picture of a person holding an opah; that will give you an idea of the size and appearance of the fish (and of the lead author of the article). The fish shown is not a particularly large specimen; apparently, some can be two meters across.

Video. There is a short video associated with the article, as supplementary material. The video shows underwater footage of an opah swimming. It is also available at YouTube. (30 seconds; no sound)

The article: Whole-body endothermy in a mesopelagic fish, the opah, Lampris guttatus. (N C Wegner, Science 348:786, May 15, 2015.) Check Google Scholar for a freely available pdf; there is one from NOAA, the government agency where this work was done.

Background post about endothermy: Were dinosaurs cold-blooded or warm-blooded? (August 23, 2014). This post suggests that dinosaurs were mesotherms -- intermediate, as are some fishes.

More: Facultative endothermy: a lizard that is warm-blooded in October (February 1, 2016).

Another comical fish... CO₂ emissions threaten clowns (September 20, 2010).

Also see:
* The oldest known dog leash? (January 23, 2018).
* The role of mutation in heart disease? (April 25, 2017).
* A drug for heart hypertrophy? (March 4, 2016).
* Fish make their own sunscreen (September 29, 2015).
* How the giant panda survives on a poor diet (August 2, 2015).
* Increased risk of congenital heart defects in offspring from older mothers: Why? and can we do anything about it? (July 18, 2015).

A simpler way to make styrene

July 10, 2015

Styrene is a major commercial chemical. Most famously, it is used to make the common and useful plastic polystyrene. A new article offers a new way to make styrene.

The following figure serves as a framework for our discussion. It outlines the current and proposed pathways to make styrene.

The key to developing the new process was finding a good catalyst. Such work typically involves a lot of trial and error building on previous experience. Catalysts are often expensive metals, and the ability of the catalyst to survive for a long time without degradation is critical to the economics. Here, the scientists found a catalyst based on rhodium that appeared quite stable over the periods tested; that was a big improvement over previous work with platinum.

In fact, they had made the change from Pt to Rh because they predicted that Rh would work better. The Pt catalyst, which contained oxidized Pt, was reacting to form Pt metal, effectively eliminating the catalyst. Rh is less likely to react this way; their results confirm the prediction.

Ultimately, the choice of a process is largely driven by economics, and further work will be needed to address that seriously. For now, the new process looks promising. As noted above, it is simpler and need less energy. It makes fewer by-products; this has two advantages: it increases the efficiency of use of the benzene (a fossil fuel resource), and it simplifies purification of the product. On the other hand, the reaction rate so far is probably not good enough, and the reaction has been studied only at lab scale.

News story: Novel catalyst used to make styrene in one step. (H Zeiger, Phys.org, May 5, 2015.)

The article: A rhodium catalyst for single-step styrene production from benzene and ethylene. (B A Vaughan et al, Science 348:421, April 24, 2015.)

If you're curious... The rhodium compound used as the catalyst is (^FlDAB)Rh(TFA)(η²-C₂H₄), where ^FlDAB is N,N'-bis(pentafluorophenyl)-2,3-dimethyl-1,4-diaza-1,3-butadiene and TFA is trifluoroacetate. There is a drawing of the structure in the article; it is compound 1 in Figure 3.

* * * * *

Posts about catalyst development include...
* A tunable catalyst (July 25, 2022).
* Low temperature treatment for auto exhaust? (February 18, 2018). Lonks to more.
* 2 + 2 = 4: Chemists finally figure it out (October 9, 2015).
* Turning lignin into a useful product (April 11, 2015).
* Photosynthesis that gave off manganese dioxide? (July 21, 2013).
* Hydrogen cars? (June 24, 2009). Go on to the discussion on the supplementary page.

More about polystyrene: Polystyrene foam for dinner? (October 19, 2015).

More about plastics...
* A "greener" way to make acrylonitrile? (January 6, 2018).
* History of plastic -- by the numbers (October 23, 2017).
* Shark skin inspires design of a new material to reduce bacterial growth (March 13, 2015).
* Degradable polyethylene isn't (October 17, 2011).

This post is listed on my page Introduction to Organic and Biochemistry -- Internet resources in the section on Aromatic compounds.

July 8, 2015

Quiz: What is it, and ... ?

July 7, 2015

1. What is it? 2. How old is it? You may well be able to guess what kind of animal this skeleton is from. As to age... Well, if we bothered to ask... Answers below. This is reduced from the figure in the news story listed below. It is probably the same as Figure 1A from the article.

Answers and discussion...

The picture shows a sponge. The picture was taken by scanning electron microscopy (SEM).

As to its age... Well, it is old. In fact, it is the oldest known sponge, as reported in a new article. It's about 600 million years old. That dates it to about 60 million years before the start of the Cambrian era, which was marked by an explosion of animal diversity.

Molecular biologists estimate that animals appeared at least 700 million years ago, but physical evidence for them is weak. The sponges are one of the oldest groups of animals. This specimen gets us a little closer to the beginning of Animalia.

The article shows many more images, both from SEM and X-ray analyses (CT scans). Some are at much higher resolution than this one. The specimen is in excellent condition. The overall anatomy is very clear, and many cell types are apparent.

The authors name this novel sponge Eocyathispongia qiania.

News story: Oldest known sponge found in China. (B Yirka, Phys.org, March 10, 2015.)

The article, which is freely available: Sponge grade body fossil with cellular resolution dating 60 Myr before the Cambrian. (Z Yin et al, PNAS 112:E1453, March 9, 2015.)

Previous post about a sponge: Theonella's secret: Entotheonella (March 18, 2014).

A post about simple animals: A novel nervous system? (July 20, 2014). This post is about comb jellies; it links to other posts about the simplest animals.

* Previous quiz: Quiz: What are they? And are they a threat to you? (October 20, 2014).
* Next: Quiz: What is it? (August 17, 2015).

Our Loki ancestor? A possible missing link between prokaryotic and eukaryotic cells?

July 6, 2015

Bacteria, archaea, eukaryotes. Three domains of equal rank, all coming from a shared ancestor. In recent decades that has been the dominant view of the top level of classifying organisms. However, an alternative view has been put forward: that the eukaryotes are more a branch off the archaea than they are a domain of equal rank. Sometimes this seemed little more than speculation, but some significant supporting evidence has emerged in recent years. Both the traditional three-domain view and the eukaryotic-branch view have been noted in Musings posts [links at the end]. In any case, we do not really understand how the eukaryotic cell arose.

We now have a report of a newly discovered microbe that may help us understand the origin of eukaryotes. It is a microbe -- an archaeon -- that is more like a eukaryote than any other known microbe. (We use "microbe" here to refer to the bacteria and archaea, collectively called the prokaryotes.) Let's look at what we know -- and don't know -- about this novel bug.

The heart of the story is based on sequencing DNA from sediments in the Arctic Ocean near a thermal vent. Preliminary analysis suggested there were some novel organisms, so sequencing was continued. The result was a fairly complete genome, with some interesting features. It is an archaeal genome; in fact, it is very near the group of archaea that has already been suggested to be closest to the eukaryotes.

Importantly, this new archaeal genome contains numerous genes that are characteristically eukaryotic-like. For example, the genome seems to code for proteins that might relate to phagocytosis, a process of cells taking up things by surrounding them with a membrane. This is a process typical of eukaryotic cells, but not of prokaryotes. Not only might this reveal the origin of phagocytosis, it could be useful for some of the suspected early steps in making the first eukaryotic cells, by taking up other bacteria, destined to become mitochondria. The scientists also got partial sequences for two other archaea that seem to be related.

The scientists have tentatively named this new microbe Lokiarchaeum. Along with the related partial sequences, it is the founding member of a suggested new phylum, the Lokiarchaeota. Interestingly, their best fit to a good family tree placed the eukaryotes with this Lokiarchaeota group.

A new family tree for diverse archaea, incorporating the Lokiarchaeota, which are newly reported here.

Focus on the yellow-shaded block. It includes the three Loki genomes (one complete and two partial) noted above; these are collectively labeled Lokiarchaeota. That yellow block also contains the Eukarya -- closer to the Lokiarchaeota than to anything else. Also note the label TACK at the right. This brackets a group of archaea that had previously been suggested to be eukaryotic-like. The new Lokiarchaeota group is within TACK, and is the closest archaea to the eukaryotes yet known.    This is Figure 2b from the article.

A picture of this new bug? We don't have one. In fact, the scientists have not seen it at all. They have not isolated it. They have inferred its existence by analyzing the DNA in an environmental sample. They find pieces of DNA that seem to connect together to make the chromosome with the properties described here. This is a common approach nowadays; it is made possible by rapid inexpensive DNA sequencing, which allows samples to be sequenced even though we do not have the organisms. The approach is called metagenomics.

What are we to believe? We have genome evidence for a novel and interesting microbe. It is a lead. It may help the scientists find the organism that goes with this genome. It may lead to finding other genomes, related or similar. When (if?) more evidence becomes available, this could lead to a better understanding of how eukaryotes arose. However, even if the current article correctly describes the new microbe, there is no assurance that it has anything to do with the ancestry of eukaryotes. Perhaps there are many other eukaryotic-like archaea out there, yet to be discovered; the current work is a reminder that there is more to discover.

This article provides some novel and tantalizing evidence, on which we can build all sorts of speculations -- and future work. An intriguing story.

News stories:
* Newly found microbe is close relative of complex life. (P Rincon, BBC, May 6, 2015.) Includes a picture of Loki's Castle, after which the new bug is named. (If you want to know who Loki was, check Wikipedia.)
* Prokaryotic Microbes with Eukaryote-like Genes Found -- Deep-sea microbes possess hallmarks of eukaryotic cells, hinting at a common ancestor for archaea and eukaryotes. (J Madhusoodanan, The Scientist, May 6, 2015.)

* News story accompanying the article: Evolution: Steps on the road to eukaryotes. (T M Embley & T A Williams, Nature 521:169, May 14, 2015.)
* The article: Complex archaea that bridge the gap between prokaryotes and eukaryotes. (A Spang et al, Nature 521:173, May 14, 2015.) Check Google Scholar for a freely available preprint pdf.

Background posts about the three-domain model and the origin of eukaryotes:
* Origin of eukaryotic cells: a new hypothesis (February 24, 2015). Another model.
* Are there really three domains of life? (January 12, 2013). Discussion of the possibility that eukaryotes arose from within the archaea. Compare the family tree shown above with the one in this post.
* Carl Woese and the archaea (January 12, 2013). Discovery of the archaea.

Major follow-up posts (Loki is an Asgard):
* An Asgard in culture (February 4, 2020).
* The Asgard superphylum: More progress toward understanding the origin of the eukaryotic cell (February 6, 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 Musings posts on the topics.

This post is noted on my page Unusual microbes.

Book... See my page Books: Suggestions for general science reading: Forterre, Microbes from Hell (2016). Forterre addresses the nature of Loki, which was published just as he was finishing his book.

Magnetic turtles

July 5, 2015

Animal migrations are fascinating. Some involve very long distances. How do the animals know where to go? Some migrations span many years, making them all the more mysterious -- and harder to study.

A new article offers a clue about sea turtle migrations. These animals are born on land, spend many years at sea, and then return to land to reproduce. Remarkably, they return to their birthplace. The new work exploits what is usually considered a difficulty of the system: the migratory cycle is very long.

It has been suspected that the turtles use some magnetic sense to find their birthplace. That hypothesis leads to an interesting prediction... Magnetic fields change. In some places, the magnetic field lines are converging over time: they are becoming closer together. In other places, they are diverging: becoming further apart. The prediction is that if the magnetic field lines are converging, the density of nesting turtles will become higher over the years.

Think about... If the magnetic field lines are converging, it means that two places that were a certain distance apart, magnetically, when the turtles were born are now closer together. In the extreme case, two places that were separate when the turtles were born may now be in essentially the same place. So when the turtles come back and look for their birthplace, they end up closer together, or, in the extreme, in the same place.

The following figure shows the data...

The graph reflects how the density of nesting turtles has changed during the study period for regions of converging and diverging magnetic isolines. An isoline is a line between places of a particular value of the magnetic field. Exactly what the y-axis shows is unclear. I think it is the average of all the changes observed for two-year steps.    This is Figure 2 from the article.

It's clear: the density of nesting turtles has been increasing in regions of converging magnetic isolines. The observation supports the hypothesis.

It is a simple and elegant experiment. It does not require collecting data about individual turtles from birth to return. (It merely requires checking the records, both of nesting sites and magnetic lines.) We also caution, as always... this is a piece of evidence, not a proof. Nevertheless, for now, one can imagine that a baby turtle is imprinted with the magnetic address of its birthplace. When it returns from the sea years later, it looks for that same magnetic address. How either of those steps is done is open.

News story: For sea turtles, there's no place like magnetic home. (Science Daily, January 15, 2015.)

* News story accompanying the article: Animal Navigation: Memories of Home. (J L Gould, Current Biology 25:R104, February 2, 2015.)
* The article: Evidence for Geomagnetic Imprinting and Magnetic Navigation in the Natal Homing of Sea Turtles. (J R Brothers & K J Lohmann, Current Biology 25:392, February 2, 2015.)

It was already known that these turtles had a magnetic sense, which they used for navigation. What's new here is showing that it plays a key role in returning to the birthplace to form a new nest.

* * * * *

Other posts about migrations include...
* Anne's journey across the Pacific (July 6, 2018).
* Offering the monarch butterflies milkweed may not be good for them (May 5, 2015).
* The First Americans: the European connection (February 8, 2014).

More about magnetic fields...
* The nature of a bio-compass? (June 10, 2016).
* Can blind rats learn to use a geomagnetic compass? (June 29, 2015).
* What if your compass pointed south? (October 24, 2014).

More about sea turtles...
* Red color vision in dinosaurs? (October 17, 2016).
* What did Osedax worms eat before there were whales? (May 30, 2015).
* Why might it be good to put lights on fish nets? (September 9, 2013).
* Where is turtle #92587? (February 22, 2011). Part of a project to track individual turtles.

July 1, 2015

Can blind rats learn to use a geomagnetic compass?

June 29, 2015

We use our senses to inform us about the environment. Using a sense involves detecting the signal, then integrating it, using our brain, so that we make use of the information. For example, our eyes detect light; they send a signal to the brain, which decides what to do with the information.

An earlier post showed that rats can make use of a novel sensory system [link at the end]. A new article presents another example.

In the new work, the rats were equipped with a geomagnetic compass, located on the head and connected to the brain. The rats learned to use the compass as information about absolute direction.

The following figure shows some examples of the results. In these experiments, blind rats were to find a food pellet in one arm of a simple T maze. The y-axis shows the percentage of successful trials vs day of testing.

In Part B (upper)... The blue curve shows the results for blind rats. They showed about 50% success over the entire time period. That is what is expected if they are making random choices about which direction to go. The red curve shows the results for the blind rats that got to use the compass. The compass sensor was ON (sending a signal) at certain time periods, as shown by the bars at the top. You can see that when the sensor was turned on, the rats quickly learned which direction to go. When the sensor was turned OFF, they lost their sense of direction. When it was turned back ON, they quickly regained their sense of direction.

Part C (lower) shows another experiment. The rats again learned to find the food by using the compass sensor. In this case, the position of the food was switched to the other arm of the maze after day 6. At that point, the high success rate turned to a high failure rate. Remember, the compass provided information about absolute direction. The rats had learned to "go east"; now, "east" was not useful, but the rats still did it. They quickly learned, and a high success rate was soon re-established.    This is part of Figure 2 from the article.

It works. Rats can use a compass. Blind rats now have a sense of direction.

Now, we need to emphasize that this does not mean that the rats understand what a compass does. The rats are responding to a signal received in the brain, and associating it with food success (or failure). But isn't that the heart of how sensory signals work? Do rats understand how odor receptors work even as they use them to find their food? Did ancient man?

Would this work for humans? Why not? Would it be good for blind people to have a compass wired into their brains? Perhaps, though there may be good alternatives for solving the particular problem. Would this be useful for sighted people? But those questions are too narrow. The present work is another example showing how much potential the mammalian brain has. It is another example of how we can develop new inputs to the brain, correcting existing defects, or adding new capabilities.

News story: Geomagnetic compass hooked to the brain allows blind rats to 'see'. (Kurzweil, April 3, 2015.)

The article: Visual Cortical Prosthesis with a Geomagnetic Compass Restores Spatial Navigation in Blind Rats. (H Norimoto & Y Ikegaya, Current Biology 25:1091, April 20, 2015.)

Background post, on adding a sensory skill: Can rats touch infrared light? (February 25, 2013). The article discussed here is reference 10 of the current article.

Is this related? Can one rat know what another rat is thinking? (April 8, 2013). Note that there is a linked post about similar work with humans.

The use of magnetic field information by animals is not, per se, novel. What's new here is how a non-natural sensor has been integrated into the rat brain. A post on magnetic field detection by animals: Magnetic field perception (June 16, 2010).

More...
* The nature of a bio-compass? (June 10, 2016).
* Magnetic turtles (July 5, 2015).

More about brains is on my page Biotechnology in the News (BITN) -- Other topics under Brain (autism, schizophrenia).

Human gracility

June 26, 2015

A pair of recent articles make some interesting measurements on humans -- and draw an interesting conclusion.

The scientists measure certain bones. They interpret the results as reflecting strength. And the conclusion is that humans are getting soft, perhaps due to our lifestyle.

Humans have become couch potatoes, due to television? No, they are looking at a longer time scale. They measure human bones that span millions of years.

Here is an example of the results...

The graph shows the trabecular bone fraction (TBF) for various bones from various primates. The TBF, shown on the y-axis, is a measure of bone density. The primates are listed across the x-axis. The first is the chimpanzee; the others are various hominins, in order by age. Results are shown for three leg bones, color coded as shown in the key (lower right).

Look at the results for the femur (thigh bone), in red (the left bar of each set). The striking result is that the TBF (or density) for this bone is lower for "recent moderns" (the right-hand set) than for any of the other primates shown here. The asterisk on the femur bar for recent moderns shows that the difference is statistically significant. The results for the tibia (long bone of the lower leg) and metatarsal (a foot bone) are similar. Trabecular bone is bone with open space in it; the marrow is in that open space. The TBF shown above is the fraction of the bone that is mineralized, as judged by examination of a cross section. This is Figure 3B from the first article. (Figure 3A shows a similar analysis for arm bones. The trend is the same, though the effect may be smaller for the arms.)

That's the main direct conclusion: modern human leg bones are less dense than in our ancestors, including the "early modern" humans. That latter category seems to include humans older than about 10,000 years. The "recent" humans are from museum collections, and are hundreds or a few thousands of years old.

What is the significance? One possibility was that bone density changed simply as the human body plan was developed. That doesn't seem supported by the results here, which show a major change in density rather recently. The lower bone density may have resulted from humans changing lifestyle in a way that reduced the mechanical loading on the bones. What was this lifestyle change? The timing might be consistent with the beginning of agriculture. Interesting speculation. (Emphasize that the results shown above are not sufficient to lead to that point. However, there is more, especially in article 2.)

In thinking about this work, it's important to keep the steps separate. The scientists suggest that humans are getting weaker. They start with measurements, and then there are stages of interpretation. There is much to wonder about, starting with the question of how representative the results are, and going on to the timing of the change. All that will probably be the subject of further discussion -- and presumably more data.

I used the term gracility in the title, but haven't used it since. What is gracility? We are more gracile than our ancestors studied here: we have less bone mass per body weight. In non-technical English, gracile means slender or graceful. There is an implication here that humans have become more graceful because we became weaker.

The articles speculate on the relevance of the findings to the likelihood of bone fracture and osteoporosis.

News story: Lightweight skeletons of modern humans have recent origin. (Phys.org, December 22, 2014.)

The articles, which are published together:
* 1) Recent origin of low trabecular bone density in modern humans. (H Chirchir et al, PNAS 112:366, January 13, 2015.)
* 2) Gracility of the modern Homo sapiens skeleton is the result of decreased biomechanical loading. (T M Ryan & C N Shaw, PNAS 112:372, January 13, 2015.) A similar analysis, with more emphasis on the timing of the change in human bone density, and what its implications are. In particular, they find a difference in bone density between forager and agriculturist humans.

More about bone density: A new, simple way to measure bone loss? (September 14, 2012).

Also see: Do animal bones have something like annual growth rings? (August 7, 2012).

June 24, 2015

Learning to use a mirror

June 22, 2015

If you see yourself in a mirror, do you recognize that it is you? If you saw a mark on the forehead of your image in the mirror, would you check your own forehead? That's a standard type of test used to determine if an animal is self-aware. Human children usually pass the test starting at 18-24 months of age. A few other animals can pass the test. People vary in how they interpret the significance. There are, perhaps, various reasons why an animal might fail the test.

A recent article makes a useful contribution to the mirror test for self-awareness. Rhesus monkeys usually do not pass the mirror test. However, the new article shows that they can be taught to do so.

The general strategy in the new work is to get the monkeys to associate their mirror image with something significant about themselves. Thus the scientists train the monkeys with marks that are irritating and they couple success with a food reward. Once the monkeys learn to pay attention to the mirror image, they do check themselves when the image shows something unusual.

Here is an example of the results with seven (male) monkeys that had been trained to pay attention to what they saw in the mirror.

A dye mark was applied to the monkey. You can see the mark at the left of the monkey's eyes. The monkey is touching the mark. As we will see in a moment, he does that only if a mirror is available.

The graph to the right summarizes the results from many tests. In this case, the test was with a red dye, as indicated by the line color. Each line is for one monkey. Each line has two points, without and with the mirror (- and + on the x-axis, labeled mirror). The y-axis is the number of times the monkey touched the mark during the allotted time. You can see that the number of proper touches increased for each monkey when the mirror was present. The red bars to the left and right of the main set of data lines show the means for the set of monkeys, with error bars. You can see that the mean increased substantially when the mirror was present. This is part of Figure 1D from the article. Additional parts of the figure show the results using other dye colors. The qualitative conclusion is the same.

There are variations of the test; the general result is the same. The monkeys that have been trained to pay attention to the mirror now pass the mirror test for self-awareness. (The monkeys differ in how well they did, as you can see above. Two of the monkeys consistently did relatively poorly, and completely failed certain tests.)

Untrained monkeys do not pass. Based on the new work, the interpretation is that the monkeys do not pay attention to the mirror image, rather than that they don't see themselves in the mirror. Is that the right interpretation? We'll see how things proceed from here. In any case, it does seem that these monkeys can at least be taught to pay attention to their image in the mirror, whatever the explanation may be.

Trained monkeys given free access to the mirror used it to examine themselves. This behavior has been found in some other animals that pass the mirror test.

News story: Monkeys can learn to see themselves in the mirror. (Science Daily, January 8, 2015.)

* News story accompanying the article: Animal Cognition: Monkeys Pass the Mirror Test. (K Toda & M L Platt, Current Biology 25:R64, January 19, 2015.)
* The article: Mirror-Induced Self-Directed Behaviors in Rhesus Monkeys after Visual-Somatosensory Training. (L Chang et al, Current Biology 25:212, January 19, 2015.)

Videos. There are six short movie files posted with the article at the journal web site. I think you need journal access to get to the movies. Each is less than one minute long. There is no narration, but they are well-labeled (and also referred to in the text). There is no sound, except for some background noise, including an occasional monkey vocalization. Movie S3 is a good place to see a monkey with a mirror.

An earlier post on the mirror test: Self (October 8, 2008) discusses work showing that a magpie can recognize itself in the mirror. The article there discusses other mirror work. As you read about mirror work, be sure to distinguish two phenomena. One is animals that can use a mirror to find things. The other is the specific recognition of self in the mirror; it is this phenomenon that is the subject here.

Previous monkey post... Use of instructional videos -- in the wild (November 3, 2014).

Fracking: the earthquake connection

June 19, 2015

Is there a connection between fracking and earthquakes? In some cases, the evidence strongly suggests clear that there is, but in other cases there is no connection. Can we make sense of all this?

Fracking, or hydraulic fracturing, is a method for breaking up rock formations that contain fossil fuels by injecting high pressure fluids into them.

Scientists have been trying to analyze the effects of fracking; perhaps a consensus is emerging on some points.
* First, it is most likely not fracking, but rather the waste water disposal associated with fracking that is the major culprit. That's an important distinction; the route to solving the problem depends on understanding what the problem really is. (As we will see, it's more complicated than this, but this is a useful point.)
* Second, the effect depends on the location -- on the ground structure. In certain areas of Oklahoma and Texas there has been a dramatic increase in earthquakes correlated with fracking. (In fact, Oklahoma has replaced California as the earthquake capital of the US.) On the other hand, fracking activities in California and North Dakota seem without effect.

We note here one new article that is part of this story. It is an analysis of the activities around Azle, Texas (just south of the Oklahoma border). This is an area of active fracking -- and a lot of earthquakes since the fracking was started. The general approach is that the scientists try to model the area, and consider what the forces are that may affect ground movement.

The following figure is a diagram of the area. As you look at the figure directly, you are looking at a cross-section, from the surface down a few thousand meters to the "basement".

That simple view might suggest that the salt water aquifer, the layer where waste water is injected, is most likely to directly affect the ground structure responsible for earthquakes. That is where large amounts of water accumulate. Further, water gets drawn from that layer, as a byproduct of the production wells. That is, the overall activity involves relatively large and rapid changes in water pressure, both increases and decreases. in that layer. That's over-simplified, of course.

The article uses the model for quantitative analysis of the forces and how they change; the general picture fits that simple overview. It is the water movements in and out of the salt water aquifer that are most likely to cause earthquakes. Waste water injection is a major part of this. These movements can create small but significant pressure changes, enough to trigger already stressed fault regions nearby. The pressure changes due to these movements are clearly larger than those due to changes in the surface lake or fresh water aquifer.

This analysis leads to suggestions about how to reduce earthquake risk from fracking. Clearly, it would be best to not inject waste water very near basement that contains potentially active faults. It also follows that people (including regulatory authorities) should be alert to increases in earthquake activity associated with fracking; the increases may well be a warning sign -- one that is easy to heed.

What's most important here is the type of analysis. It is probably one of the best analyses yet done on such a system. It leads to interesting conclusions, but it also has limitations. The authors emphasize the need for more data to allow better modeling. As noted below, industry has raised some concerns about the model. If that leads to good open discussion about the modeling, that's good over the long term. Analysis such as this leads to better understanding of the risks, and allows proper action to minimize harm.

News stories:
* SMU-led seismology team reveals Azle findings: Combination of gas field fluid injection and removal is most likely cause of 2013-14 earthquakes. (Southern Methodist University (SMU), April 21, 2015.) From the lead institution, which is in Dallas, near the study area. Excellent overview of the work, with good information about context. The page links to various items of news coverage.
* Five Questions about SMU's New Azle Earthquake Study. (S Everley, Energy In Depth, April 21, 2015. Now archived.) This page is from an industry group. Not surprisingly, it expresses an industry-biased position, and raises some questions about the study. What I found striking about the page was how much industry agrees with. Clearly, industry is concerned about an over-reaction: using the fear of induced earthquakes to impose major restrictions on fracking. Of course, they will tend to under-estimate the risk and resist even minor restrictions. Open discussion, with many views represented and based on good science, is the way forward. Regulatory agencies should look at all the evidence. In fact, regulatory agencies in both Oklahoma and Texas have signaled their interest in the kind of analysis reported here.

The article, which is freely available: Causal factors for seismicity near Azle, Texas. (M J Hornbach et al, Nature Communications 6:6728, April 21, 2015.)

Posts about fracking include:
* Fracking and earthquakes: It's injection near the basement that matters (April 22, 2018).
* Hydraulic fracturing (fracking) and earthquakes: a direct connection (February 13, 2017).
* Fracking: one scientist's perspective (January 5, 2016).
* Quality of oil and gas wells -- fracking and conventional (August 18, 2014).
* Shale gas recovery using hydraulic fracturing (fracking) (October 7, 2013). Useful overview of fracking.

More about earthquakes...
* Does the moon affect earthquakes? (October 21, 2016).
* How PBRs survive major earthquakes; why being near two faults may be safer than being near just one (September 22, 2015).
* Earthquake: Are the geologists responsible for the damage? (November 17, 2014).
* Could we block seismic waves from earthquakes? (June 23, 2014). Links to more.

June 17, 2015

The advantage of menopause: grandma knows where dinner is

June 15, 2015

Menopause -- the loss of reproductive ability in older females -- is a somewhat mysterious phenomenon to biologists. It's not common; it is found in only a few animals besides humans. The key question that concerns biologists is: what is its advantage to the species? Biologists suspect that the older females, while no longer reproducing themselves, help promote the survival of the younger animals, through some form of care-giving. This is sometimes called the "grandmother effect", but it is largely a hypothesis.

In an earlier post, Musings noted a study of killer whales (orcas), one of those few species that has a menopause. A long term study of an orca population suggested that the presence of older (menopausal) females promoted survival, especially for males. [link at the end]. There was an effect, but there was no evidence reported there for any explanation.

A recent article, with further observations of that same killer whale population, offers more. It looks at which whales provide leadership during foraging. The following graphs summarize the key findings...

The figure shows who provides leadership in the whale excursions. The x-axis shows a measure of leadership, the y-axis shows how often it occurs. (It is hard to explain exactly what either scale is showing, but the idea is simple enough. The basic observation is that the whale in front of a group that is swimming together is called the leader. The rest is data presentation, which is complex.) In frame C (upper), there are results for male and female whales. You can see that the curve for females (pink) is shifted towards the right. That is, the females have higher leadership scores; the females show leadership more often than males.

In frame D (lower), the results for females are subdivided into two groups: those of reproductive age and those that are postreproductive (menopausal). You can see that the curve for postreproductive females (darker) is shifted towards the right. This means that postreproductive females show leadership more often than those of reproductive age.    This is Figure 1 parts C and D from the article.

In both cases above, the effect is quantitative, not absolute. This is not a highly differentiated society, with a distinct role for the menopausal females. The observation is that the menopausal females are more likely to be leaders.

Further analysis suggested that the leadership role of the menopausal females was greatest in times of food shortage. That is, it may be that the role of these elder females is most important in times of hardship. It may be that they hold the cultural knowledge about where the food is. But careful, we are going beyond the data. (The graph showing this effect, Figure 2, is not very convincing. The conclusion by the authors is based on a more thorough statistical analysis.)

That's it. The results suggest that menopausal females play an enhanced role as leaders -- in killer whale populations.

News stories:
* Menopausal killer whales are family leaders. (N Weiler, Science, March 5, 2015.)
* Old mothers know best: Killer whale study sheds light on the evolution of menopause. (Science Daily, March 5, 2015.)

The article, which is freely available: Ecological Knowledge, Leadership, and the Evolution of Menopause in Killer Whales. (L J N Brent et al, Current Biology 25:746, March 16, 2015.) A very readable article.

Background post about whale menopause: Killer whales: menopause (October 1, 2012).

Previous post about whales: If it quacks like a whale... (August 25, 2014).

Other dinner stories include...
* Polystyrene foam for dinner? (October 19, 2015).

The aroma of rain

June 13, 2015

A light rain falls. It smells good! Why? Because the impact of the raindrops on the soil aerosolizes the soil surface, releasing soil chemicals into the air.

That may sound reasonable. What's new is that scientists at MIT have captured the process with high-speed video. A recent article reports their findings.

Here is one small set of frames from their videos, just as a teaser.

A water drop hits the ground and bursts, resulting in a pillar of water rising into the air above. The water carries with it volatiles from the soil. It all happens in less than 2 milliseconds.    This is Figure 1 parts d-g from the article.

Of course, there is more to it. What happens depends on the speed of the falling rain drops and on the nature of the soil surface. The aroma will depend on what is in the soil. But the key point here is that the scientists have opened this up for study. They address some of the variables, but start by simply getting a sense of their experimental system.

The experimental conditions are described by two parameters, W_e and P_e. These are defined, but not clearly described in the article. In part, W_e represents the energy of the water droplet and P_e represents the porosity of the surface it hits. The scientists vary both parameters over wide ranges; it seems that aerosol generation is best if the two values are of similar magnitude.

Movies. There are several short videos with the article. However, there is a single longer video at YouTube; it shows the results for many trials, with various conditions. Start by exploring it. In each sequence, you are watching a water drop hit a tiny bit of soil. You will see columns of water rise from the surface. If you get a little bored with it, skip ahead to about 4 1/2 minutes. At that point, a wind is added, labeled "air blowing". Look at what it does to the droplets. Movie. (YouTube, 5 minutes -- representing perhaps 2 seconds total of action. No sound.)

News stories:
* Why Does Rainfall Leave Behind a Scent? (J Maynard, Tech Times, January 16, 2015.)
* Sure can smell the rain. (G-Soil, Soil System Sciences Division of the European Geosciences Union, February 24, 2015.) The English is a bit rough here, but the page starts with a quotation from a Verdi opera.
* Rainfall can release aerosols, study finds. (J Chu, MIT News, January 14, 2015.) From the lead institution.

The article: Aerosol generation by raindrop impact on soil. (Y S Joung & C R Buie, Nature Communications 6:6083, January 14, 2015.)

More raindrops...
* Fossil raindrops and the density of the ancient atmosphere (May 6, 2012). (And post immediately following it.) 2.7 billion years old.
* How big are rain drops? And why? (July 23, 2009).

And also... Weather report from Titan: Clouds? Puddles? Does that mean it rained? (April 6, 2011). I wonder what it smells like. And whether anyone is there smelling it.

More droplets:
* How water droplets damage hard surfaces (June 18, 2022).
* What determines the size of liquid droplets from a sprayer? (September 21, 2018).

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

The mystery of the first dinosaur found in the state of Washington

June 12, 2015

At the right is the bone that is of interest here. The smaller of the bones shown here -- the one the people are examining -- is the actual fossil that was found. This is one of the figures from the news story listed below. Their figure legend: "Burke Museum Curator of Vertebrate Paleontology Dr. Christian Sidor, and Brandon Peecook, University of Washington graduate student, compare Washington's first dinosaur fossil to the cast of a femur (thigh bone) of another theropod dinosaur."

That's it. It is the first dinosaur fossil from the state of Washington. It's identified as a leg bone from a theropod, the kind of dinosaur typified by Tyrannosaurus rex. The people in the figure above are the authors of a new article describing the find.

So what's the mystery? The western United States has been the source for many dinosaur bones. Why is this one so special -- other than the local excitement of Washington state getting its first? Is there some reason why that state had not previously provided dinosaur fossils? In fact, there shouldn't be dinosaur fossils in Washington. The land area we now call Washington state was pretty much under water during the age of the land animals we know as dinosaurs.

The bone was found in the San Juan Islands, off the coast of the mainland. It had clam shells in the hollow part. The authors suspect that this bone was washed up to Washington over the ages, probably from much further south. But they don't know. For now, the state of Washington proudly displays its first dinosaur fossil in its state museum -- and wonders why it is there. Another reminder that the fossil record is not simple.

News story: Burke Museum Paleontologists Discover the First Dinosaur Fossil in Washington State. (Burke Museum of Natural History and Culture, University of Washington, May 19, 2015. Now archived.)

The article, which is freely available: The First Dinosaur from Washington State and a Review of Pacific Coast Dinosaurs from North America. (B R Peecook & C A Sidor, PLoS ONE 10:e0127792, May 20, 2015.)

We use the term dinosaur here in the traditional sense. With the general recognition that modern birds are part of the dinosaur lineage, birds are properly called dinosaurs. The term non-avian dinosaurs would be appropriate here.

A recent post with another caution about the fossil record: What did Osedax worms eat before there were whales? (May 30, 2015).

More that doesn't belong in Washington state: Could a common food plant be used to make rubber? (March 27, 2015).

Previous post about dinosaurs: What caused the dinosaur extinction? Did volcanoes in India play a role? (April 13, 2015).

Of birds and dinosaurs... How the birds survived the extinction of the dinosaurs (June 6, 2014).

T rex census (May 25, 2021).

June 10, 2015

What's the connection: rotten eggs and high-temperature superconductivity?

June 8, 2015

There are two addenda to this post, dated July 15 and September 12, 2015. They add information and formal publications.

It's probably well known that the famous odor of rotten eggs is due to hydrogen sulfide, H₂S.

It's probably not well known that the material that holds the record for high temperature superconductivity is that same H₂S. In fact, it was only reported last December. The article reporting it has not yet been officially published, but it is receiving considerable attention, so let's look. The claim must be taken as tentative, and there is uncertainty about what chemical is actually doing the superconducting. Nevertheless, it's an interesting development.

There is a claim, and there are results to support it. Here are some results...

The graph shows the electrical resistance of the sample (y-axis) at various temperatures (T; x-axis). Focus on the right-hand (green) curve. This is for "sulfur hydride" (another name for hydrogen sulfide). It is at a pressure of 177 gigapascals. (1 GPa = 109 Pa ~ 10,000 atmospheres.) Superconductivity is a low-temperature phenomenon, so look at the curve here starting from a high T, at the right. That is, "normal" is to the right (high T), and "things happen" as you go to the left (low T). You can see that the resistance of the sample drops slowly as T is reduced (move to the left) -- until about T =185 K. At that point, the resistance drops precipitously to near zero, and remains there as T is reduced further.    This is Figure 1b from the Drozdov article.

That curve demonstrates superconductivity, the flow of electricity without resistance. The T where the resistance drops rapidly and approaches zero is called the critical temperature for superconductivity, or T_c. (Remember, conductivity is the reciprocal of resistance. Zero resistance means the sample is superconducting.) For this sample of H₂S, T_c is 185 K. The previous record for high T_c was 164 K.

The red curve? That is for sulfur deuteride, the same chemical but with the heavy isotope of hydrogen called deuterium. Comparison of the curves for different isotopes shows that the mass of the hydrogen is important. This is an important finding for those working on the theory of superconductivity, but we will leave it for now.

In another experiment reported in the same article, the scientists measured T_c = 191 K for a sample of H₂S. The data for this is shown in the tiny inset of their Figure 2b. Getting the higher T_c required some tricks in sample preparation. This may be a clue about the nature of the superconducting material; we'll note this again below.

There are two general types of superconductivity. One is called conventional, and conforms to a theory worked out many years ago. The other doesn't follow this "BCS" theory -- and is not understood. The record for highest T_c for the conventional superconductors is 39 K. That record of 164 K noted above is for one of those mystery-class superconductors. You can see that the mystery superconductors are well ahead of the ones that are understood.

What about the superconductivity of H₂S? Scientists have worked on the theory. In fact, theory predicts that H₂S will be a superconductor, of the "conventional" BCS type. More specifically, a recent article suggested that H₂S will superconduct up to about 80 K. Testing that prediction was the motivation for the current work. The current work confirms that H₂S superconducts -- but finds a T_c about 100 kelvins higher than expected!

And that brings us to the second part of this story. It is likely that it is not really H₂S that is superconducting. We hinted at this above when we noted that getting the T_c = 191 K result required some fiddling. It is likely that the H₂S first undergoes a chemical reaction at the ultra-high pressures -- making a new material that is the actual superconductor. What might that new material be? Perhaps H₃S, according to some of the modeling. H₃S? Think... 3 H₂S --> 2 H₃S + S. Something like that. Strange things happen at those pressures. It is known that S is not a good superconductor, but the compounds with more H may well be good superconductors.

One group has even predicted that the T_c of the high pressure H₂S, whatever it is at that pressure, would be 194 K -- very close to the 191 K observed.

So what do we have, if the new work is confirmed? A record high temperature for superconductivity. The new record (185 K or perhaps even 191 K) is a significant improvement over the previous 164 K, and a huge improvement over what had been found for "conventional" BCS superconductors. Further, it is with a simple chemical -- though perhaps it is not as simple as we might think under the extreme conditions.

For practical use, one would like to have superconductivity at high temperature and low pressure; ambient conditions would be fantastic. For physicists, superconductivity is still full of surprises. Finding that H₂S -- or H₃S -- is now the high T record holder, and is "conventional", is just the latest surprise.

This post is based mainly on the December article, which announced the experimental result.

News stories:
* Superconductivity record breaks under pressure. (E Cartlidge, Nature News, December 12, 2014.) Good overview.
* High Temperature Superconductivity Record Smashed By Sulphur Hydride. (Physics arXiv Blog, December 9, 2014.) A little more technical, with good consideration of why physicists are cautious about accepting the new claim.

The article, which is freely available: Conventional superconductivity at 190 K at high pressures. (A P Drozdov et al, preprint posted at ArXiv, December 1, 2014.) The status of this article is not clear. However, it is being widely discussed, as the following articles attest.

Follow-up, if you want to go further...

News story, for article #1, below: Secret of record-breaking superconductor explained. (H Johnston, Physics World, April 24, 2015.)

The articles:
1) High-Pressure Hydrogen Sulfide from First Principles: A Strongly Anharmonic Phonon-Mediated Superconductor. (I Errea et al, Physical Review Letters 114:157004, April 17, 2015.)
2) What superconducts in sulfur hydrides under pressure and why. (N Bernstein et al, Physical Review B 91:060511, February 2015.) Check Google Scholar for a freely available copy.

Another case of an abrupt transition from less conducting to more conducting, in this case as the pressure increases: Metallic hydrogen? (March 16, 2012). From the same lab. The article discussed in this 2012 post is reference 17 of the current article. (Caution... The claim here has been challenged; see the linked follow-up post.)

A major new development which can be seen as a follow-up to the current work: Superconductivity in lanthanum hydride: a new temperature record (June 8, 2019).

And then... Superconductivity at room temperature -- at last (October 18, 2020).

Another conductivity story: Electricity in DNA: guarding your genes? (December 16, 2009).

More on unusual chemistry at high pressures:
* How many atoms can one nitrogen atom bond to? (January 17, 2017).
* Novel forms of sodium chloride, such as NaCl₃ (January 17, 2014). By the way, the pressure used in the current work is about three times that used in the work discussed in this earlier post on sodium chlorides.

The biology of hydrogen sulfide, H₂S...
* Why does a durian smell so bad? (February 14, 2017).
* Garlic or rotten eggs? (February 8, 2010).

* Previous "What's the connection" post... Quiz: What's the connection... (February 14, 2012).
* Next: What's the connection: blue cheese, rotten coconuts, and the odorous house ant? (August 24, 2015).

More, July 15, 2015...

There is some new information available. The authors of the article posted at ArXiv last December have extended the work. They have now shown an additional property that helps to characterize what they observed as bona fide superconductivity. In fact, they now claim 203 K as T_c, a bit higher than before. A news story from Nature News outlines this, and also notes that other labs have confirmed the findings (thought not yet published).

Here is the new item from Nature News... Superconductivity record bolstered by magnetic data. (E Cartlidge, Nature News, June 29, 2015.)

It links to a new article from the authors of the work -- still only at ArXiv, where it is freely available. The new article is reference 2 of this news story.

This story is developing, but we must caution again that we lack formally published articles.

More, September 12, 2015...

Briefly, the story is that hydrogen sulfide has been shown to act as an electrical superconductor at higher temperatures than found previously for any substance. It seems likely that the actual superconducting material is not H₂S itself, but a reaction product under the high pressures used, likely H₃S.

The work has generated much excitement, but so far all we have had are preprints posted at ArXiv. We now have a formally published article. The more recent article posted at ArXiv, noted in the July 15 addendum, has now been published in Nature. There is no new content, but the news stories are new. The one from Nature News notes the very limited independent replication of the work so far, based on informal inquiry of those likely to be able to do so. I should add that the information on this point here is somewhat different from what the same author said in his previous news story. A caution to keep in mind.

Remember, if you cannot access the Nature article, the versions posted at ArXiv are freely available. The news stories in Nature are freely available; they link to the ArXiv items.

News stories:
* New temperature record: Hydrogen sulfide becomes superconductive under high pressure at minus 70 degrees Celsius. (Phys.org, August 18, 2015.)
* Superconductivity record sparks wave of follow-up physics. (E Cartlidge, Nature News, August 17, 2015.) Includes a useful list of references to the related articles.

* News story accompanying the article: Superconductivity: Extraordinarily conventional. (I I Mazin, Nature 525:40, September 3, 2015.)
* The article: Conventional superconductivity at 203 kelvin at high pressures in the sulfur hydride system. (A P Drozdov et al, Nature 525:73, September 3, 2015.)

The measles vaccine: What does it protect against?

June 6, 2015

If you answered measles, that's a good start.

However, there may be much more to the story. A new article suggests that the measles vaccine reduces the rate of mortality due to all infectious causes.

Let's look at some of the evidence behind this claim...

The graph compares the mortality (death) rate due to non-measles infectious diseases with the incidence of measles, over a 25 year period in England and Wales. The measles vaccine was introduced there in about 1968. The first observation is that there is a general correlation: the higher the incidence of measles (x-axis), the higher the mortality due to other infectious diseases (y-axis).

The data points on the scatter plot are color-coded by year; see the color key at the upper right. Simplifying a bit to get you started... The reddish points are for early years, pre-vaccine; these years tend to have high measles incidence. Bluish points are for later years, mostly after the vaccine was introduced; these years tend to have lower measles incidence -- and lower mortality due to other infectious diseases. For example, you can see that most of the bluish points are low on the y-axis scale. It is intriguing that the mortality rate for the non-measles diseases is lowest after the introduction of the measles vaccine. This is Figure 1E from the article. The full figure also shows similar analyses for the United States and Denmark. The dates analyzed are different for each country, partly because the measles vaccine was introduced at different times in the different countries. The general trend was the same in each case.

That graph, alone, does not show the reason for the correlation. There is clearly a lot of scatter in the data; the correlation coefficient shown is significant but not high. The graph is a hint, not an answer. It is a hint that there may be something interesting going on; it is (part of) the starting point for further investigation.

Where does one look for a possible connection? To the immune system. It has been known for some time that measles suppresses the immune system. That can lead to an enhanced susceptibility to other infections. For a few months -- it was thought. In fact, more recent work has shown that measles causes loss of memory cells in the immune system, an effect that may last for a few years.

Here is the idea that is developing... Measles is not only a serious disease in its own right, but it increases deaths due to other diseases by damaging the immune system. The measles infection can eliminate cells in the immune system that protect a person against other diseases. The measles vaccine protects against measles, and in so doing protects against all the other diseases that measles infection would allow.

It's an interesting story; we'll see how well it holds up upon further examination.

News stories:
* Measles Weakens the Immune System for Years. (K Smith-Strickland, Discover, May 7, 2015.)
* What the Measles Vaccine Could Do for Public Health -- Measles may weaken immune system for several years, vaccine may indirectly prevent other infectious diseases. (B Greenwood, dailyRx News, May 9, 2015. Link is to an archived copy.)

The article: Long-term measles-induced immunomodulation increases overall childhood infectious disease mortality. (M J Mina et al, Science 348:694, May 8, 2015.)

Recent posts about measles:
* Fallout from the Ebola outbreak: more measles? (April 28, 2015).
* What if Mickey Mouse got measles? (January 27, 2015).

There is a section of my page Biotechnology in the News (BITN) -- Other topics on Measles. It lists related posts.

Using a plasma to kill norovirus

June 5, 2015

Norovirus is one of the most important agents of food poisoning. It is easily transmitted -- and hard to inactivate.

A recent article explores an unusual approach for reducing the amount of norovirus on surfaces, and offers some encouraging results. Here is an example of the results...

The graph shows the reduction in the amount of norovirus (y-axis) vs treatment time (x-axis). Note that the y-axis is a log scale; -1 on the y-axis means there was a 10-fold reduction. Three conditions are shown, with different symbols and lines. The general picture is that the treatment leads to around a 10-fold reduction in the amount of virus. Longer treatments give greater virus reduction, at least for a while.    This is Figure 2 from the article.

What is this treatment? As the label on the x-axis indicates, it is "cold plasma". Plasma is a form of matter that consists largely of charged particles (ions); the ions are highly reactive, and that is the basis of how the plasma kills.

Is this useful? The results here show that this particular type of plasma has some effectiveness in killing norovirus on surfaces. That's a start. The authors argue that the method is practical, say, for common surfaces in a hospital -- and that it would lead to a significant reduction in virus load. However, the article does not have any direct comparison of this method to others, although we know that killing norovirus is difficult. Bottom line? An intriguing result, which deserves follow-up.

News stories:
* Cold plasma treatment cuts norovirus germs. (Science Daily, January 13, 2015.)
* Cold plasma kills off norovirus, German scientists find. (Cleanroom Technology, February 19, 2015.) Caution, this page mixes up bacteria and viruses. The page is from equipment folks, not microbiologists.

The article, which is freely available: Inactivation of a Foodborne Norovirus Outbreak Strain with Nonthermal Atmospheric Pressure Plasma. (B Ahlfeld et al, mBio 6:e02300-14, January 2015.)

Norovirus is a difficult virus to work with. There is no good lab assay for infectious virus. The current work used PCR analysis of the viral RNA. It is plausible that this assay underestimates the effectiveness of the killing.

The cold plasma is being investigated for other medical applications. It is considered safe for humans; I do wonder how solid that view is.

A norovirus story: Possible transmission of norovirus via reusable grocery bag (May 21, 2012).

More... An organoid for the gut: at last, a culture system for norovirus (October 30, 2016).

Perspective... The cost of food poisoning (October 14, 2014).

An early Musings post on food poisoning is... Killer chickens (December 2, 2009). It includes an extensive list of related posts.

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

Another application of plasma: Improving soybean oil by using high voltage plasma (January 9, 2017).

Also see... An antiviral coating for medical textiles (July 12, 2020).

June 3, 2015

A clinical trial of ice cream

June 2, 2015

It's good.

This is one of those stories that sounds odd in some ways. On the other hand, it is actually a rather nice piece of science. It deals with an important issue. It is based on an interesting premise, and involves a nice test, even if rather small.

The premise? That probiotic bacteria night help prevent tooth decay in children. The scientists, from dental schools in India, choose to examine two species of bacteria commonly considered probiotic: Bifidobacterium lactis and Lactobacillus acidophilus. It's not obvious they would be good choices as dental probiotics, but there is some background work supporting the choice.

How do we deliver dental probiotics to children? Food, perhaps. And what is every child's favorite food -- world wide? Ice cream, apparently. The authors spend some time in the article making the case for ice cream.

The trial? Give children ice cream that contains the probiotic bacteria. Test them. Of course, we need a placebo: ice cream that doesn't have the bacteria added.

The scientists thus arrange for the children to get their ice cream. This is a short and simple trial; what they do is to check the children's saliva for caries-promoting bacteria, Streptococcus mutans. The ice cream treatment, with or without probiotics, is for 7 days. The scientists measure the bacteria in the children's saliva before and after the treatment, as well as at a couple of later times to see if the effect persists.

It worked. The children with the probiotic-containing ice cream had fewer of the bad bacteria. The effect wasn't big, but it seemed significant. An encouraging first result. Perhaps ice cream with a higher load of the probiotic bacteria, and used over a longer time, would be more effective. The effect wore off a few months after the ice cream treatment stopped; not a surprise.

It's a small step, and needs further work. In particular, they need to show whether it actually affects tooth decay over the long term. All they measured here was a short term "proxy"; since it was encouraging, they need to move on and measure "the real thing". Doing that will require that they find more children willing to endure the treatment.

News story: Probiotic ice cream may boost oral health for kids. (S Daniells, NutraIngredients-USA.com, April 28, 2015.) I am unfamiliar with the source, but the page appears to be a good presentation of the work.

The article, which is freely available: Effect of Probiotic Containing Ice-cream on Salivary Mutans Streptococci (SMS) Levels in Children of 6-12 Years of Age: A Randomized Controlled Double Blind Study with Six-months Follow Up. (D Ashwin et al, Journal of Clinical and Diagnostic Research, 9:ZC06, February 2015.)

More about probiotic bacteria...
* Would a probiotic reduce sepsis in newborn babies? (October 20, 2017).
* Staph fighting Staph: a small clinical trial (April 8, 2017).
* How to administer Bt toxin to people? (May 16, 2016).
* Could we treat obesity with probiotic bacteria? (August 5, 2014).
* How probiotics work: a clue? (October 11, 2010). Discusses Lactobacillus.

More dairy...
* The nutritional value of yogurt? (September 28, 2018).
* The oldest known piece of cheese (April 25, 2014).

More about tooth decay: Is fluoride neurotoxic to the human fetus? (December 13, 2017).

SyAMs: Synthetic drugs that act like antibodies

May 31, 2015

Antibodies are useful drugs, but they are expensive, and their size limits how they can be used. Can we do better? Can we design small, cheap molecules that would do the job? It's a tall order, but a recent article offers some encouraging results, at least in principle. Simply trying to do it requires a careful look at what it is antibodies do.

Here is the idea...

If this works as intended, then the immune system cell should be activated if added to the prostate cancer cells plus the SyAM, which brings them together. As a first step to testing this, the scientists used PSMA-tagged beads (rather than cancer cells); that's done for experimental convenience. Here are some results...

This is a test to see if the three-part system shown above works. We'll leave the technical details, and simply note that the y-axis is a measure of whether the immune cells are activated. Look at the blue bars -- the ones to the right of the dashed vertical line. They show the activation as a function of SyAM concentration (x-axis). You can see that the activation increases as the SyAM concentration increases. That's good. The x-axis scale is odd, so be careful about interpreting it. The main point is that the bars are in order of increasing concentration. However, they are not evenly spaced, on either a linear or logarithmic scale. The "1" in the header and x-scale refers to compound 1, which is the SyAM of interest.    This is Figure 2 part F from the article.

So it works. At least it works with tagged beads. It actually took some further development to get a SyAM that worked with real cancer cells, but they achieved that, too. They have made a synthetic molecule that acts like an antibody. It's impressive. It's also not clear how useful it is -- at this point. This "small" molecule is rather big. It was expensive to design and it would be expensive to make. It remains to be seen whether something useful can come of this, but it is a fascinating development. The current article offers the first steps, and led to useful progress as well as considerable understanding.

News stories:
* New class of synthetic molecules mimics antibodies. (Science Daily, December 17, 2014.)
* The Immune System, In Pill Form: SyAMs May Treat Cancer, HIV, And Autoimmune Diseases. (Medical Daily, February 11, 2015.)

The article: Chemically Synthesized Molecules with the Targeting and Effector Functions of Antibodies. (P J McEnaney et al, Journal of the American Chemical Society (JACS) 136:18034, December 31, 2014.)

A post about using an antibody therapeutically: Rotavirus: passive immunization via food (January 10, 2014).

A post that introduced the general Y-shape of antibodies: A more powerful method for measuring what is in a cell (July 23, 2013).

More about antibodies: Should we make antibodies to HIV in cows? (November 14, 2017).

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

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

May 27, 2015

What can we learn by looking at the DNA in vampire bat feces?

May 27, 2015

We can learn what they eat.

Analyzing feces for remains is a common way to study what an animal eats. However, vampire bats consume only the blood of their prey, and blood doesn't leave remains. Or does it?

A new article examines vampire bat feces for DNA. The scientists can identify the source of the DNA; that source was the bats' prey.

To do this, the scientists worked out a simple DNA test that allowed them to distinguish the source of DNA found in the bat feces. They focused on a single (mitochondrial) gene; the DNA sequences for this gene for several relevant organisms were already in the databases. The scientists amplified the DNA from the feces, and after treatment with selected restriction enzymes, ran it on a gel. The gel pattern distinguished the source of the DNA: pig, chicken, cow, dog, human, vampire bat. They worked this out with controlled experiments using captive vampire bats fed a single type of blood. They then looked at samples from "the wild" -- 18 villages in Brazil's Amazonia.

The following graph shows what kind of DNA was found in feces of vampire bats collected from villages in two localities (groups of villages).

The figure shows that the strongest signal is for pig, with much smaller signals for chicken and cattle. We'll explain the detail of the y-axis scale later, but what you see here is the authors' main conclusion. This is part of Figure 3 from the article. The other parts show the separate results for the two localities; they are similar.

In addition to the three food sources shown above, a low level of dog DNA was found in bats from one area. Human DNA was not found; the authors do note that attacks of vampire bats on humans were reported in one village under study. None of several other possible wild vertebrates were detected; apparently these bats have adapted to living around humans populations and their farmed animals -- even in the rather primitive Amazon jungle. No "host" (vampire bat) DNA was detected.

Now, things aren't quite that simple... The graph above shows a preference for eating pig. However, the raw data showed that about 2/3 of the DNA samples were from chicken. That is, chicken was the most common prey. Why does the graph say pig? The scientists normalized the raw results by the availability of the various prey. That is, they divide the number of DNA samples found for each prey by the population size for that animal. When they do that, they get the "selection ratio", which is what is shown on the y-axis above. The value shown for pig is about 8; this means that the bats choose pig about 8 times more often that expected from their availability. Chicken may be the most common prey, but when population size is taken into account, it seems that the bats prefer pig.

Comment... Normalization is obviously a good idea. Clearly the availability of various prey affects how often they are consumed. However, I'm not at all sure that normalizing the raw data by the number of available prey is the right approach. After all, pigs are much bigger than chickens. If the data were normalized by surface area, surely the preference for pig would be lost. Would that be better? I don't know. How does a vampire bat choose its food? Is a large animal a better target? The authors present both raw data and the results normalized by number (shown in the figure above). They mention the size issue, as well as other possible reasons for the bats preferring one or another food. These include that pig blood may be more nutritious than chicken blood. My point here should be taken as a question, not a criticism.

News story: Vampire bats have a taste for bacon. (C Cesare, Science, April 10, 2015.) Bad title... They don't eat bacon; they consume blood.

The article, which may be freely available: Prey preference of the common vampire bat (Desmodus rotundus, Chiroptera) using molecular analysis. (P E D Bobrowiec et al, Journal of Mammalogy 96:54, February 2015.)

More about vampire bats:
* The biological basis of sanguivory (March 2, 2018).
* How to find the blood (August 29, 2011).

Previous post about bats: The use of wing clicks in a simple form of echolocation in bats (May 22, 2015).

More about pork... Cooking pork (June 4, 2011).

Other vampires: Quiz: What is it? (November 20, 2012).

More about feces:
* What can we learn from 17,000-year-old cat feces? (September 16, 2019).
* The effect of defecation by whales on global warming (August 2, 2010).

How graphs can mislead

May 24, 2015

A new article discusses how graphs, especially bar graphs, can be misleading. In fact, that is the central topic, and purpose, of the article.

The following figure illustrates the concern...

What's the point? Each of those data sets looks different. A careful scientist will have different reactions to the data in frames B and E. Yet each data set is summarized by the same bar graph. If all we see is the bar graph, then we don't know what the data is behind it.

The table below the graphs makes the same point in a different way. The table shows the p values that would be calculated for each data set. That is the probability that the observed distribution would be found by chance. To make things even more interesting, three different ways of calculating p are shown. You can see that the p values range from 0.035 to 0.128. It's common to use p = 0.05 as a cutoff for whether the results are statistically significant. The bar graph in frame A may or may not show a statistically significant difference -- depending on what the data is behind it (and depending on the test used).

Why is the bar graph a problem? The bar graph is a summary of the data. In contrast, the other frames show the actual data. (Simple analogy... The mean of a set of data is a single number that summarizes the data set. It doesn't tell you about how the points are arranged.) The authors argue that all too often authors of articles show a summary when it would be better to show the actual data. Summaries are useful. They hide the details, and help us see the big picture. They hide the details, and keep us from seeing what is going on. Take your choice. At least, be aware of the choice; don't just blindly substitute a summary for the real thing.

Bad graphs is a pet peeve of mine. I've noted some bad graphs from time to time... graphs that are poorly labeled, poorly laid out, too crowded to be readable; various reasons. I've even thought of collecting bad graphs -- and perhaps featuring them somewhere. The current article is a part of that story. And it is getting attention among scientists.

When you make a graph, for whatever reason, think about what it is for. Choose a graph that shows what you want to show. It's even reasonable that you may want to make more than one graph of the same results.

From the abstract of the article: "We recommend training investigators in data presentation, encouraging a more complete presentation of data, and changing journal editorial policies."

News story: Data Presentation Matters: A Partial Solution to the Reproducibility Crisis. (Mike the Mad Biologist, April 28, 2015.)

The article, which is freely available: Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm. (T L Weissgerber et al, PLoS Biology 13:e1002128, April 22, 2015.)

One reason for crowded graphs in scientific journals is that some journals restrict how much space graphs can have. At times, the journals effectively insist that the graphs be too small to read. One such journal with such a policy offers its own feature articles with graphs that are often incomprehensible, for one or another reason. My sense is that the graphs are made by artists not scientists. The first purpose of a graph is to convey information.

An example of a post where I noted a confusing graph: Where is the control knob for global warming? (November 16, 2010). (I'm sure there are others, even "better" ones. But offhand, I don't know where.)

One issue above is the meaning of p values. We have discussed that before, such as: More on the story of p (March 2, 2014).

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

May 20, 2015

Can you make a 777 by printing it?

May 19, 2015

777? As in Boeing 777 passenger jet.

No. But engineers at GE Aviation have (almost) printed a jet engine, albeit a small one. It's more an engine for a hobbyist's remote-controlled model airplane than for a 777. Still, it is a functioning jet engine.

The parts. All of these parts were printed. (However, the assembled engine contained some parts that were from sources other than printing.) This is reduced from a figure in the Kurzweil news story; an equivalent figure is in the GE story. Both of those pages include a picture of the assembled engine; it provides a sense of scale.

They have also printed a part for the 777, and it was recently officially approved by the (US) Federal Aviation Administration (FAA) for use -- on real 777s. (It's a T25 sensor housing; no matter.)

3D printing, or additive manufacturing, is a technology that is rapidly developing. It builds on the long-familiar inkjet printer. We've noted other achievements from time to time; some are listed below. 3D printing is actually a set of technologies, as scientists learn new ways to use materials. In this case, they are printing metals.

Let's modify that first negative answer I gave above. How about... Not yet.

There is no peer-reviewed article here. This post is based on two pages from GE, which Kurzweil picked up. We briefly note them as newsworthy events.

News story: A 3D-printed mini jet engine that performs at 33,000 RPM. (Kurzweil, May 13, 2015.)

Here are the two GE pages. Both are linked to in the Kurzweil story.
* These Engineers 3D Printed a Mini Jet Engine, Then Took it to 33,000 RPM. (M Keller, GE Reports, May 9, 2015. Now archived.) Includes a video of the engine in operation.
* The FAA Cleared the First 3D Printed Part to Fly in a Commercial Jet Engine from GE. (GE Reports, April 14, 2015. Now archived.)

Here are a couple of previous posts on 3D printing; they link to more.
* 3D printing for space: a titanium woov, and more (April 29, 2014).
* 3D printing: simple inexpensive prosthetic arms (January 29, 2014).

Among posts on airplanes... An ion-drive engine for an airplane? (February 15, 2019).

The iron war

May 17, 2015

A recent article makes an interesting contribution to a couple of stories. First, iron is an important nutrient. It is essential for all aerobic organisms. However, it can be difficult to obtain, since the common form of iron is quite insoluble in neutral solution. Second, pathogens and hosts engage in evolutionary warfare. Hosts develop resistance to pathogens; pathogens overcome host resistance. Repeat. Over and over. It is sometimes argued that such "warfare" is a major driving force behind evolutionary development. (That idea is sometimes referred to as the Red Queen hypothesis. There is lots of action, but no one gets anywhere.)

The current article connects those two stories. Pathogens and host both require iron as a nutrient. In a pathogen-infected host, they compete for the same iron. The article provides evidence for the evolutionary war as they compete for the iron.

The following figure shows the idea...

There are three frames in the figure. We need to understand the first, at the left, in some detail, before following what happens later.

In that first frame several things are depicted. The two dark round things (upper right) are parts of a transferrin molecule. Transferrin is a protein that vertebrates use to carry iron ions. The small reddish circles are iron ions, Fe3+. You can see a small red Fe3+ circle on each large dark transferrin circle. The green oblongs are for the transferrin receptor. (There are two oblongs. They are actually different, but we can largely ignore that here.) The transferrin receptor is also called transferrin binding protein (Tbp) in some organisms. The big horizontal structure is a cell. The upper (lighter) part is the cell membrane. The lower part is the cytoplasm. (No, the C at the lower left doesn't stand for cell. It identifies this as part C of a larger figure.) How does this all work? The transferrin receptor spans the membrane. Transferrin binds to the receptor. The receptor takes iron ions from the transferrin and releases them to inside the cell (at the bottom). That's the basic idea of how transferrin, along with transferrin receptor, works. Now what? Well, in this figure, that membrane is a bacterial cell membrane. It is the membrane of an invading pathogen -- and the pathogen needs Fe3+, too. It makes its own analog of a transferrin receptor, to steal the host's iron. That's what the iron war is about. The next two frames are variations of that left-hand frame. They show some of the war moves, over evolutionary time. The host can score by mutating its transferrin so that it can't bind to the pathogen's receptor. This is shown in the middle frame. There is a little off-color region near the bottom of the transferrin; that represents a mutation -- which prevents binding to the receptor. The inverted T-shaped symbol ( ⊥ ) between the transferrin and the receptor is a common way to show that a step is blocked. (Of course, the mutant transferrin still binds fine to the host's own receptor.) The pathogen can score by mutating its receptor protein so that it now binds the host's new transferrin. This is shown in the right-hand frame. The transferrin has that same mutation as before (light patch); the receptor now has a "matching" light patch. The mutant pathogen receptor now binds the mutant transferrin, and the pathogen is back in business.    This is part C of the Figure in the news story accompanying the article.

That's the idea. Remember, the figure is a cartoon -- of what we think is happening. Evidence? The article examines the genes for human transferrin and for certain bacterial transferrin receptors. The results show hot-spots for mutational changes at precisely those sites of contact. That is, mutations are more frequent at the contact sites than at other sites. That's evidence that selection has occurred. The frequency of a mutant gene depends on how often the mutation occurs, but also on how well the mutant gene fares over time. Mutations that provide an advantage increase in frequency; that is "positive selection". In this case, the evidence suggests that both host and pathogen are making changes supported by positive selection.

Why is there a selection for these mutations? According to the model (and the cartoon figure above), it is because the host transferrin mutations reduce the ability of pathogens to damage the host, and because the pathogen mutations increase the ability of the pathogen to survive. The scientists examine the ability of certain transferrin receptor proteins to bind to certain transferrins, and the results are largely as one might predict from that model. They do not have direct evidence that the mutations provide the suggested benefit; that is an inference from the description of the mutations, and is probably testable.

That's how the iron war is fought. No one is winning. The Red Queen would understand.

News stories:
* Yarr! Humans evolving to escape from bacterial iron piracy -- An evolutionary arms race keeps humans and bacteria right where they started. (D Gitig, Ars Technica, December 13, 2014.) Explains the reason for the name Red Queen hypothesis, if you don't know it.
* Humans Battle Bacteria over Iron as an Evolutionary Prize. (GEN, December 12, 2014.)

* News story accompanying the article: Genetics: The battle for iron -- Evolutionary analysis shows how a mammalian iron transport protein evolves to avoid capture by bacteria. (A E Armitage & H Drakesmith, Science 346:1299, December 12, 2014.)
* The article: Escape from bacterial iron piracy through rapid evolution of transferrin. (M F Barber & N C Elde, Science 346:1362, December 12, 2014.)

More about the iron limitation for growth: Fertilizing the ocean may lead to reducing atmospheric CO₂ (August 24, 2012).

Another post dealing with positive selection of two traits together: Butterflies and UV vision (June 29, 2010).

More about selection... A gene that reduces the chance of successful pregnancy: is it advantageous? (May 18, 2015). This is the post immediately above.

More about membranes: How flippase works (September 25, 2015).

The aphid-bacterium symbiosis: a step toward manipulating it

May 15, 2015

Let's look at some results... The following figure shows how two different strains of aphid fared upon being heated.

The two strains are in the two columns; we'll explain what they are later. There are three types of measurements, one in each row. Look at the top row of results... In this row, the data are for the time it took for adults to emerge. For the left-hand strain (labeled LSR1), this was just under 7 days in the "control" (20 °C; dark bars); it increased to over 8 days when treated with heat (4 hours at 35 °C, at a particular stage of development; light bars). The difference was statistically significant, as shown by the asterisks. In contrast, the right-hand strain showed only a small increase, which was not statistically significant. That is, the right-hand strain seems to be relatively heat-resistant, compared to the left-hand strain.

The other two rows show other measurements in the same system. The middle row is for the weight of the adults; the bottom row is for the number of progeny. In both of these cases, the results are in agreement with the conclusion from the top row: the right-hand strain is relatively heat-resistant.    This is Figure 3 from the article.

What is the difference between these two aphid strains? Why is one more heat-resistant?

To understand this, we need to recall that these aphids carry symbiotic bacteria, called Buchnera. The key in the current experiment is that the scientists replaced the Buchnera that were found normally in strain LSR1 with a more heat-resistant strain. Giving the aphids a more heat-resistant Buchnera made the aphids more heat-resistant.

The name of the right-hand strain is LSR1<5AY. The name describes that this is strain LSR1 with Buchnera from strain 5AY. Note that the direction of the "arrowhead" in the name points to the direction that the bacteria were transferred.

How did they do the replacement? It was known that the LSR1 aphid contained heat-sensitive Buchnera. Step 1 of the replacement procedure was to use the heat treatment to reduce (if not eliminate) the endogenous Buchnera. Step 2 was to inject new Buchnera into the developing aphids. It worked, as the results shown above document.

The major advance in this work was developing the ability to replace one kind of Buchnera with another. This was novel; normally the bacteria are transmitted "vertically", from mother to offspring, not via the environment. Further, the bacteria themselves are obligate symbionts, which cannot be grown in lab culture. The replacement technique allows the kind of experiment seen above. The results show the usefulness of such an experiment: we learn rather directly how the bacterial symbiont affects the host physiology. More will come from this system -- undoubtedly.

News story: Transferring primary symbionts: a missed link? (the aphid room, January 25, 2015.) This news story is no longer available, and is not at the Internet archive. Its original URL was https://theaphidroom.wordpress.com/2015/01/25/transferring-primary-symbionts-a-missed-link/.

* Commentary accompanying the article: Interchangeable allies: Exploiting development and selection to swap symbionts. (N M Gerardo, PNAS 112:1923, February 17, 2015.)
* The article: Experimental replacement of an obligate insect symbiont. (N A Moran & Y Yun, PNAS 112:2093, February 17, 2015.)

More about aphids:
* Underground messaging between bean plants (July 29, 2013).
* Are aphids photosynthetic? (September 17, 2012).
* Red and green aphids (June 2, 2010).

More about bacterial symbionts:
* Can Wolbachia reduce transmission of mosquito-borne diseases? 1. Introduction and Zika virus (June 14, 2016).
* Origin of eukaryotic cells: a new hypothesis (February 24, 2015).
* A quasi-quiz: The fate of bone and wood on the Antarctic seafloor -- and the discovery of new bone-eating worms (August 20, 2013).
* A new organelle "in progress"? (September 13, 2010).

May 13, 2015

The artificial trees in the artificial forest are now fixing CO₂ (and making high-value products) -- naturally

May 13, 2015

About two years ago Musings presented a new system for artificial photosynthesis developed in the lab of Peidong Yang and colleagues at UC Berkeley [link at the end]. By "artificial photosynthesis" we refer to a non-biological process for capturing solar energy and using it to make chemicals of interest. The process uses semi-conductors and nanowires, products of the chem lab. One important point was that the process was modular: they had solutions for parts of the photosynthesis problem, but one could see how these might interact with other modules -- or even be replaced by better modules for the current processes. What was cute about the process was that it looked like a system of artificial trees in an artificial forest -- at the micro scale. I encourage you to read that earlier post somewhere along the way here.

A new article reports new developments in the system: it now fixes CO₂ and makes higher value products. And it does these things "naturally".

The following figure is the authors' summary of the process. It serves as an overview both of natural photosynthesis and their own work, previously and now. It suffers from some bad artwork with the lettering; that seems to be present in all versions of the figure I can find, even at the highest resolution. I'll fill in the text.

How do they get their system to make acetate -- and more? They add bacteria to it. That is, at this point, they make use of the natural ability of bacteria to fix CO₂, given a boost from the electrons of the artificial photosynthesis system. Acetate is one simple product of this bacterial CO₂ fixation. Then, to make the more complex products, they add more bacteria, which convert the acetate to more products.

The new process is a hybrid of chemistry and biology. The initial steps are artificial photosynthesis; the final steps use existing biological processes. Is that allowed? Is that good? The goal is to make a practical process; all options are allowed -- to compete. What they have shown here is that it is possible to make the two types of systems compatible, thus allowing for a hybrid system.

Caution... In the background post we noted that the process was not very efficient. That's still true. This is lab research, developing a new type of process. Substantial improvements in efficiency are needed to make it economical. The scientific progress is exciting (and fun); practical use is a way's off, if it comes at all.

News stories:
* UC Berkeley hybrid semiconductor nanowire-bacteria system for direct solar-powered production of chemicals from CO₂ and water. (Green Car Congress, April 10, 2015.)
* Major Advance in Artificial Photosynthesis Poses Win/Win for the Environment -- Berkeley Lab Researchers Perform Solar-powered Green Chemistry with Captured CO₂. (L Yarris, Lawrence Berkeley National Laboratory, April 16, 2015.) From the lead institution. (The scientists work jointly at the University of California Berkeley and Lawrence Berkeley National Laboratory, a common arrangement.)

The article: Nanowire-Bacteria Hybrids for Unassisted Solar Carbon Dioxide Fixation to Value-Added Chemicals. (C Liu et al, Nano Letters 15:3634, May 13, 2015.)

Background post about the system: An artificial forest with artificial trees (June 7, 2013). Includes pictures of both forest and trees.

Another follow-up: More from the artificial forest with artificial trees (August 31, 2015).

A recent post about bacteria using electrons from the outside: A battery for bacteria: How bacteria store electrons (May 2, 2015).

If you're into the waste product -- maybe even dependent on it... A whiff of oxygen three billion years ago? (April 6, 2015).

More about solar energy development: The energy landscape: looking ahead (August 16, 2015).

Next post on photosynthesis: Photosynthetic sea slugs; species vary (June 9, 2015).

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.

Is the lychee (litchi) a toxic food?

May 11, 2015

The lychee is a subtropical tree; its fruit (or nut) is widely consumed. Yet, in some areas that grow lychee, large numbers of children get sick each year around the time of the lychee harvest; the fatality rate is around 30% (at least of those who get medical attention). The symptoms start with convulsions, and often include extremely low blood sugar; the condition is referred to as a hypoglycemic encephalopathy.

What's going on? A series of articles over the last couple of years has led to a fairly strong hypothesis: lychee contains a poison -- similar to one found in some of its close relatives. The poison is not very potent, but children are susceptible, especially if they are otherwise malnourished.

This is an incomplete story. But it is strong enough and specific enough to lead to actions and further testing. One report has shown that giving an afflicted child intravenous sugar may be of benefit; see the MMWR article listed below. Questions remain. In addition to testing and extending the basic hypothesis... The role of fruit flesh vs seed is one issue. Both pesticides and viruses have been suggested as causal agents in other work, though no specifics were identified. Is there a role for either of these, perhaps in addition to the poison? There is reason to connect the outbreak in India, the focus here, with similar outbreaks in other lychee-growing countries, but, again, this needs to be confirmed.

There is nothing in this work that questions the ordinary consumption of lychee fruit. However, since the story is incomplete, we cannot exclude that more subtle or long term effects of ordinary consumption may be found at some point.

Here are the structures of the key chemicals suspected as neurotoxic from lychee (left) or ackee (right). (Stereochemistry not shown.)

I have named them as derivatives of standard amino acids. You can see that each contains the same unusual group, methylenecyclopropyl, attached to the terminal carbon of a standard amino acid. The only difference between the two is an extra C just before that group in the ackee poison; this reflects the difference between glycine and alanine.    These are my drawings, using the free chemical drawing program ChemSketch.    (If you would like to try ChemSketch, see my page ChemSketch - An Introductory Guide.)

News stories, primarily relating to article #1:
* A compound in litchi behind mystery brain disease? (N Gopal Raj, The Hindu, February 5, 2015.) Good overview.
* Litchi Toxin May Give Rise to Mysterious Epidemic in India. (Tropical Fruit Forum, International Tropical Fruit Growers, January 30, 2015.)

Two recent articles, both freely available:
1) Outbreaks of Unexplained Neurologic Illness -- Muzaffarpur, India, 2013-2014. (A Shrivastava et al, Morbidity and Mortality Weekly Report (MMWR) 64:49, January 30, 2015.) A report from two hospitals in a lychee-growing region. Among other things, the article notes a somewhat lower death rate in the second year, when they immediately treated the hypoglycemia. This was not a controlled trial, and the significance of the finding is uncertain.
2) Probable Toxic Cause for Suspected Lychee-Linked Viral Encephalitis. (P S Spencer et al, Emerging Infectious Diseases 21:904, May 2015.) A half-page note suggesting a connection between the lychee disease and a disease caused by eating ackee fruit. (Their reference #6 is the article I list above as #1.)

Recent posts about food poisoning include:
* Fugu poisoning incident in the United States (January 5, 2015). This also involves a poison that is endogenous to the food.
* Food poisoning outbreak: Listeria infections from caramel apples and fresh apples (January 14, 2015). This involves a food contamination issue.

More fruit... Why does a durian smell so bad? (February 14, 2017).

Another story about a neurotoxic amino acid derivative... How BMAA may cause motor neuron disease -- a clue? (July 1, 2014). There is no connection between these stories, and no implication that the toxic amino acids work the same way.

Another toxin: A new botulinum toxin -- and a story of how we deal with dangerous things (July 11, 2015).

Also see: Killer chickens (December 2, 2009). This is an early post about one food issue; it now includes links to a wide range of posts about food poisoning.

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

Xystocheir bistipita is really a Motyxia: significance for understanding bioluminescence

May 9, 2015

Scientists recently re-discovered a long-lost species of millipede in the California foothills. Examination of it has led to some interesting developments.

Let's start with some data...

	The figure shows two species of millipede, labeled at the top. The top row shows photographs of the animals taken with ordinary lighting. The bottom row shows photographs of the same animals taken in the dark. The only light is from the animals themselves.
You can see that both animals produce light. The inset for frame D (lower right) is a close-up of part of that animal, for emphasis.    This is Figure 1 from the article. I have added the labels at top and left. The scale bars are 5 millimeters.

What do we do with this information? The first issue deals with the identification of the animal at the right. It's quite rare; the recent finding was the first in decades. This animal was not known to be bioluminescent; it had been classified as Xystocheir bistipita. Now, knowing it is luminescent, the scientists have reclassified it as Motyxia bistipita, putting it with other luminescent millipedes.

More importantly, the scientists did some gene analyses of the available species of Motyxia, as well as some related non-luminescent species. By examining the sequences of the same genes over many species, they reconstructed a genealogy -- the most likely order in which the species developed. They found that the brightness of the luminescence generally increased during evolutionary history. The current species, now called Motyxia bistipita, is both the dimmest and the oldest Motyxia.

What does that mean? The common view has been that luminescence in millipedes is a defense mechanism. These animals are poisonous; the light they emit warns predators to avoid a toxic meal. But perhaps this was not the original role of bioluminescence. The scientists suggest that the luminescence was originally part of a response to stress -- perhaps heat stress in the hot mountains. The stress resulted in free radicals; proteins designed to protect against free radicals happened to be luminescent. That is, the protein was primarily an anti-oxidant; luminescence was a side effect. The development of the luminescence as a predator defense came later, building on the low level of luminescence already present for another reason.

It's an interesting model. It illustrates how a gene originally playing one role can get co-opted for another. So far as I can tell, the model is basically just that at this point; there is little evidence for it, beyond finding the general trend that the level of luminescence has increased in younger species. It will be interesting to see how this story develops. Are there alternative models that would fit the data? Is it possible to test the model or any alternative models? In any case, we know a little more about luminescent millipedes than we did.

News stories:
* Researchers shine light on origin of bioluminescence. (Phys.org, May 4, 2015.)
* New Glowing Millipede Found; Shows How Bioluminescence Evolved -- Some California millipedes first evolved bioluminescence to cope with harsh desert living, according to scientists who may have cracked the mystery of glowing millipedes. (C Arnold, National Geographic, May 4, 2015. Now archived. ) Includes some nice video. However, the story incorrectly identifies the source of the millipedes. They are not from the Sierra Nevada range, but from the coastal range, near San Luis Obispo.

The article, which is freely available: Discovery of a glowing millipede in California and the gradual evolution of bioluminescence in Diplopoda. (P E Marek and W Moore, PNAS 112:6419, May 19, 2015.)

The discussion of the role of bioluminescence here is for this group of millipedes. Don't extend it to any other groups of bioluminescent organisms. Bioluminescence plays different roles for different organisms.

More about bioluminescence:
* Milky seas: now observable from space (September 27, 2021).
* Observing inside animals with an improved bioluminescence system (April 6, 2018).
* Lux aeterna: Mushrooms; Mozart (December 7, 2009). Note a follow-up post listed there.

There is a section of my page Internet resources: Chemistry - Miscellaneous on Chemiluminescence.

Also see... Unusual synthesis of cadmium telluride quantum dots (February 15, 2013).

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

Hybrid formation between organisms that diverged 60 million years ago

May 8, 2015

Do you think that humans and lemurs could form a hybrid? That seems preposterous. But a new article reports what appears to be an example of two organisms that diverged about the same time doing exactly that.

The evidence? It's shown at the right: a fern, in nature, that seems to be a hybrid of two types of fern that diverged 60 million years ago.    This is reduced from the figure in the news story listed below.

How do we know it is a hybrid? The original observation was that it looked like a hybrid of two known ferns. Now, scientists have analyzed the DNA of the newly discovered fern, and shown that it consists of genes from those two other fern species. They estimate that those parent ferns diverged 60 million years ago. More specifically... The scientists analyzed one particular region of the genome in detail. They found four copies of the region, indicating that the new fern is tetraploid. Two of those copies correspond very closely to what is found in one of the suspected parents; the other two copies correspond to the other parent. The copies are so close to those of the parents that the scientists believe the hybrid formation was quite recent; there has been little time for the hybrid to diverge from its parent species.

The hybrid fern grows fine, and can be propagated by rhizomes (or "cuttings"), as often true for plants, simple or complex. It seems to be a sterile hybrid, not capable of sexual reproduction. That shows there is a barrier between the two species that hybridized. Nevertheless, it is remarkable that a viable hybrid can form at all.

What does this mean? Is it just that ferns, a very old group, evolve more slowly? The authors suggest that it might have something to do with them being fertilized passively, by the wind. That is, they lack much of the specialization of reproductive organs found in many organisms; maybe this allows them to remain partially compatible over longer time. It will be interesting to see what more can be learned by studying this fern, or by using it as a clue for further work on how species become distinct.

The way the hybrid is named is interesting. The hybrid is called ×Cystocarpium roskamianum. The first character of the name is a times sign, which denotes a hybrid. The parents are ferns of the genera Cystopteris and Gymnocarpium.

News story: Distant species produce 'love child' fern after 60-million-year breakup. (Science Daily, February 13, 2015.)

The article: Natural Hybridization between Genera That Diverged from Each Other Approximately 60 Million Years Ago. (C J Rothfels et al, American Naturalist 185:433, March 2015.) Check Google Scholar for a pdf copy from the authors.

Previous post about ferns: Chromosomes -- 180 million years old? (April 18, 2014). Interestingly, this post makes a point somewhat similar to the current post: that ferns haven't changed much over tens of millions of years. The evidence is completely different.

* A recent post about hybrid formation in nature... What if two of the world's most destructive pests spent the evening together in Fort Lauderdale? (April 4, 2015).
* Also see... Development of a new species of lizard in the lab (May 20, 2011).

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

If you have forgotten what a lemur is...
* Underground hibernation in primates? (October 6, 2013).
* and maybe... Quiz: What's the connection... (February 14, 2012).

May 6, 2015

Offering the monarch butterflies milkweed may not be good for them

May 5, 2015

Monarch butterflies are beautiful, and they have a fascinating life cycle. They migrate long distances, with each migration actually involving multiple generations of animals.

Some populations of monarchs are in serious decline. One factor may be the loss of their special food: milkweed. This was discussed in an earlier post [link at the end]. If that is true, then maybe it would be good to plant more milkweed, to attract the monarchs.

A new article raises a concern about that suggestion. It's an interesting story, perhaps less complete than the news coverage might suggest.

The following figure summarizes a key finding. It shows the level of parasite infection of various populations of monarch butterflies from the eastern United States.

The figure shows the results for four populations (x-axis), with data for two years for each population. The y-axis shows the fraction of the population that is "heavily infected" with a particular parasite of concern. The striking observation is that the right-hand bars are very high. It will serve our purposes here to simply separate the results into two groups: the high bars of the right-hand population, and all the others, which are low.    This is Figure 2 from the article.

What is special about the high-bar population? It is a population of monarchs that does not migrate, but rather stays in the southern US year-round; it is labeled "winter-breeding". Why don't they migrate? Apparently because they have plenty of food where they are. Plenty of milkweed.

The other three sets are for monarchs that are migratory. (Don't try to make sense of the labels without reading the article for details.)

One interesting comparison is between the populations labeled "coastal overwintering" and "winter-breeding". These are populations from about the same area of the southern US. The former is from a migrating population; the latter is from a non-migrating population. The latter, the non-migrating population, has a much higher parasite load.

Here is the issue... The monarchs that do not migrate have more parasites; that is the basic observation. Why don't they migrate? Because they have plenty of food where they are. Why do they have more food? Apparently because they are in areas where is a type of milkweed that grows year-round.

And here is the concern... If people plant milkweed, they are likely to plant the type that grows year-round. That is not the type that grows wild in the east. The monarchs will eat it just fine. They'll eat it year-round -- instead of migrating, and that may not be good for their health. Migration helps to reduce the parasite load.

That's the argument. The results certainly are interesting, and there is logic to the argument. However, it is not clear that all the points are causally connected. It would be nice to see some follow-up, directly comparing the behavior -- and parasite load -- of monarchs offered year-round and summer-only milkweed. As the authors note, simply cutting back the year-round milkweed during the winter may serve the purpose.

In the meantime, if you want to feed the monarchs, don't over-do it.

News story: Plan to save monarch butterflies backfires. (L Wade, Science, January 13, 2015.) Good overview. As the picture suggests, the infection discussed here starts with the larval stage of the butterfly eating the milkweed.

The article: Loss of migratory behaviour increases infection risk for a butterfly host. (D A Satterfield et al, Proceedings of the Royal Society B 282:20141734, February 22, 2015.) Check Google Scholar for a copy.

Background post on monarch butterflies: Genetically modified crops and the fate of the monarch butterfly (April 1, 2012). Includes a picture, with links to more -- and to a site about a California population of the monarchs.

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

Also see: Which came first: butterflies or flowers? (March 9, 2018).

Claim of oldest fossilized cells refuted

May 3, 2015

Here are two sets of figures from a new article. Each set contains three photos of mineral materials, taken by light microscopy. Do you think these are samples of fossils from living organisms? (The three photos in each set go together.)

Figure 3, parts x, y & z.	Figure 5, parts b, c & d.
	↑ Above (Fig 5):    Scale bars (bottom, left or right) are all 10 micrometers. ← Left (Fig 3):    There is a single scale bar, to the left of the top frame, in white. It is 14 µm in frame x, and 10 µm in y and z. Don't worry about the bewildering array of scale bars. Size per se is not an issue here.

Intriguing, aren't they?

Some people see signs of biology in them. They do look something like modern cyanobacteria. Scientists have been arguing about the nature of these samples for years. The stakes are high: if they are from living organisms, they would be evidence for some of the earliest forms of life on Earth. These samples are about 3 1/2 billion years old.

The article examines them more closely than ever before, with the latest technology -- and more information about their context. The conclusion? The one on the left (Figure 3) is not biological, but the one on the right (Figure 5) is. That distinction is important, because Figure 3 is the older material; in fact, it has been claimed to represent the oldest known cells. It was a controversial claim; the authors here suggest it should be discarded. In terms of the timeline of life, it doesn't make much difference: the samples in Figure 5 are almost as old -- only 30 million years younger.

The big message here is the difficulty of telling for sure which ancient samples are biological and which are not. Not only does our casual inspection of the figures above leave the question open, but so does much of the technical analysis. The authors of the new work suggest they have improved methods, and that they can tell. We'll see how well their claim stands up.

What did they do? It's not easy to explain concisely. They used electron microscopy, and looked at the fine details around what appeared to be the cell wall structure. It just didn't look "right" for the samples of Figure 3 -- didn't look like authentic biological material.

But as I hinted above, context was a big clue. Further examination of the Fig 3 materials has suggested they are of high temperature origin. That raised suspicion and led to the more careful analysis. The authors found the differences in detail, and suggest a model for how the cell-like structures arose from flow of hot fluids.

News stories:
* Oldest fossils controversy resolved. (Science Daily, April 20, 2015.)
* Early life hunt inspired by oldest fossils debate. (Oxford University, April 20, 2015.) From the lead institution.

The article: Changing the picture of Earth's earliest fossils (3.5-1.9 Ga) with new approaches and new discoveries. (M D Brasier et al, PNAS 112:4859, April 21, 2015.)

Posts about other old fossils and such include:
* A 1.6 billion-year-old macroscopic multicellular eukaryote? (June 13, 2016).
* Quiz: What is it? (September 23, 2014). The first animals, from around 600 million years ago. The featured specimen is actually a living animal, but the post compares it with early fossils.
* Fossil raindrops and the density of the ancient atmosphere (May 6, 2012). (And post immediately following it.) 2.7 billion years old.
* The earliest biomineralization? (January 24, 2012). Skeletons, 750 million years old.
* The Antikythera device: a 2000-year-old computer (August 31, 2011).
* The oldest known multicellular organisms? (August 21, 2010). 2.1 billion years old.

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

A battery for bacteria: How bacteria store electrons

May 2, 2015

Let's jump in and look at some results. The experiment involves measuring the number of electrons stored in a rock.

In this experiment, two types of bacteria were grown together, with some magnetite, Fe3O4. The growth conditions were switched between light and dark at various times, indicated by the vertical dashed lines. The light and dark growth periods are labeled by the sun and crescent moon, respectively.

The scientists measured the number of electrons in the magnetite. They did this, indirectly, by measuring a property called the magnetic susceptibility, κ (kappa). The graph shows κ on the y-axis; more precisely, it shows Δκ (delta kappa), the change in that property, in percent. You can think of that as a measure of the number of electrons; we'll explain this a little more below. Observe... During the first growth period, in light, κ decreases. It then increases during the next growth period, which is in the dark. That pattern is repeated: κ decreases in each growth period in the light, and increases in each growth period in the dark. It works over the 240 hours (10 days) of the experiment.    This is Figure 2B from the article.

What's going on?

1) One type of bacteria used here produces excess electrons; they are shunted into the magnetite, reducing Fe³⁺ to Fe²⁺.

2) The other type of bacteria used here takes electrons from the magnetite, oxidizing Fe²⁺ to Fe³⁺.

The value of κ reflects the two forms of iron ion. More specifically, κ effectively measures Fe²⁺. Thus the oxidation step (#2), which removes electrons and lowers the amount of Fe²⁺, lowers κ -- and vice versa.

The bacteria of step 1 are iron-reducing bacteria; they reduce the Fe³⁺ to Fe²⁺. The bacteria of step 2 are photosynthetic; they are using the light energy to fuel their growth. They also need electrons, and they get electrons they need from the magnetite.

Overall, the magnetite is effectively serving as a battery, being charged by one type of bacteria during the "night", and discharged by the other during the "day". All the steps here were known; what is new is showing that they can be coupled together, leading to measurable cyclic changes in the electron status of the rock as the environment changes.

This is in the lab under controlled conditions. I wonder what's going on in nature.

The bacteria are Geobacter sulfurreducens and Rhodopseudomonas palustris, respectively.

Magnetite is a common mineral; it contains iron in both the 2+ and 3+ forms. The work here was done with pure synthetic magnetite, in a very fine particulate form.

News story: Bacteria can use magnetic particles to create a 'natural battery'. (Science Daily, March 26, 2015.)

The article: Redox cycling of Fe(II) and Fe(III) in magnetite by Fe-metabolizing bacteria. (J M Byrne et al, Science 347:1473, March 27, 2015.)

On related bacterial tricks...
* On sharing electrons (May 3, 2011). This case may involve direct transfer of electrons from one organism to another; in contrast, the current post involves storing the electrons.
* On sharing electrons -- II (June 9, 2013). A discussion.

More on magnetite... Magnetic field perception (June 16, 2010).

Posts on batteries include...
* Making lithium-ion batteries more elastic (October 10, 2017).
* Flow battery (January 4, 2016).
* Boiled batteries (July 19, 2010).

Also see...
* How seismic waves travel through the Earth: effect of redox state (June 8, 2018).
* The artificial trees in the artificial forest are now fixing CO₂ (and making high-value products) -- naturally (May 13, 2015).

There is more about energy on my page of Internet Resources for Organic and Biochemistry - Energy resources.

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