The Mason’s Apprentice

My latest Seed column slipped quietly onto the interwebs last week — it’s an overview of how the glues that hold multicellular organisms together first evolved in single celled creatures, represented today by the choanoflagellates.

Just as a teaser, the next print edition that should be coming out soon will continue the focus on enlightening organisms of remarkable simplicity with a description of the results of the Trichoplax genome. Get it! You will also be rewarded with a great issue focusing on science policy.

Epidexipteryx

The Mesozoic was inhabited by some strange-looking critters, and here’s another example: a Jurassic dinosaur called Epidexipteryx, which has spiky teeth, big claws, fluffy feathers all over its body, and four long decorative feathers coming off a stumpy tail. It resembles a particularly ugly bird with a nasty bite, but it couldn’t fly — none of the feathers covering its forelimbs are pennaceous, but are more like an insulating fur. Or, alternatively, its feathers were all about display, a possibility suggested by the odd long feathers of the tail. Here are the bones; as you can see, the integument is remarkably well preserved, with a scruffy ruff of short, non-shafted feathers over the body and limbs, and a surprising spray of just four very long feathers coming off the tail.

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(Click for larger image)
a, Main slab; b, c, skull in main slab (b) and counterslab (c); d, four elongate ribbon-like tail feathers; b’, c’, line drawings of b and c, respectively. Abbreviations: l1, l2 and l7, 1st, 2nd and 7th left teeth of upper jaw; l1′, r1′ and r5′, 1st left, 1st right and 5th right teeth of lower jaw; l2 and r2, 2nd left and right teeth of upper jaw.

And here’s what it would have looked like in life (only the colors are imaginary). It would have been about the size of a pigeon — I think a pack of these scurrying about New York’s Times Square would be both scenic and would quickly clean up the pigeon problem there.

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For all the details, read the write-up on Tetrapod Zoology.

Zhang F, Zhou Z, Xu X, Wang X, Sullivan C (2008) A bizarre Jurassic maniraptoran from China with elongate ribbon-like feathers. Nature 455:1105-1108.

Here’s something else Darwin didn’t have

Tracking of the HMS Beagle by a manned space station. I don’t know why; maybe those pre-Victorian Space Engineers had their steam-powered space-stations all tied up trying to find the source of the Nile or plotting invasion routes into Afghanistan, or something. This time around our 21st century panjandrums of outer space have their priorities a bit more in focus, and NASA has committed to using the ISS to watch the new Voyage of the Beagle. Read the Beagle Project for more details.

I’m just relieved that finally we’ve found something useful for these space nuts to do — providing supplemental assistance to a biological and historical project, instead of noodling around staring at space rocks, space debris, and space vapor.

A step closer to efficient solar power?

I have to confess that the title of this paper, The remarkable influence of M2δ to thienyl π conjugation in oligothiophenes incorporating MM quadruple bonds, is Greek to me, that the abstract was impenetrable, and the paper itself was thoroughly incomprehensible. I’m a biologist, not a chemist or materials engineer! Fortunately, there are a couple of summaries that simplify the explanation enough that I can understand the gist of it, and it’s cool stuff. Researchers have made a new material that promises to greatly increase the efficiency of solar cells. It works by collecting photons over a wider spectrum of wavelengths and by using both fluorescence and phosphorescence to create an electron flow, allowing it to both collect more energy per unit area and facilitating the production of current.

This is promising news, and also illustrates why we need to fund basic research — these are the kinds of discoveries that can’t be simply planned and forced into existence, but require the liberty of the research enterprise to explore new ideas freely.

Don’t get too excited just yet, though. The research has uncovered useful properties of a combination of molecules that have only been tested in minute quantities. It remains to be seen if it can be scaled up efficiently, if it can be made cost-effective, and whether it can be simply made to work at a practical level. It’s still an exciting idea — they’re talking about nearly 100% efficiency.

Sometimes ink is just ink

At first, I was a bit disappointed in this result, but then I realized it’s actually rather interesting in a negative sense. Investigators tested the effects of squid ink on other squid; the entirely reasonable idea being that it could contain an alarm pheromone that would have the function of alerting neighboring squid in the school of trouble. It works — adding ink to a tank of Caribbean reef squid sends them scurrying away.

However, when they removed the pigments from the ink and added that, the squid couldn’t care less. That says there is no chemical signal, only a visual signal.

That makes sense, I suppose — oceans are big and would dilute any chemical signal fairly rapidly, so pheromones would only work well over a fairly short range (although some fish certainly do have extremely sensitive olfactory senses, so it could be done). Still, Aplysia eject some potent chemical signals with their secretions, which work when directly squirted into the face of a predator, so there was a chance the cephalopods might have evolved something similar.

Will the availability of C-sections give humans bigger brains?

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While Steve Jones might think human evolution has stopped, I have to say that that is impossible. If human technology removes a selective constraint, that doesn’t stop evolution — it just opens up a new degree of freedom and allows change to carry us in a novel direction.

One interesting potential example is the availability of relatively safe Cesarean sections. Babies have very big heads that squeeze with only great difficulty through a relatively narrow pelvis, so the relationship in size between head diameter and the diameter of the pelvic opening has been a limitation on human evolution. We know this had to be a factor in our evolution: the average newborn mammal has a cranial capacity that is roughly 50% of the adult size, chimpanzee babies have heads about 40% of the adult size, but human babies have crania that are only 23% of what they will be in adults. While our brains have gotten larger over evolutionary time, they have not gotten proportionally larger in utero, because large-headed babies increase the difficulty of labor and cause increased mortality in childbirth. If childbirth could bypass the pelvic bottleneck, that would allow for fetal heads to grow larger without increasing the risk of killing mother and/or child.

And childbirth is a risky proposition for women; 529,000 die every year from this natural process (although only about 1% of those deaths occur in places where women have access to good, modern medical facilities — hooray for modern medicine). About 8% of those deaths occur from obstructed labor, where the fetus is unable to proceed through the birth canal for various reasons, and these are the kinds of birth problems that can be circumvented by C-sections. In practice, teaching health care workers how to carry out emergency C-sections has been tested in regions in Africa, where it has actually worked well at reducing maternal mortality.

This is the subject of an article by Joseph Walsh in the American Biology Teacher, which suggests that C-sections will have an effect on human evolution.

“Nothing in biology makes sense except in the light of evolution.” This was the title of an essay by geneticist Theodosius Dobzhansky writing in 1973. Many causes have been given for the increased Cesarean section rate in developed countries, but biologic evolution has not been one of them. The C-section rate will continue to rise, because the ability to perform a safe C-section has liberated human childbirth from natural selection directed against too small a maternal pelvis and too large a fetal head. Babies will get bigger and pelves will get smaller because there is nothing to prevent it.

The evidence so far is entirely circumstantial, but Walsh makes an interesting case. There are several correlations that imply an effect, but I can’t help but think there are alternative explanations that may swamp out any heritable, evolutionary effect. The kinds of evidence he describes are:

  • A known trend for increasing birth weight in the US, by about 40 g over 18 years in one study. It’s there, all right, but these studies don’t demonstrate a genetic component to increased size — it could be a consequence of better nutrition and medical care.

  • An increasing frequency of C-sections. Again, this isn’t necessarily genetically based at all, but could be a consequence of fads in medicine, or social factors, such as an increase in the likelihood of medical malpractice suits making doctors more cautious.

  • Walsh describes a couple of studies that seem to show that cephalopelvic disproportion (small pelvis or large babies or both together) does have a genetic component. So at least it is likely that there are heritable variations in these parameters that could influence the likelihood of obstructed labor.

  • There is statistical variation in neo-natal mortality that varies with birth weight in a suggestive way. Low birth weight clearly puts infants at risk, and there is an optimum weight around 3600 grams for newborns that minimizes mortality. Death rates also rise with increasing birth weight above the optimum. There is some data that suggest that availablity of modern medical care and C-sections reduces infant mortality at larger birth weights.

That increasing availability of C-sections might lead to an evolutionary shift towards increasing cranial capacity at birth is a reasonable hypothesis, but I’m not convinced that it has been convincingly demonstrated yet. There are too many variables that effect brain size at birth to make a clean analysis possible; in addition, many of the measures are indirect. Often, we use birth weight as a proxy for cranial capacity, and that means the numbers and correlations are sloppier than they should be. Many of the measurements made are of factors that are readily influenced by the environment, which makes it difficult to imply that these are the product of genetics.

So the idea is weakly supported, but tantalizing. Even as a purely theoretical exercise, though, what it does say is that it is obvious that human culture cannot end human evolution…all it can do is shape the direction in which it can occur.

Walsh J (2008) Evolution & the Cesarean Section Rate. The American Biology Teacher 70(7):401-404.

Old scientists never clean out their refrigerators

Blogging on Peer-Reviewed Research

We all know the story of the Miller-Urey experiment. In 1953, a young graduate student named Stanley Miller ran an off-the-wall experiment: he ran water, methane, ammonia, and hydrogen in a sealed flask with a pair of electrodes to produce a spark, and from those simple building blocks discovered that more complex compounds, such as amino acids, were spontaneously produced. Stanley Miller died in 2007, and in going through his effects, the original apparatus was discovered, and in addition, several small sealed vials containing the sludge produced in the original experiment were also found.

This isn’t too surprising. I’ve gone through a few old scientists’ labs, and you’d be surprised at all the antiquities they preserved, all with notes documenting exactly what they are. It’s habit to keep this stuff.

Now the cool part, though: the scientists who unearthed the old samples ran them through modern analysis techniques, which are a bit more sensitive than the tools they had in the 1950s. In 1953, Miller reported the recovery of five amino acids from his experiment. The reanalysis found twenty two amino acids and five amines in the vials. He was more successful than he knew!

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Moles (relative to glycine = 1) of the various amino acids
detected in the volcanic apparatus vials. Amino acids underlined have not been previously
reported in spark discharge experiments. Values for amines are minimum values because of loss due to their volatility during workup.

Yes, I know that Miller’s reducing atmosphere is no longer considered to be an accurate representation of the ancient earth’s atmosphere. However, the experiment still supported a key idea: that the synthesis of these organic compounds did not require any kind of guiding hand, but would naturally emerge from unassisted chemical reactions. Furthermore, the authors of this paper argue that while it was not a good model of the global atmosphere, it might still model local conditions in isolated areas.

Geoscientists today doubt that the primitive atmosphere had the highly reducing composition Miller used. However, the volcanic apparatus experiment suggests that, even if the overall atmosphere was not reducing, localized prebiotic synthesis could have been effective. Reduced gases and lightning associated with volcanic eruptions in hot spots or island arc-type systems could have been prevalent on the early Earth before extensive continents formed. In these volcanic plumes, HCN, aldehydes, and ketones may have been produced, which, after washing out of the atmosphere, could have become involved in the synthesis of organic molecules. Amino acids formed in volcanic island systems could have accumulated in tidal areas, where they could be polymerized by carbonyl sulfide, a simple volcanic gas that has been shown to form peptides under mild conditions.

So good work, Dr Miller!

Johnson AP, Cleaves HJ, Dworkin JP, Glavin DP, Lazcano A, Bada JL (2008) The Miller Volcanic Spark Discharge Experiment. Science 322(5900):404.

Watching every cell of the developing zebrafish

Blogging on Peer-Reviewed Research

How can I respond to a story about zebrafish, development, and new imaging and visualization techniques? Total incoherent nerdgasm is how.

Keller et al. are using a technique called digital scanned laser light sheet fluorescence microscopy (DSLM) to do fast, high-resolution, 3-D scans through developing embryos over time; using a GFP-histone fusion protein marker, they localize the nucleus of every single cell in the embryo. Some of the geeky specs:

  • 1500×1500 pixel 2-D resolution

  • 12 bits per pixel dynamic range

  • Imaging speed of 10 million voxels per second

  • Complete scan of a 1 cubic millimeter volume in 3µm steps in 90 seconds

  • Efficient excitation (5600 times less energy than a confocal, one million times less than a two-photon scope) to minimize bleaching and photodamage

Trust me, this is great stuff — as someone who was trying to do crude imaging of fluorescently labeled cells in the 1980s using a standard fluorescence scope and storing stills on VHS tape, this is all very Buck Rogers. Just load your embryo into the machine, start up the scanner, and it sits there collecting gigabytes of data for you for hours and hours.

But wait! That’s not all! They’ve also got sophisticated analysis tools that go through the collected images and put together data projections for you. For instance, it will color code cells by how fast they are migrating, or will count cell divisions. Similar tools have been available for C. elegans for a while now, but they have an advantage: they’re tiny animals where you might have to follow a thousand cells to get the full story. In zebrafish, you need to track tens of thousands of cells to capture all the details of a developmental event. This gadget can do it.

Here, for instance, are a couple of images to show what it looks like. The right half is the raw embryo, where each bright spot is a single cell nucleus; the left is one where the pattern of cell movement is color-coded, making it easier to spot exactly what domains of cells are doing.

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Cell tracking and detection of cell divisions in the
digital embryo. (A) Microscopy data (right half of embryo:
animal view maximum-projection) and digital embryo (left
half of embryo) with color-encoded migration directions (see
movie S9). Color-code: dorsal migration (green), ventral
migration (cyan), towards/away from body axis (red/yellow),
toward yolk (pink).

I grabbed one of their movies and threw it on YouTube for the bandwidth-challenged. It’s not very pretty, but that’s the fault of reducing it and compressing it with YouTube’s standard tools. This is an example with color-coded migration (blue cells are relatively motionless, orange ones are moving fast), and you can at least get the gist of what you can detect. You can see the early scrambling of cells in the blastula, migration during epiboly and blastopore closure, and convergence in the formation of the body axis fairly easily. Well, you can if you’re familiar with fish embryology, anyway.

This crappy little video doesn’t do it justice, however. Take a look at the Zebrafish Digital Embryo movie repository for much higher resolution images that are crisp and sharp and unmarred by compression artifacts. It contains DivX and Quicktime movies that are somewhat large, 10-40M typically, that represent visualizations of databases that are several hundred megabytes in size.

What can you do with it? They describe observations of early symmetry breaking events; patterns of synchrony and symmetry in cell divisions; direct observations of the formation of specific tissues; and comparisons with mutant embryos that reveal differences in cell assortment. It’s fabulous work, and I think I’m going to be wishing for a bank of big computers and lasers and scopes for Christmas—only about $100,000 cheap! Until then, get a fast internet connection and browse through the movies.

Keller PJ, Schmidt AD, Wittbrodt J, Stelzer EHK (2008) Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy. Science 2008 Oct 9. [Epub ahead of print].

Physics is important to us biologists, too

The Canadian Undergraduate Physics Conference is in trouble — government support has been flat, and corporate support has been declining. They are really in trouble: here’s what I got from one of the people working on it:

The CUPC is the largest conference in North America organized entirely by undergraduate students. It brings together students from across Canada and the world studying a vast array of subject areas from mathematical and theoretical physics to medical biophysics to engineering and applied physics. This important event gives many students their first experience with academics outside of the classroom, and helps to cultivate an interest in research and higher study. I, and every one else working on the organization of this event, would therefore be extremely grateful if you would be willing to post a link to your blog for the conference (http://cupc.ca/) and ask for donations (which are accepted on the site). The conference is in only a few short days and we are desperate for funds. If the we cannot find adequate support, this will be the 44th and final CUPC, which will be a tremendous shame for science education.

If you can, donate. If you know any potential sponsors who care about undergraduate physics research, pass the word on.

Fossil daisy-chain

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Here’s a very strange fossil from the Chengjiang Lagerstätte, an early Cambrian fossil bed from 525 million years ago. It’s a collection of Waptia-like arthropods, nothing unusual there; these are ancient creatures that look rather like headless shrimp. What’s weird about it is the way the individuals are locked together in a daisy chain, with the telson (tail piece) of each individual stuck into the carapace of the animal behind. It’s not just a fluke, either — they have 22 fossil chains, and just one animal all by its lonesome.

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(Click for larger image)
Waptia-like arthropod, Lower Cambrian, Haikou, Yunnan. (A) Individual with twisted abdomen, part of chain, Yunnan Key Laboratory for Palaeontology, YKLP 11020a. (B) Chain, about 20 individuals, various dorsoventral-lateral orientations, composite image (joined at cpt/p arrow), YKLP 11020a and YKLP 11020b. (C) Individual linked to carapace behind, lateral view, part of chain of nine individuals, YKLP 11021. (D) Isolated individual, subventral view, YKLP 11019. (E to G) Reconstruction shown in dorsal, ventral, and right lateral views, respectively. Scale bars in (A), (C), and (D) indicate 1 mm; in (B) and (E) to (G), 5 mm. b, s, and t indicate bent, stretched, and telescoped individuals, respectively; cpt, counterpart; f, facing direction; p, part; and tw, twisted.

They do not look like animals that were constrained in a burrow, or that were crawling over the surface. Rather, they had been swimming together in a chain at death, and the whole chain fell to the sea bed, bending and kinking but still remaining firmly locked together.

Why were they doing this? My first thought was of sex; everyone knows how dragonflies and damselflies lock together for mating, but of course that would predict pairs of individuals, not 20 at a time. It also reminded me of the Drosophila mutant fruitless, in which male flies court other male flies, and they spontaneously form conga lines in the culture bottles. That’s also unlikely, since that kind of behavior doesn’t lead to a consistent pattern of successful reproduction, but maybe if these animals were hermaphroditic, it might work. It’s not a behavior that any modern arthropods show, however.

The authors consider the possibility it is a feeding strategy, but that’s even worse: they’re locked basically mouth to anus, which would mean the fellow at the end of the line gets a very unpleasant diet. They conclude that the most likely explanation is that this represents a migratory behavior, perhaps involved in daily vertical migration. It may have been that strings of these animals would link up and paddle together to move to new feeding sites, where they separated and dispersed until the time came to move elsewhere.

Hou X-G, Siveter DJ, Aldridge RJ, Siveter DJ (2008) Collective Behavior in an Early Cambrian Arthropod. Science 322(5899):224.