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?

Blogging on Peer-Reviewed Research

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!

i-fd77777a341fb3ccad00b07dda6d2e80-miller.jpg
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.

i-a993b2c6d92e3964a73f6707b3cee9ca-dslm.jpg
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.

i-099b6d5f75230997e3080f6338fac631-waptia.jpg
(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.

Jellyfish gettin’ it on, baby

This is too much verisimilitude. The movie below is of the mating behavior of the jellyfish Carybdea sivickisi, and the first thing you’ll notice is that the scientists have set it to good old classic porn music.

The second thing you’ll notice, that I found annoying, is that they used too high a power objective to film it, so everything is jerking everywhere and none of the participants stay in the field of view for any length of time. Why is it that porn is afflicted with so many gynecological close-ups? Come on, set the mood, show us whole individuals instead of fragmented zooms of body parts.

Hawaii’s shame

This is shocking news, but not too surprising: I know a few of the people in this facility, and when I talked to them last they were deeply concerned about this possibility. The University of Hawaii is planning to shut down the Kewalo Marine Laboratory. They’re doing it so they can funnel more money into the expansion of a cancer research center, which is certainly valuable, but not at the expense of closing half of their marine facilities. This is especially shocking because heck, when students here in the cold and land-locked midwest talk to me about going into marine biology, many of them ask about Hawaii — it’s only natural that they’d imagine a tropical island would be a haven for that kind of research, and it is. It’s just that the state doesn’t support it. This is an ironic fact:

The Kewalo scientists said that Florida, also an ocean state, has 22 marine labs. “Even Georgia would have more marine labs (four) than Hawaii” if the Kewalo facility goes, said Michael Hadfield, biosciences research center faculty member and former director.

So I should tell my students that Georgia would be a better place to study marine biology? That’s nice for the South, not so nice for Hawaii.

And it’s not as if Kewalo has been unproductive — they’ve turned out some amazing work. Mark Martindale is there, as the director. The man is a Very Big Name in the field of evo-devo — go back through my evo-devo posts, and he keeps popping up everywhere. He’s working on early pattern formation in the metazoans, and his papers are indispensable in understanding early evolutionary events.

An old friend of mine, Elaine Seaver, is also there and doing fabulous work on a promising new system, the polychaete worm Capitella. If you want to know about body plan evolution, we need the kind of comparative approach she’s taking.

Write. Contact:

Gary Ostrander

Vice Chancellor for Research & Graduate Education
Hawaiʻi Hall 211
2500 Campus Road
Honolulu, HI 96822
808-956-7837

Let them know what an incredibly short-sighted decision this is, and what a failure of vision in the making. Not only does it harm the university immediately, damaging their reputation and costing them a useful facility, but think of the message it’s sending, that productive and esteemed faculty at the University of Hawaii can have their work so cavalierly dismissed and their laboratories demolished.

GFP wins Nobel Prize!

The Nobel in Chemistry this year goes to Osamu Shimomura, Martin Chalfie, and Roger Tsien for the discovery of Green Fluorescent Protein, GFP. That’s well deserved — GFP is a wonderful tool, a simple protein that fluoresces. There are lots of fluorescent compounds out there, and most of them require some kind of artificial injection or application to get them into cells — they basically allow you to determine that “a needle was stuck in here“, and also to allow us to visualize the morphology of individual cells, which is all very useful, and there’s quite an industry built around making new probes of this sort. GFP is different. It allows one to use the molecular biology of the cell to generate your green glowing compound. If you want to know when and where a particular gene of interest is expressed, for instance, you just make a construct that couples the regulatory elements of that gene to a GFP gene, and presto, where ever the gene you’re following is turned on, so is GFP, and the cell lights up like a little Christmas tree decoration. That’s powerful stuff: it gives us a tool to follow patterns of gene expression visually, in real time, in living cells.

i-3e2d5a2a71247b754798265bf82dda3e-squid.gif

Wave those arms in praise of MSKGEELFTG VVPVLVELDG DVNGQKFSVS GEGEGDATYG KLTLNFICTT GKLPVPWPTL VTTFSYGVQC FSRYPDHMKQ HDFFKSAMPE GYVQERTIFY KDDGNYKTRA EVKFEGDTLV NRIELKGIDF KEDGNILGHK MEYNYNSHNV YIMGDKPKNG IKVNFKIRHN IKDGSVQLAD HYQQNTPIGD GPVLLPDNHY LSTQSALSKD PNEKRDHMIL LEFVTAARIT HGMDELYK!

    1 atgagtaaag gagaagaact tttcactgga gtggtcccag ttcttgttga attagatggc 
   61 gatgttaatg ggcaaaaatt ctctgtcagt ggagagggtg aaggtgatgc aacatacgga 
  121 aaacttaccc ttaattttat ttgcactact gggaagctac ctgttccatg gccaacactt 
  181 gtcactactt tctcttatgg tgttcaatgc ttctcaagat acccagatca tatgaaacag 
  241 catgactttt tcaagagtgc catgcccgaa ggttatgtac aggaaagaac tatattttac 
  301 aaagatgacg ggaactacaa gacacgtgct gaagtcaagt ttgaaggtga tacccttgtt 
  361 aatagaatcg agttaaaagg tattgatttt aaagaagatg gaaacattct tggacacaaa 
  421 atggaataca actataactc acataatgta tacatcatgg gagacaaacc aaagaatggc 
  481 atcaaagtta acttcaaaat tagacacaac attaaagatg gaagcgttca attagcagac 
  541 cattatcaac aaaatactcc aattggcgat ggccctgtcc ttttaccaga caaccattac 
  601 ctgtccacac aatctgccct ttccaaagat cccaacgaaa agagagatca catgatcctt 
  661 cttgagtttg taacagctgc taggattaca catggcatgg atgaactata caaa

And the Nobel Prize goes to…

It looks like Alex’s predictions for the Nobel Prise this year did not come to pass — although I was thinking McCulloch and Till were likely, so I was wrong, too. The Nobel for Physiology or Medicine has just been announced, and the winners are Harald zur Hausen, for discovering that HPV causes cervical cancer, and Françoise Barré-Sinoussi and Luc Montagnier for the discovery of HIV. It’s a viral year this time around.