Squid in space

The last mission of the space shuttle will contain a student-initiated experiment: a collection of bobtail squid embryos will be launched into space. Which is cool, I suppose. I like squid, I like space, I like science, I like student research, let’s just throw them all into one big tossed salad of extravagantly expensive tinkering.

So why am I so disappointed?

Because the experiment is so trivial and uninteresting. The squid Euprymna has a commensal relationship with the luminescent bacterium, Vibrio. Early in their development, special organs in the squid are colonized by the bacteria; the squid provides a privileged environment for Vibrio growth, the bacteria give Euprymna a glowing organ that is thought to camouflage itself when viewed from below against a moonlit sky. This is a really cool phenomenon that has engaged the interest of many researchers, and there is serious work being done on the genetics and development of the symbiosis.

But, you know, I’ve never seen any speculation that gravity is a significant factor in the interaction. There’s cilia, and there are secreted amino acids, there is a mucus trap, and there’s a venting process, but gravity? Why would that matter?

I suspect the experiment was chosen because it’s easy for the shuttle engineers and technicians. Load up some chambers with embryos, launch it into space where it will require minimal attention from the crew, assay the results, that is, the development of the light organ, when it returns to earth. The results don’t matter. NASA will check off an item on a list, and say, yep, we did experimental embryology on the shuttle, and we gave a little bit of space to a student research project.

And what will the results be? Most likely, the light organ will be colonized and develop perfectly normally, because there’s no reason to think that microgravity will affect it. Or there will be abnormalities, which could either be because delicate embryos do not take well to the abuse of a shuttle launch, so we’re seeing the effect of stress, or there will be some surprising peculiarity in development that suggests maybe microgravity does make a difference, but repeating and expanding the experiment to puzzle out what’s going on will be out of the question.

I get the impression that NASA is simply filling a quota of interdisciplinary research for PR purposes, with only a nominal investment in the project. I wish I could be more of a cheerleader for the combination of space and developmental biology, but I haven’t yet seen an engaging project that would actually help me understand anything. There’s good science that we do because we really want to find an answer, and there’s lazy science that we do just because we can. This is an example of the latter, I’m sorry to say.

SDB 2011: Posters!

Those of you who’ve been to a poster session at a science meeting know that they’re noisy and chaotic and entirely reliant on interaction to work…so I’m not even going to try and describe it. Instead, I strong-armed Eric Röttinger into describing his poster on video for me, and here it is. He’s describing his work on Kahikai, an online database for collecting information about the development of marine invertebrates.

Paul Nelson takes a stab at Ontogenetic Depth again…which makes me go stab-stab-stabbity-stab

Paul Nelson has deigned to write a two-part essay on “Ontogenetic Depth“, his sciencey made-up term for a metric that he claims makes evolution essentially impossible. We’ve been wrangling over this for a long time — he and Marcus Ross introduced this in a poster at the Developmental Biology meetings in 2004, titled “Understanding the Cambrian Explosion by Estimating Ontogenetic Depth”, and in our conversation at that time I certainly got the impression that he and Ross were busy collecting this peculiar thing alien to creationists called “data”. I have asked him multiple times over the last 7 years how to estimate this hypothetical number; at the meetings, I recall asking him specifically how I would go back into my lab and measure it in my zebrafish. He was evasive. We’ve been trying to get him to explain this datum, which was his pretext for getting into a professional meeting, and gotten nothing.

Well, now we’re done. His first point in his first essay is that “ontogenetic depth” is “A Biological Distance That’s Currently Impossible to Measure”.


So what the heck were Paul Nelson and Marcus Ross doing? Nelson was certainly doing his best to pretend that they were actually doing real work on this metric, but I should have known better: a failed young-earth creationist philosopher could not possibly have been soiling his hands with empiricism. Now he’s frantically arguing that it doesn’t matter, that once upon a time no one knew the distance from the earth and the sun, but they could at least name the concept, so he can take credit for at least recognizing a real problem, and he can also patronizingly thank me for pointing out that they don’t actually have the tools right now to actually measure it.

Wait, how can they thank me for that? I’m picturing Nelson and Ross sitting at a microscope and looking at eggs of a nematode or a zebrafish or a frog, rubbing their hands in anticipation of a productive morning, and then staring at each other and wondering what to do next…and end up inventing a term for something that they don’t know how to measure. And then a year or so later, Nelson encounters me, I peevishly tell him that he doesn’t know how to measure cell division and differentiation in terms of a single numeric metric, and seven years after that, Nelson finally slaps his forehead and admits “Hey, we don’t know how to measure that!”

I don’t want credit for pointing out the obvious to the clueless, especially not when they’re that slow.

His first essay is an exercise in rationalizing away how he could propose this obstacle to evolution while not having the slightest idea how to measure it. His second essay is an exercise in demonstrating that he doesn’t understand basic biology. He has gussied it up with brightly colored diagrams of cell pedigrees that he purports illustrate the problem, but I think are actually more intended to distract and confuse and make you think he’s actually thought deeply about the subject.

Here’s the gist of his conceptual difficulty: he can’t imagine how the first metazoan got from a crude colonial state, where it’s just a mass of identical cells clumped together, to a state in which regions are consistently specialized for specific functional roles, with the simplest example of an animal that contains only two cell types, a mass of somatic cells that take care of feeding and motility, and a smaller mass of germ cells that do the job of reproduction. Why, that would require a whole series of mutations that selection can’t possibly explain! How could selection possibly create a cell that contains a series of instructions to build a cell type that isn’t going to reproduce?

I’m wishing that Nelson hadn’t chosen to focus on biology. If only he were a creationist philosopher of physics, he’d be the one asking, “magnets, how do they work?” and somebody else would get the job of correcting him.

Nelson summarizes the problem as, at the minimum in the simplest possible metazoan, a three step sequence. First, cells have to divide and stick together; second, they have to have a way to make daughter cells differ from one another; and third, there has to be inheritance of that differentiated state in sublineages. He claims that in none of these steps can selection be involved; this complex process had to evolve independently of any selective effects.

That’s nonsense. The first metazoan already had all the tools needed to build these steps, honed by a billion years or more of selection in single-celled organisms. All three of his steps are found in bacteria.

Step one is simply cell adhesion. Step two is gene regulation. Step three is epigenetics. That’s it. These aren’t glorious novelties invented by the first animals, they inherited this toolkit from their ancestors. Bacteria have been sticking together for billions of years, and they’ve been responding to their local environment by shifting patterns of gene expression for just as long. A bacterium in a sugar-rich environment vs. a bacterium in a sugar-poor environment will make long term changes in gene activity that can persist for a few generations using exactly the same mechanisms as an animal embryo sets up germ and somatic tissues; has Nelson never heard of Jacob and Monod?

Nelson’s argument goes beyond pure ignorance, however. He also recruits Lewis Wolpert to his side, which is remarkable. Wolpert is a brilliant and influential developmental biologist who shaped many of our ideas about differentiation, pattern formation, and evolution. He cites Wolpert as postulating as serious problems for evolution the origin of the egg, and in particular implying that Wolpert sees metazoan evolution as violating a principle. Here’s what Nelson says about a particular paper Wolpert wrote.

Evolutionary developmental biologist Lewis Wolpert — whom no one, even in his wildest delirium, would ever mistake for an ID theorist — had long critiqued the scenario on functional grounds, using what he called “the continuity principle.” (1994) The continuity principle requires that any change occurring in an evolutionary transformation be biologically possible, that is, viable and stably heritable in the next generation.

Whoa — eminent anti-creationist scientist critiques an evolutionary explanation! I’m sure this must make you wonder, familiar as you are with creationist tactics, what Wolpert actually said. Judge for yourself, here’s the abstract for Wolpert’s paper, does it sound like he’s on Nelson’s side at all?

A scenario for the evolution of a simple spherical multicellular organism from a single eukaryotic cell is proposed. Its evolution is based on environmentally induced alterations in the cell cycle, which then, by the Baldwin effect, become autonomous. Further patterning of this primitive organism–a Blastaea, could again involve environmentally induced signals like contact with the substratum, which could then become autonomous, by, perhaps, cytoplasmic localization and asymmetric cell division. Generating differences between cells based on positional information is probably very primitive, and is well conserved; its relation to asymmetric cell division is still unclear. Differentiation of new cell types can arise from non equivalence and gene duplication. Periodicity also evolved very early on. The origin of gastrulation may be related to mechanisms of feeding. The embryo may be evolutionarily privileged and this may facilitate the evolution of novel forms. Larvae are secondarily derived and direct development is the primitive condition as required by the continuity principle.

This is a paper in which Wolpert explains how multicellularity could have evolved, directly answering the questions Nelson raised with his supposedly problematic three steps. How did Paul Nelson miss that?

But wait! There’s more Wolpert abuse!

Nelson has found a paper by Wolpert in which he points out a serious problem in a particular evolutionary strategy, and Nelson, apparently primed by a selective reading of science papers for the magic words “problem”, “difficulty”, “impossible”, or “unlikely” has seized upon it as another instance of Eminent Scientist Critiquing Evolution.

What mechanism is coordinating gene expression among all the members of the colony, such that only one cell lineage will evolve to carry the complete instruction set required to specify the form of the whole? How are mutations — occurring in all individual cells of the colony — transmitted to the next generation? If individual cells continue to reproduce via normal fission, or budding, notes Wolpert, “cell lineages [will be] mutating in all sorts of directions in genetic space.” (2002, 745) Given such genetic chaos, he argues, “we consider it practically impossible” for the collection of cells to “yet retain the ability to evolve into viable new forms.”

Sounds dreadful. I give up, I guess evolution must actually be impossible.

Hang on, though, maybe we should read Wolpert’s paper first. And there what you discover is a story that you would not have expected from Nelson’s peculiarly distorted coverage. It’s a short paper where the authors consider alternative reproduction strategies: not all animals go through a single-cell stage in reproduction, you know. Some, like hydra, reproduce by budding, where a small collection of cells, not just one egg or sperm cell, splits off to form an independent organism. Wolpert is considering which solution is more advantageous for evolution, going through a single-cell bottleneck or through a larger population that would reduce the dangers of mutations? And that’s where Wolpert’s criticisms lie: the asexual budding solution is the focus of his critique, and which is where Nelson draws his quotes highlighting the difficulty of evolution.

In a hydra-like organism that only reproduces by asexual budding, it is impossible to evolve significant changes. There is no way that the genes in the huge number of cells involved in budding can change at the same time, and mutations in individual cells mean that they no longer share the behavioural rules of the majority. It is only through a coherent developmental programme, with all cells possessing the same genes, that organisms can evolve, and this requires an egg.

Huh. So Wolpert is arguing that development from a multicellular propagule is much less evolutionarily flexible than evolution from a single-celled egg. His thesis is explaining why we develop from eggs, not that our evolution is unlikely.

We consider it practically impossible to have many asexual, differentiated cell lineages mutating in all sorts of directions in genetic space and yet retain the ability to evolve into viable new forms. This may not be completely impossible but, taking the broad view in evolutionary terms, organisms that develop from an egg would displace those that do not.

Dang, Paul Nelson. You should be smart enough to know that you don’t quotemine claims from the science literature in an argument with someone who has actually read that literature.

Clarifying tetrapod embryogenesis, accurately

Clarifying tetrapod embryogenesis, accurately
By OldCola

[Note from pzm: The text of this one is a little rougher than I like, but the content is interesting and addresses the claims of a character who has been lurking about here for a while, and whose work I’ve criticized before. If nothing else, I’d also like to see a few science posts submitted as guest articles, so think of this as priming the pump.]

The article, “Clarifying tetrapod embryogenesis, a physicistʼs point of view,” by V. Fleury, hasn’t steered the revolution expected by Fleury in evo-devo. Two years after the publication, cited by one (Fleury himself), the article seems to have being more useful to clarify the way he perceives the world, then anything related to the tetrapods embryogenesis. And the most useful elements are to be found on the Web, not in the article per se. Direct questions remain unanswered, critics are threatened by legal action for defamation, and hierarchical superiors are solicited to politely ask the critics to STFU.

While Fleury must be aware by now of major flaws in the way he represented several of the articles he used as sources of information, and of several inconsistencies of his model and the way he extrapolates his own data, he doesn’t seem to have done anything to correct them. The article remains available unchanged, a shame for EPJ AP editorial board (and Editor-in-Chief Dr Drévillon B. in particular), sufficiently shameful at least for the guy who invited the review, for Fleury to avoid disclosing his name.

A new element comes to complete Fleury’s quest:

The pattern of tetrapods exist in the platonician space of forms, just like the sphere. You can write its essence without evolutionnary arguments.

V. Fleury, Dynamic topology of the cephalochordate to amniote morphological transition: A self- organized system of Russian dolls, C. R. Biologies (2011), doi:10.1016/j.crvi.2010.11.009

During evolution of vertebrates a sequence of events is empirically observed: first, animals are bilateral, but they have no heart, no head, and no surrounding bag during development (these primitive animals are called cephalochordates [1]).

From the very first phrase of the Introduction, you know hope that no biologist read the manuscript before it was accepted for publication. And certainly not any evo-devo person, which would be the right choice for a referee for this kind of subject.

Cephalochordates are certainly not vertebrates and they certainly have a head, the sub-phylum being named after the fact that the notochord extends into that head. One may think that Fleury misused the word “head”, meaning “skull” or whatever, but if you read the French summary of the paper you do get the same information, Cephalochordata don’t have a “tête” (French for “head”).

And he dare give a reference! But if you had the courage to read his previous article (for a review) you may be familiar with the strange way Fleury reports his readings (at least the way he understood them), in an absolutely surreal way, including data from his own lab! If not, there is a brand new example in this one (see below).

By the title you may have expected to read about comparative embryology/anatomy that will enlighten you on the relations between the body plans of cephalochordates and amniotes. If so, you will be deceived. Fleury focuses entirely on chicken embryos, hoping to prove experimentally the existence of some kind of order in the ontogeny of the chicken that reflects an order in the phylogeny of chordates. The reading is interesting not to learn anything about evolution or embryology (or physics by the way), but to see how an a priori can lead someone to mess up things badly. Fleury observes the world through a keyhole shaped by Plato a long time ago and he seeks some equivalent of the Holly Grail: a way to write the essence of the pattern of tetrapods without evolutionary arguments, as it “exist in the platonician space of forms, while avoiding being embarrassed by the bullshit produced by embryologists, geneticists or evo-devo people.

The aim of this work is to support that “the formation of amniotes would be a deterministic attractor of a physical process over a flat visco-elastic plane,” and that the formation of the heart and the chorion (you should pronounce it amnios to make sense) are the consequence of the body’s growth along the anteroposterior axis.

Thus, any embryo with the amniotic (and chorionic) cavity formed before the beginning of gastrulation would falsify Fleury’s model definitively. I’ll come to that later.

While aware of the lateral folding of the embryo around an antero-posterior (AP) axis, Fleury avoid to discuss it as his model don’t explain it. Cardiac tubes are formed as mirror structures at both sides of and parallel to the AP axis, they migrate to the midline where they fuse to form the heart and they are already pre-determined to produce almost fully developed hearts if by some mutation their migration to the midline is impaired. Cardiac formation is not caused by the the cephalic fold renamed “cardiac fold” by Fleury.

The fact that the cephalic and caudal folds forming the anterior and posterior intestinal portals are distant in time by almost 24 h doesn’t bother him and his model lack any modality that would explain the latency for the formation of the posterior intestinal portal. On the contrary, he manage to represent the two folds as the result of the AP axis extension in a single schema, as being the consequences of a single phenomenon, “[f]or the sake of clarity“. He is not at his first temporal jump of embryonic structures, even of imaginary ones.
What kind of physicist could have reviewed the manuscript without requiring some kind of explanation about this particularity?

There is nothing really new in his description of the development of the chicken embryo, except the errors and omissions which make it unusable. One may prefer a classic textbook, published a while ago: Patten, B.M. (1920). The Early Embryology of the Chick. Philadelphia: P. Blakiston’s Son and Co. You can browse through it at UNSW Embryology pages, where the scans of the illustrations are of much better quality.

Some data may be interesting for people interested by the dynamics of the embryo formation, the article being based on time lapse videos of the developing embryo. There is no much of it and the graphics seem to report on single experiments (no number of observed embryos given, no variance bars on the graphics). What is really new for me, is that Fleury found a way to report a “rate of variation of the radius” of an ellipse, with a major vs minor axis ratio of ~1,5 (fig 3, a, 0′), giving a single value! Any mathematician around to explain us this?

As Fleury decided to rename the formation of the subcephalic pocket “cardiac fold”, and he was seeking some symmetry at the caudal region, he also renamed the subcaudal pocket “cardiac fold” and he triumphantly mention the “aneural heart” of the hagfish as an evidence of the power of prediction of his model. Now, the caudal heart of the hagfish is just a pair of specialized structures on the caudal veins, parallel to the AP axis, as the primitive heart tubes, separated by a cartilage septum and they are innervated! Jensen, in the Introduction of his paper clearly explain the anatomy of the circulatory system of the hagfish and what elements are innervated, or not. Either Fleury didn’t bothered reading the paper or he is simply unable to understand what he is reading (or both, your guess). It would have be nice if he had read the paper, because he passed over the existence of the portal heart and of what some people call the cephalic hearts of the hagfish (specialized gill musculature which propel the blood through the arterial circulation). There is even an illustration for people bored by textual explications (fig 4). Such a little animal, so many hearts and not enough folds to explain them. Unnerving.

Patten starts his Introduction by a very wise advice:

The only method of attaining a comprehensive understanding of embryological processes is through the study and comparison of development in various animals.

As I said, any embryo with the amniotic cavity formed before the beginning of gastrulation would falsify Fleury’s model definitively. Let me present you an artist’s rendition of Dr Fleury at his early youth, second week of development

Capture d'écran 2011-02-21 à 18.24.47.png


The illustration is from the online Human Embryology course notes (clic the image for the full page). I’m not sure they had in mind Vincent Fleury when they draw this cartoon, but it’s the best I can offer you: A cute embryo with his amniotic cavity lined with cells from the epiblast and his primary yolk sac lined by cells derived by the hypoblast. The Heuser’s membrane is still attached to the extraembryonic reticulum.
A few days later, the secondary yolk sac had formed and the chorionic cavity was installed.


At this stage little Vincent was still bilaminar with fully formed amniotic and chorinic cavities.

Those of you interested to learn about embryo’s folding can also visit Folding of the germinal disk and the generation of the abdominal wall, in which case the comparison of the two foldings (cephalo-caudal and lateral), animation is a must for the visitor, and certainly for Fleury.

How sad that a great model from an experimentalist working all day with embryos, goes down the drain after being confronted to elements of chapter 5 of a Human Embryology textbook.

Several questions come in mind in this situation, the first one being: who the hell reviewed the manuscript. Not a biologist, probably not a physicist (he should have ask for a mechanism explaining the delay of formation of the caudal fold). Not a second year student of biology or medicine neither; she would have spotted the problem with the amniotic and chorionic cavities subito presto.
Fleury’s precedent paper was an invited review by one of the editors of a journal of physics. You can’t blame the guy for being unable to understand the bunch of errors the review contains. OK, you can blame him for not having a specialist’s opinion on the final piece of work. Misplaced trust. And sometimes, some physicists are just pissed-off by life scientists. Fleury didn’t even dared to give his name.

This time, the journal is a publication of the French National Academy of Science and it displays “Biologies” on the cover. Shame on them. Until this paper is retracted who would trust the “Development and reproduction biology” section of the journal, or the journal at all? I wouldn’t, would you?

Therefore, this suggest” is one fabulous transition.

The Methods section of the paper may be interesting if you plan a few experiments with chicken embryos, but dramatically incomplete. The most interesting part is missing: the references of the software and the method Fleury is using for PIV, which gives him astonishing images. I would like to be able to check by myself, previous interpretations of experimental data, even the ones generated in his lab, by Fleury being as much surreal as his usual stuff. Hopefully he could complete this section in the comments of this post.

In Heart formation, Fleury undergo to explain how the heart is formed by the heart fold. Here is the first part where it goes really bad. I can understand the frustration of a physicist who would like to have more data concerning the biomechanics of the process, and hopefully somebody else than Fleury will go for them. But there is no need to reinvent the wheel, there are nice descriptions of the movements by which the heart tubes are forming, how the lateral folding of the embryo make them join along the anteroposterior axis and describing their fusion to produce the unique heart tube [1]. Certainly, the 125° rotation of the heart fields and the lateral folding of the embryo necessary for the normal cardiogenenic process are not perpendicular to the anteroposterior axis and doesn’t fit Fleury’s model, but it isn’t reasonable to just ignore them. You can’t just ignore what it doesn’t fit your model to make it sound plausible.
Anyway, even the fusion of the primary heart tubes doesn’t seem to be necessary to support the development and morphogenesis of the heart, up to some point: “a highly differentiated four-chambered mammalian heart” in the case of Foxp4 mutant mice embryos [2].

The point of junction of the cardiac tubes do travel caudaly along the anteroposterior axis of the embryo, but that’s just the point of junction…

An interesting description of the heart formation can be found in a relatively old textbook: The Early Embryology of the Chick (pp 68-72, fig. 26 & 27, with emphasis for fig 27) [3]

For those who will take the time to read the paper, please pay attention to the part discussing the role of chemotactic forces ; Fleury didn’t managed yet to understand morphogenic gradients and that most of them are embedded into the cells and the extracellular matrix.

You may need to go through the whole section about the Chorion formation to understand that Fleury discuss just about the amniotic folds of the chorion and completely ignores the rest of it. It’s just that it isn’t folded in the right direction for his model. On the other hand the amniotic folds of the chorion are folded in the right way and Fleury carefully studied the ways the meet around a single point. Not only it’s weird how he doesn’t discuss the lateral part of the amniotic folds (absolutely necessary to form the amnios and the dorsal part of the chorion), but not perpendicular to the anteroposterior axis, but somehow he manage to found a single rate of variation of the radius of an ellipse!

Patten [3] offers a series of diagrams showing the growth and foldings of the somatopleure which form the amnios, from transverse sections of the embryo, in fig 30 and from longitudinal sections in fig. 32. That gives a global image of the tissue growth, in all directions, not just the keyhole presentation Fleury is giving in his article.

While Fleury is aware that the cephalic and caudal amniotic folds appear at different developmental stages, he present their occurrence as being caused by the “extension of the median axis” without explaining what may be the mechanical causes for the delay of almost 24h for the apparition of the caudal amniotic fold. “For the sake of clarity” he present them in the same figure (4b of his paper) as if they occurred in the same time. As much clarity as usually.

1. Heart Field: From Mesoderm to Heart Tube, Radwan Abu-Issa, and Margaret L. Kirby, Annual Review of Cell and Developmental Biology Vol. 23 (2007): 45-68, doi: 10.1146/annurev.cellbio.23.090506.123331

2. Advanced Cardiac Morphogenesis Does Not Require Heart Tube Fusion, Shanru Li, Deying Zhou, Min Min Lu, Edward E. Morrisey, Science Vol 305 (2004): 1619-1622, doi: 10.1126/science.1098674
3. Patten, B.M. (1920). The Early Embryology of the Chick [link to scans in pdf at archive.org]. Philadelphia: P. Blakiston’s Son and Co. You can browse through it at UNSW Embryology pages, where the scans of the illustrations are of much better quality.

V. Fleury, Dynamic topology of the cephalochordate to amniote morphological transition: A self-organized system of Russian dolls, C. R. Biologies (2011), doi:10.1016/j.crvi.2010.11.009

Will radiation hormesis protect us from exploding nuclear reactors?

That reputable scientist, Ann Coulter, recently wrote a genuinely irresponsible and dishonest column on radiation hormesis. She claims we shouldn’t worry about the damaged Japanese reactors because they’ll make the locals healthier!

With the terrible earthquake and resulting tsunami that have devastated Japan, the only good news is that anyone exposed to excess radiation from the nuclear power plants is now probably much less likely to get cancer.

This only seems counterintuitive because of media hysteria for the past 20 years trying to convince Americans that radiation at any dose is bad. There is, however, burgeoning evidence that excess radiation operates as a sort of cancer vaccine.

As The New York Times science section reported in 2001, an increasing number of scientists believe that at some level — much higher than the minimums set by the U.S. government — radiation is good for you.

But wait! If that isn’t enough stupid for you, she went on the O’Reilly show to argue about it. Yes! Coulter and O’Reilly, arguing over science. America really has become an idiocracy.

I only know about hormesis from my dabbling in teratology; a pharmacologist or toxicologist would be a far better source. But I know enough about hormesis to tell you that she’s wrong. She has taken a tiny grain of truth and mangled it to make an entirely fallacious argument.

Radiation is always harmful — it breaks DNA, for instance, and can produce free radicals that damage cells. You want to minimize exposure as much as possible, all right? However, your cells also have repair and protective mechanisms that they can switch on or up-regulate and produce a positive effect. So: radiation is bad for you, cellular defense mechanisms are good for you.

Hormesis refers to a biphasic dose response curve. That is, when exposed to a toxic agent at very low doses, you may observe an initial reduction in deleterious effects; as the dose is increased, you begin to see a dose-dependent increase in the effects. The most likely mechanism is an upregulation of cellular defenses that overcompensates for the damage the agent is doing. This is real (I told you there’s a grain of truth to what she wrote), and it’s been observed in multiple situations. I can even give an example from my own work.

Alcohol is a teratogenic substance — it causes severe deformities in zebrafish embryos at high doses and prolonged exposure, on the order of several percent for several hours. I’ve done concentration series, where we give sets of embryos exposures at increasing concentrations, and we get a nice linear curve out of it: more alcohol leads to increasing frequency and severity of midline and branchial arch defects. With one exception: at low concentrations of about 0.5% alcohol, the treated embryos actually have reduced mortality rates relative to the controls, and no developmental anomalies.

If Ann Coulter got her hands on that work, she’d probably be arguing that pregnant women ought to run out and party all night.

We think there is probably a combination of factors going on. One is that alcohol is actually a fuel, so what they’re getting is a little extra dose of energy; it’s also deleterious to pathogens, so we’re probably killing off bacteria that might otherwise harm the embryos, and we’re killing those faster than we are killing healthy embryonic cells. It’s the same principle behind medieval beer and wine drinking — it was healthier than the water because the alcohol killed the germs.

However, the key thing to note about hormetic effects is that they only apply at low dosages. Low dosages tend to be where the damaging effects are weakest, anyway, and where the data are also the poorest. The US government recommendations for radiation exposure are based on a linear no threshold model in which there is no hormesis to reduced effects at low concentrations for a couple of reasons. One is methodological. The data we can get from high exposures to toxic agents tends to be much more robust and consistent, and we do see simple relationships like a ten-fold increase in dose produces a ten-fold increase in effect, whereas at low doses, where the effects are much weaker, variability adds so much noise to the measurements that it may be difficult to get a repeatable and consistent relationship. So the strategy is to determine the relationships at high doses and extrapolate backwards.

Then, of course, the major reason recommendations are made on the simple linear model is that it is the most conservative model. The data are weaker at the low end; there is more variability from individual to individual; the safest bet is always to recommend lower exposures than are known to be harmful.

In the low dosage regime, these responses get complicated at the same time the data gets harder to collect. This is why it’s a bad idea to base public policy on the weakest information. I’ll quote a chunk from a review by Calabrese (2008) that describes why you have to be careful in interpreting these data.

In 2002, Calabrese and Baldwin published a paper entitled “Defining hormesis” in which they argued that hormesis is a dose-response relationship with specific quantitative and temporal characteristics. It was further argued that the concept of benefit or harm should be decoupled from that definition. To fail to do so has the potential of politicizing the scientific evaluation of the dose-response relationship, especially in the area of risk assessment. Calabrese and Baldwin also recognized that benefit or harm had the distinct potential to be seen from specific points of view. For example, in a highly heterogeneous population with considerable inter-individual variation, a beneficial dose for one subgroup may be a harmful dose for another subgroup. In addition, it is now known that low doses of antiviral, antibacterial, and antitumor drugs can enhance the growth of these potentially harmful agents (i.e., viruses), cells, and organisms while possibly harming the human patient receiving the drug. In such cases, a low concentration of these agents may be hormetic for the disease-causing organisms but harmful to people. In many assessments of immune responses, it was determined that approximately 80% of the reported hormetic responses that were assessed with respect to clinical implications were thought to be beneficial to humans. This suggested, however, that approximately 20% of the hormetic-like low-dose stimulatory responses may be potentially adverse. Most antianxiety drugs at low doses display hormetic dose-response relationships, thereby showing beneficial responses to animal models and human subjects. Some antianxiety drugs enhance anxiety in the low-dose stimulatory zone while decreasing anxiety at higher inhibitory doses. In these two cases, the hormetic stimulation is either decreasing or increasing anxiety, depending on the agent and the animal model]. Thus, the concepts of beneficial or harmful are important to apply to dose-response relationships and need to be seen within a broad biological, clinical, and societal context. The dose-response relationship itself, however, should be seen in a manner that is distinct from these necessary and yet subsequent applications.

I know, the Cabrese quote may have been a little dense for most. Let me give you another real world example with which I’m familiar, and you probably are, too.

Here in Minnesota in the winter we get very snowy, icy conditions. If I’m driving down the road and I sense a slippery patch, what I will immediately do is become more alert, slow down, and drive more carefully — I will effectively reduce my risk of an accident on that road because I detected ice. This does not in any way imply that ice reduces traffic accidents. Again, with the way Ann Coulter’s mind works, she’d argue that what we ought to do to encourage more responsible driving is to send trucks out before a storm to hose the roads down with water instead of salt.

Ann Coulter is blithely ignoring competent scientists’ informed recommendations to promote a dangerous complacency in the face of a radiation hazard. She’s using a childish, lazy interpretation of a complex phenomenon to tell people lies.

Calabrese EJ (2008) Hormesis: Why it is important to toxicology and toxicologists. Environmental Toxicology and Chemistry 27(7):1451-1474.

Brachiopods: another piece in the puzzle of eye evolution


About 600 million years ago, or a little more, there was a population of small wormlike creatures that were the forebears of all modern bilaterian animals. They were small, soft-bodied, and simple, not much more than a jellyfish in structure, and they lived by crawling sluglike over the soft muck of the sea bottom. We have no fossils of them, and no direct picture of their form, but we know a surprising amount about them because we can infer the nature of their genes.

These animals would have been the predecessors of flies and squid, cats and starfish, and what we can do is look at the genes that these diverse modern animals have, and those that are held in common we all inherited together from that distant ancestor. So we know that flies and cats both have hearts that are initiated in early development by the same genes, nkx2.5 and tinman, and infer that our common ancestor had a heart induced by those genes…and that it was only a simple muscular tube. We know that modern animals all have a body plan demarcated by expression of Hox genes, containing muscles expressing myoD, so it’s reasonable to deduce that our last common ancestor had a muscular and longitudinally patterned body. And all of us have anterior eyes demarcated by early expression of pax6, as did our ancient many-times-great grandparent worm.


We do not have fossils of these small, soft organisms, but that’s no obstacle to picturing them. You just have to see the world like a modern molecular or developmental biologist. One of the graphical conceits of the Matrix movies was that the hero could see the hidden mathematical structure of the world, which was visualized as green streams of symbols flowing over everything. We aspire to the same understanding of the structure of life, only what we see are patterns of genetic circuity, shared modules that are whirring away throughout development to produce the forms we see with our eyes; and also, unfortunately, we currently only see these patterns spottily and murkily. There is no developmental biologist with the power of Neo yet, but give us a few decades.

There’s another thing we know about these ancient ancestors: they had two kinds of eyes. ciliary and rhabomeric. Your eyes contain ciliary photoreceptors; they have a particular cellular structure, and they use a recognizable form of opsin. A squid has a distinctly different kind of photoreceptor, called rhabdomeric, with a different cell structure and a different form of opsin. We humans also have some rhabdomeric receptors tucked away in our retinas, while invertebrates have ciliary receptors as well, so we know the common ancestor had both.

Now this ancestral population eventually split into two great tribes, the protostomes, which includes squid and flies, and the deuterostomes, which includes cats and starfish. It should be an obvious indication of the general state of that ancestor that it represents all that those four diverse animals have in common. It also tells us that while that ancestor had eyes, they were almost certainly very simple, and could have been nothing more than a patch of light-sensitive cells, or perhaps even single cells, as we see in some larval eyes.

What we think happened at this division is that both tribes took the primitive eyes and specialized them independently. Each group evolved under similar constraints: they needed directionally-sensitive eyes that could tell what direction a source of illumination was coming from (and these would eventually form true image-forming eyes), and they also needed sensors to detect general light levels — is it day or night, are we in the open or under a rock? Think of it like a camera system: there is a part that gets all the attention, the lens and image-forming chip, but there’s also a light meter that senses ambient light levels.

The two tribes made different choices, though. The protostomes pulled the rhabdomeric photoreceptor out of their toolbox, and used that to make the camera; they used the ciliary photoreceptor to make their light meter. The deuterostomes (actually, just us chordates) instead used the ciliary photoreceptor for their camera, and the rhabdomeric photoreceptor for the light meter. It’s the same ancestral toolkit, but we’ve just specialized in different ways.

At least, that’s the general model we’ve been exploring. A new discovery at the Kewalo Marine Laboratory, one of the premiere labs for evo-devo research, has made the interpretation a little more complex.

That discovery is that brachiopod larvae, which are protostomes, have been found to have directionally sensitive eyes…which are ciliary. A protostome should have directionally sensitive eyes that are rhabdomeric. How interesting!

Brightfield microscopy of a Terebratalia transversa larva, with red eye spots visible in the apical lobe (black arrows). (A) Dorsal view. (B) Lateral view.

In addition to being ciliary in structure, these eyes express ciliary opsin. They are also true cerebral eyes, also expressing pax6 and having a nervous connection to the central nervous system.

Notice what is going on here: a protostome is building a camera, and unlike all the other protostomes we’ve observed, it’s pulled a ciliary photoreceptor out of its pocket to make it. This is a surprise, but it doesn’t upset any theories too much — it just means we need to explore a couple of alternative explanations. We don’t have answers to resolve these hypotheses yet — we need more data and experiments — but it’ll be fun to watch the work roll onward.

One explanation is illustrated in A, below. The initial animal state was to build directional, cerebral eyes using rhabdomeric photoreceptors. The vertebrates are oddballs who swapped in ciliary receptors instead, while these larval eyes in brachiopods are major peculiarities, an evolutionary novelty which resembles a cerebral eye, but is actually non-homologous. This seems unlikely to me; there are multiple elements of the eye circuitry at work in these eyes, and if they’re using the same gene circuitry, we ought to recognize them as homologous at the molecular level…the only one that counts.

The second explanation in B is that all of these cerebral eyes are homologous, but that the receptor type is more plastic than we thought — it’s relatively easy to switch on the ciliary module vs. the rhabodmeric module, so we would expect to see multiple flip-flops in the evolutionary record.

If we accept that it’s easy to switch receptor type, though, then why assume that the last common ancestor had a directional, cerebral eye that was rhabdomeric? It could have been ciliary, which is also a more parsimonious explanation, because it requires only one switch of types in the protostomes, shown in C.

(Click for larger image)

Alternative hypothesis on the evolution of photoreceptor deployment in cerebral eyes. Schematic representation of three hypotheses accounting for the deployment of ciliary photoreceptors in the cerebral eyes of Terebratalia and vertebrates, versus rhabdomeric photoreceptors in Platynereis and other protostomes. (A) Deployment of rhabdomeric photoreceptors as the ancestral state in cerebral eyes, with the larval eyes of Terebratalia, containing ciliary photoreceptors, representing an evolutionary novelty. The deployment of ciliary photoreceptors is the result of a substitution (with ciliary photoreceptors having replaced rhabdomeric photoreceptors in the cerebral eyes) early in the chordate lineage. (B) Larval eyes in Terebratalia are homologous to the cerebral eyes in other protostomes, but ciliary photoreceptors have been substituted for rhabdomeric photoreceptors, as in the vertebrates. (C) Ciliary photoreceptors in cerebral eyes represent the ancestral condition, inherited by Terebratalia and vertebrates. Deployment of rhabdomeric photoreceptors in the cerebral eyes of Platynereis and other protostomes are the result of substitution events.

Whichever hypothesis pans out, though, the important message is that photoreceptor type is a more evolutionarily labile choice than previously thought. What I want to see is more research into photoreceptor development in more exotic invertebrates — that’s where we’ll learn more about our evolutionary history.

I have to mention a couple of other cool features of this paper. If you ever want to see a minimalist directional eye, here it is: the larval eye sensor of brachiopods consists of two cells, a lens cell that actually does the job of light detection, and a pigment cell that acts as a shade, preventing light from one direction from striking the lens cell. That’s all it takes.


I lied! That isn’t a minimal directional eye at all: here it is.


This rather blew my mind. The brachiopod gastrula senses light. The figure above is of a very early stage in development, when the organism is little more than a couple of sheets of cells with no organs at all, only tisses in the process of forming up into rough structures. It definitely has no brain, no nervous tissue at all, and no eyes…and there it is, that dark blue smear is a region selectively expressing ciliary opsin as if it were a retina. Furthermore, when tested behaviorally (mind blown again…behavior, in a gastrula), populations in a light box show a statistical tendency to drift into the light. Presumably, light stimulation of the opsin is coupled to the activity of cilia used for motility in the outer epithelium of the embryo.

Amazing. It suggests how eyes evolved in multicellular organisms, as well — initially, it was just localized general expression of light-sensitive molecules coupled directly to motors in the skin, no brain required.

Passamaneck Y, Furchheim N, Hejnol A, Martindale MQ, Lüter C (2011) Ciliary photoreceptors in the cerebral eyes of a protostome larva. EvoDevo, 2:6.

Conservative self-identifies with single-celled brainless organism

Among my usual flood of daily email, I frequently get tossed onto mailing lists for conservative think tanks. Why? I don’t know. I suspect that it’s for the same reason I also get a lot of gay porn in my email: not because I follow it or asked to be added, but because some tired d-bag with no imagination thinks its funny to dun me with more junk. The joke’s on them, though: I might keep it around and skim the stuff now and then to get inspiration for a blog post, and then click-click — a few presses of a button and I add the source to my junk mail filter, and never see it again.

No, I didn’t get inspired by gay porn today, but by drivel from some freakish conservative think tank called the Witherspoon Institute, about which I know next to nothing except that they’re another of those organizations that cloak themselves in the Holy Founding Fathers of America to promote illiberal non-freethinking anti-government BS. This latest is by a philosopher criticizing a book about modern reproductive biotechnologies. He doesn’t like ’em. Not one bit, no sir.

But you know an essay from a philosopher is going to be pretty much worthless when it opens and closes with references to… C.S. Lewis. I don’t know why that man gets so much happy clappy press from believers. I suspect he must have sold his soul to the devil.

Anyway, the bizarre part is in the middle, where Justin Barnard is poleaxed by the author’s, Steven Potter’s, willingness to destroy human embryos. Potter apparently considers several of the sides of the debate, but fails to come down on the side of the Religious Right, that is, that embryos are absolutely and undeniably full human beings from the instant of fertilization, instead espousing the dreadful notion that the definition of personhood falls into a huge gray area.

Potter’s own attempt to wrestle with the morality of destroying human embryos is philosophically, if not biologically, confused from the start. He begins by claiming that “each egg and sperm has the potential to make a person.” Biologically, this is simply false. Gametes, by themselves, have no intrinsic developmental potential for human personhood. Of course, Potter knows this. So his use of “potential” is likely more latitudinarian. Still, three pages later, Potter describes the zygote as having “remarkable potential.” “It can,” he explains, “turn itself into a person.” Ironically, Potter fails to recognize that this potentialist understanding of human personhood is at odds with his rather surprising admission of the embryological facts. Potter writes, “Of course we all began as a zygote. Everyone does.” What is shocking about this concession is what it so obviously entails–an entailment that seems lost on Potter. If I, the human being I am today, “began as a zygote,” then the zygote that began the-human-being-I-am-today was me–i.e., it was a human person. It was not merely a cell with “remarkable potential” to become me. It was me.

If anyone is confused here, it’s Barnard. Of course each egg and sperm has the potential to form a person, especially when we throw biotechnology into the equation, as the book he’s reviewing explicitly does. We already have techniques to revert and differentiate a sperm cell into an egg. For that matter, given time and research, we’ll be able to reprogram just about any cell into a totipotent state, and clone someone from a cheek swab. Does Mr Barnard regard every cell he sheds as a potential person?

Perhaps he wants to argue that a sperm or egg cell doesn’t have the potential for personhood without a human assist. But then by that limitation the zygote has to be excluded as well — no human zygote can develop to term without the extreme cooperation of another individual. Try it; extract a fertilized egg and set it in a beaker by your nightstand, and wait for a baby to crawl out. Won’t happen. A uterus and attendant physiological and behavioral meat construct, i.e., woman, is also an amazing piece of biotechnology that is a necessary component of the developmental process.

But the real blow to this whole “potential” argument is damaged irreparably by Barnard’s last few sentences — was he going for a reductio here? Is the entire essay an exercise in irony? ‘Cause that dope was dumb.

Yes, Mr Barnard began as a zygote. That does not mean the zygote was Mr Barnard. My car began as a stack of metal ingots and barrels of plastics; that does not imply that an ingot of iron is a car. My house began as a set of blueprints and an idea in an architect’s mind; nobody is going to pay the architect rent for living in his cranium or on a stack of paper in a cabinet. The zygote was not Justin Barnard, unless Justin Barnard is still a vegetating single-celled blob, in which case I’d like to know how he typed his essay.

Since Barnard claims to be a philosopher, I’ll cite another, a guy named Aristotle. This is a quote I use in the classroom when I try to explain to them how epigenesis works, in contrast to preformation. Aristotle did some basic poking around in chicken eggs and in semen, and he noticed something rather obvious—there were no bones in there, nor blood, nor anything meatlike or gristly or brainy. So he made the simple suggestion that they weren’t there.

Why not admit straight away that the semen…is such that out of it blood and flesh can be formed, instead of maintaining that semen is both blood and flesh?

Barnard is making the classic preformationist error of assuming that everything had to be there in the beginning: I am made of bones and blood and flesh and brains and guts and consciousness and self-identity, therefore the zygote must have contained bones and blood and flesh and brains and guts and consciousness and self-identity.

It didn’t.

Why not admit straight away that the zygote is such that out of it selfhood may arise, rather than maintaining that the zygote is the self?

In that case we have to recognize that the person is not present instantaneously at one discrete moment, but emerges gradually over months to years of time, that there were moments when self was not present and other moments when self clearly was present, and moments in between where there is ambiguity or partial identity or otherwise blurry gray boundaries. This is a conclusion that makes conservative ideologues wince and shy away — I think it’s too complicated for their brains, which may in some ways be equivalent to the gormless reflexive metabolic state of the zygote — but it is how science understands the process of development.

The new phrenology

Morphological variation is important, it’s interesting…and it’s also common. It’s one of my major scientific interests — I’m actually beginning a new research project this spring with a student and I doing some pilot experiments to evaluate variation in wild populations here in western Minnesota, so I’m even putting my research time where my mouth is in this case. There has been some wonderful prior work in this area: I’ll just mention a paper by Shubin, Wake, and Crawford from 1995 that examined limb skeletal morphology in a population of newts, and found notable variation in the wrist elements — only about 70% had the canonical organization of limb bones.



I’ve also mentioned the fascinating variation in the morphology of the human aorta. Anatomy textbooks lay out the most common patterns, but anyone who has taught the subject knows that once you start dissecting, you always find surprises, and that’s OK: variation is the raw material of evolution, so it’s what we expect.

The interesting part is trying to figure out what causes these differences in populations. We can sort explanations into three major categories.

  1. Genetic variation. It may be the the reason different morphs are found is that they carry different alleles for traits that influence the developmental processes that build features of the organism. Consider family resemblances, for instance: your nose or chin might be a recognizable family trait that you’ve inherited from one of your parents, and may pass on to your children.

  2. Environmental variation. The specific pattern of expression of some features may be modified by environmental factors. In larval zebrafish, for instance, the final number of somites varies to a small degree, and can be biased by the temperature at which they are raised. They’re also susceptible to heat shock, which can generate segmentation abnormalities.

  3. Developmental noise. Sometimes, maybe often, the specific details of formation of a structure may not be precisely determined — they wobble a bit. The limb variation Shubin and others saw, for example, was almost entirely asymmetric, so it’s not likely to have been either genetic or environmental. They were just a consequence of common micro-accidents that almost certainly had no significant effect on limb function.

When I see variation, the first question that pops into my head is which of the above three categories it falls into. The second question is usually whether the variation does anything — while some may have consequences on physiology or movement or sexual attractiveness, for instance, others may really be entirely neutral, representing equivalent functional alternatives. Those are the interesting questions that begin inquiry; observing variation is just a starting point for asking good questions about causes and effects, if any.

I bring up this subject as a roundabout introduction to why I find myself extremely peeved by a recent bit of nonsense in the press: the claim that liberal and conservative brains have a different organization, with conservatives having larger amygdalas (“associated with anxiety and emotions”) and liberals having a larger anterior cingulate (“associated with courage and looking on the bright side of life”).


I don’t deny the existence of anatomical variation in the brain — I expect it (see above). I don’t question the ability of the technique, using MRI, to measure the dimensions of internal structures. I even think these kinds of structural variations warrant more investigation — I think there are great opportunities for future research to use these tools to look for potential effects of these differences.

What offends me are a number of things. One is that the interesting questions are ignored. Is this variation genetic, environmental, or simply a product of slop in the system? Does it actually have behavioral consequences? The authors babble about some correlation with political preferences, but they have no theoretical basis for drawing that conclusion, and they can’t even address the direction of causality (which they assume is there) — does having a larger amygdala make you conservative, or does exercising conservative views enlarge the amygdala?

I really resent the foolish categorization of the functions of these brain regions. Courage is an awfully complex aspect of personality and emotion and cognition to simply assign to one part of the brain; I don’t even know how to define “courage” neurologically. Are we still playing the magical game of phrenology here? This is not how the brain works!

Furthermore, they’re picking on a complex phenomenon and making it binary. Aren’t there more than one way each to be a conservative or a liberal? Aren’t these complicated human beings who vary in an incredibly large number of dimensions, too many to be simply lumped into one of two types on the basis of a simple survey?

This is bad science in a number of other ways. It was done at the request of a British radio channel; they essentially wanted some easily digestible fluff for their audience. The investigator, Geraint Rees, has published quite a few papers in credible journals — is this really the kind of dubious pop-culture crap he wants to be known for? The data is also feeble, based on scans of two politicians, followed by digging through scans and questionnaires filled out by 90 students. This is blatant statistical fishing, dredging a complex data set for correlations after the fact. I really, really, really detest studies like that.

And here’s a remarkable thing: I haven’t seen the actual data yet. I don’t know how much variation there is, or how weak or strong their correlations are. It’s because I can’t. This work was done as a radio stunt, is now being touted in various other media, and the paper hasn’t been published yet. It’ll be out sometime this year, in an unnamed journal.

We were just discussing the so-called “decline effect”, to which my answer was that science is hard, it takes rigor and discipline to overcome errors in analysis and interpretation, and sometimes marginal effects take a great deal of time to be resolved one way or the other…and in particular, sometimes these marginal results get over-inflated into undeserved significance, and it takes years to clear up the record.

This study is a perfect example of the kind of inept methodology and lazy fishing for data instead of information that is the root of the real problem. Science is fine, but sometimes gets obscured by the kind of noise this paper is promoting.

I have to acknowledge that I ran across this tripe via Blue Girl, who dismisses it as “sweeping proclamations about the neurophysiological superiority of the liberal brain”, and Amanda Marcotte, who rejects it because “This kind of thing is inexcusable, both from a fact-based perspective and because the implication is that people who are conservative can’t help themselves.” Exactly right. This kind of story is complete crap from the premise to the data to the interpretations.

The molecular foundation of the phylotypic stage


When last we left this subject, I had pointed out that the phenomenon of embryonic similarity within a phylum was real, and that the creationists were in a state of dishonest denial, arguing with archaic interpretations while trying to pretend the observations were false. I also explained that constraints on morphology during development were complex, and that it was going to take something like a thorough comparative analysis of large sets of gene expression data in order to drill down into the mechanisms behind the phylotypic stage.

Guess what? The comparative analysis of large sets of gene expression data is happening. And the creationists are wrong, again.

Again, briefly, here’s the phenomenon we’re trying to explain. On the left in the diagram below is the ‘developmental hourglass’: if you compare eggs from various species, and adults from various species, you find a diversity of forms. However, at one period in early development called the phylytypic stage (or pharyngula stage specifically in vertebrates), there is a period of greater similarity. Something is conserved in animals, and it’s not clear what; it’s not a single gene or anything as concrete as a sequence, but is instead a pattern of interactions between developmentally significant genes.


The diagram on the right is an explanation for the observations on the left. What’s going on in development is an increase in complexity over time, shown by the gray line, but the level of global interactions does not increase so simply. What this means is that in development, modular structures are set up that can develop autonomously using only local information; think of an arm, for instance, that is initiated as a limb bud and then gradually differentiates into the bones and muscle and connective tissue of the limb without further central guidance. The developing arm does not need to consult with the toes or get information from the brain in order to grow properly. However, at some point, the limb bud has to be localized somewhere specific in relation to the toes and brain; it does require some sort of global positioning system to place it in the proper position on the embryo. What we want to know is what is the GPS signal for an embryo: what it looks like is that that set of signals is generated at the phylotypic stage, and that’s why this particular stage is relatively well-conserved.

One important fact about the diagram above: the graph on the right is entirely speculative and is only presented to illustrate the concept. It’s a bit fake, too—the real data would have to involve multiple genes and won’t be reducible to a single axis over time in quite this same way.

Two recent papers in Nature have examined the real molecular information behind the phylotypic stage, and they’ve confirmed the molecular basis of the conservation. Of course, by “recent”, I mean a few weeks ago…and there have already been several excellent reviews of the work. Matthew Cobb has a nice, clean summary of both, if you just want to get straight to the answer. Steve Matheson has a three part series thoroughly explaining the research, so if you want all the details, go there.

In the first paper by Kalinka and others, the authors focused on 6 species of Drosophila that were separated by as much as 40 million years of evolution, and examined quantitative gene expression data for over 3000 genes measured at 2 hour intervals. The end result of all that work is a large pile of numbers for each species and each gene that shows how expression varies over time.

Now the interesting part is that those species were compared, and a measure was made of how much the expression varied: that is, if gene X in Drosophila melanogaster had the same expression profile as the homologous gene X in D. simulans, then divergence was low; if gene X was expressed at different times to different degrees in the two species, then divergence was high. In addition, the degree of conservation of the gene sequences between the species were also estimated.

The prediction was that there ought to be a reduction of divergence during the phylotypic period. That is, the expression of genes in these six species should differ the least in developmental genes that were active during that period. In addition, these same genes should show a greater degree of evolutionary constraint.

Guess what? That’s exactly what they do see.

Temporal expression divergence is minimized during the phylotypic period. a, Temporal divergence of gene expression at individual time points during embryogenesis. The curve is a second-order polynomial that fits best to the divergence data. Embryo images are three-dimensional renderings of time-lapse embryonic development of D. melanogaster using Selective Plane Illumination Microscopy (SPIM).

That trough in the graph represents a period of reduced gene expression variance between the species, and it corresponds to that phylotypic period. This is an independent confirmation of the morphological evidence: the similarities are real and they are an aspect of a conserved developmental program.

By the way, this pattern only emerges in developmental genes. They also examined genes involved in the immune system and metabolism, for instance, and they show no such correlation. This isn’t just a quirk of some functional constraint on general gene expression at one stage of development, but realy is something special about a developmental and evolutionary constraint.

The second paper by Domazet-Loso and Tautz takes a completely different approach. They examine the array of genes expressed at different times in embryonic development of the zebrafish, and then use a comparative analysis of the sequences of those genes against the sequences of genes from the genomic databases to assign a phylogenetic age to them. They call this phylostratigraphy. Each gene can be dated to the time of its origin, and then we can ask when phylogenetically old genes tend to be expressed during development.

The prediction here is that there would be a core of ancient, conserved genes that are important in establishing the body plan, and that they would be expressed during the phylotypic stage. The divergence at earlier and later stages would be a consequence of more novel genes.

Can you guess what they saw? Yeah, this is getting predictable. The observed pattern fits the prediction.

(Click for larger image)

Transcriptome age profiles for the zebrafish ontogeny. a, Cumulative transcriptome age index (TAI) for the different developmental stages. The pink shaded area represents the presumptive phylotypic phase in vertebrates. The overall pattern is significant by repeated measures ANOVA (P = 2.4 3 10-15, after Greenhouse-Geisser correction P = 0.024). Grey shaded areas represent ± the standard error of TAI estimated by bootstrap analysis.

So what does this all tell us? That the phylotypic stage can be observed and measured quantitatively using several different techniques; that it represents a conserved pattern of development gene expression; and that the genes involved are phylogenetically old (as we’d expect if they are conserved.)

Domazet-Loso and Tautz propose two alternative explanations for the phenomenon, one of which I don’t find credible.

Adaptations are expected to occur primarily in response to altered ecological conditions. Juvenile and adults interact much more with ecological factors than embryos, which may even be a cause for fast postzygotic isolation. Similarly, the zygote may also react to environmental constraints, for example, via the amount of yolk provided in the egg. In contrast, mid-embryonic stages around the phylotypic phase are normally not in direct contact with the environment and are therefore less likely to be subject to ecological adaptations and evolutionary change. As already suggested by Darwin, this alone could explain the lowered morphological divergence of early ontogenetic stages compared to adults, which would obviate the need to invoke particular constraints. Alternatively, the constraint hypothesis would suggest that it is difficult for newly evolved genes to become recruited to strongly connected regulatory networks.

They propose two alternatives, that the phylotypic stage is privileged and therefore isn’t being shaped by selection, or that it is constrained by the presence of a complicated gene network, and therefore is limited in the amount of change that can be tolerated. The first explanation doesn’t make sense to me: if a system is freed from selection, then it ought to diverge more rapidly, not less. I’m also baffled by the suggestion that the mid-stage embryos are not in direct contact with the environment. Of course they are…it’s just possible that that mid-development environment is more stable and more conserved itself.

What we need to know more about is the specifics of the full regulatory network. A map of the full circuitry, rather than just aggregate measures of divergence, would be nice. I’m looking forward to it!

The creationists aren’t, though.

Domazet-Loso, T., & Tautz, D. (2010). A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature 468 (7325): 815-818. DOI: 10.1038/nature09632

Kalinka, A., Varga, K., Gerrard, D., Preibisch, S., Corcoran, D., Jarrells, J., Ohler, U., Bergman, C., Tomancak, P. (2010). Gene expression divergence recapitulates the developmental hourglass model. Nature 468 (7325): 811-814 DOI: 10.1038/nature09634

My mouse has two daddies


This is awesome news. Biologists have figured out how to enable two male mice to have babies together, with no genetic contribution from a female mouse. I, for one, look forward to our future gay rodent overlords.

It was a clever piece of work. Getting progeny from two male parents has a couple of difficulties. One is that you need an oocyte, which is a large, specialized, complex cell type, and males don’t make them. Not at all. You can tear a boy mouse to pieces looking for one, and you won’t find a single example—they’re a cell found exclusively in female ovaries.

Now you might think that all we’d have to do is grab one from a female mouse, throw out its nuclear contents, and inject a male nucleus into it, but that doesn’t work, either. The second problem is that during the maturation of the oocyte, the DNA has to be imprinted, that is, given a female-specific pattern of activation and inactivation of genes. If that isn’t done, there will be a genetic imbalance at fertilization, and development will be abnormal. What we need to be able to do is grow an oocyte progenitor with male DNA in a female ovary.

So that’s what was done, and here’s how.


Start with Father #1, whose cells all contain an X and a Y chromosome. Connective tissue cells were extracted from the mouse (in this case, an embryo), and then reprogrammed by viral transduction with modified copies of the genes Pou5f1, Sox2, Klf4, and Myc. This step produces induced pluripotent stem cells (iPS cells), or cells that have the ability to develop into all (probably) of the tissues of the body. These cells are then grown in a dish.

The next step is to give Father #1’s cells a sex change operation. This turns out to be trivial: in culture, cells can spontaneously lose a chromosome by non-disjunction, and 1-3% of the cells will lose their Y chromosome, and convert to X0. No Y chromosome means it is now a functionally female cell.

There is a significant difference between humans and mice here. Sometimes (about 1 in 5,000 births) humans are born with only one X chromosome, a condition called Turner syndrome. These individuals appear to be entirely normal females, except for some minor cosmetic differences, an unfortunate predisposition to a few problems like heart disease, and of particular relevance here, are also sterile. Mice are different: Turner syndrome mice are fertile. Apparently, mice have a god-given edge in the gay reproduction race.

Once a population of Father #1’s cells that are X0 are identified, they are then injected into a female mouse blastocyst to produce a chimera, an embryo with a mix of host cells (which are genetically XX) and donor cells (which are X0). That they’re mixed together in the resulting offspring doesn’t matter; it may be a callous way of looking at it, but the only purpose of the host XX cells is to provide a female mouse environment to house Father #1’s X0 cells that end up in the ovaries.

That’s the result of all this tinkering: a female mouse is born with a subset of Father #1’s reprogrammed cells nestled in her ovaries, where they mature in a female body and differentiate into oocytes. The oocytes divide by meiosis, producing egg cells that contain either one X chromosome, or no sex chromosome at all (0).

Finally, Father #2 comes into the picture. Father #2 is an ordinary male, with testes containing cells that go through meiosis and mature into ordinary sperm containing either one X chromosome or one Y chromosome. These sperm are used to fertilize eggs from the chimeric female, which, by all the shenanigans describe above, are derived from Father #1. Both male (XY) and female (X0) progeny ensue. That this actually occurred was thoroughly confirmed by testing the progeny for genetic markers from both fathers…and it’s true. The only genetic contributions were from the dads, and nothing from the host mother.

Now you may be sitting at home with your dearly beloved gay partner and wondering whether you will be able to have babies together someday. Or perhaps you’re a narcissistic man sitting at home alone, thinking you’d like to have babies with yourself, if only you could convince a few of your cells to make eggs (this is another possibility: there is no barrier to this technique being applied in cases where Father #1 is also Father #2, except that it is incestuous to the max). I expect it will be possible someday, but it isn’t right now. There are a few obstacles to doing this in humans.

  1. We haven’t worked out that genetic reprogramming trick for humans yet, so we don’t have a technique for producing pluripotent stem cells from your somatic cells. Give it time, though, and keep funding adult stem cell research, and it’ll happen.

    Also note the rule of unintended consequences. The fundy fanatics have been anti-embryonic stem cell research for years, and one of their tactics has been to insist that adult stem cell research is far more important. In the long run, it is…and oh, look what we’ll be able to do!

  2. The reprogramming trick involves viral transfection, the insertion of mutant copies of a few specific genes. This is probably not desirable. All kids are mutant anyway, but this is adding a specific, constant kind of mutation to all of the individuals produced by this method.

  3. It still requires a woman, and a woman who has been embryonically modified as a blastocyst at that. Did you know women have rights, including the right to not be a vessel for a scientific experiment? It’s true. They also take years and years to grow to sexual maturity, so even if you got started right now it would be a dozen years before she started making oocytes for you, and by the way, she’d inform you that she only produces eggs for herself, not you.

    There may be ways around this, but the techniques aren’t here yet. To produce eggs, we really don’t need the whole woman, just the ovary: another goal of stem cell research is to regrow organs from cells in a dish, for instance to build a new heart or pancreas for transplantation. Consider ovaries on the list of organs.

  4. That difference between mice and humans, that X0 mice are fertile while X0 women are not, seems like a serious problem. We apparently need the pair of X chromosomes working together to provide the correct gene dosage for normal maturation of the egg. It just means that we need to add an extra step to the procedure for people, though: transfer by injection an extra X chromosome from a donor cell from Father #1 to the X0 cells, producing a composite XX cell derived entirely from a male.

  5. The fundies will go raving apeshit bonkers. So what else is new?

  6. OK, there are also some serious ethical concerns that would need to be worked out, independent of the Bible-thumping theocratic sex police. As you can see from the recipe above, this is a procedure that involves extensive manipulation of embryos, almost all of it experimental, and the end result is…a baby. We should be conscientious in our care in any procedure that can produce human beings, especially if there is risk of producing damaged human beings. This can also only be categorized as a kind of expensive luxury treatment, and it’s difficult to justify such elaborate work for solely egotistical gratification. Especially for you, nerd-boy masturbating alone at home. (But learning more about the mechanisms of reproduction is more than enough to justify this work in mice, at least).

Wait…all this is just for male gay couples. What about nurturing lesbians who want to have children together? That has another tricky problem: you need a Y chromosome to induce normal sperm differentiation, and lesbian couples don’t have any of those. At all. They’re going to have to go to a male donor for a genetic contribution, diluting the purity of the genetic side of the procedure. However, that has a technology in the works to help out already: see obstacle #4 above. We’ll have to isolate iPS cells from Mother #1, inject a donor Y chromosome into them, cultivate chimeric male (or chimeric testis in a dish) to produce sperm, and then fertilize eggs from Mother #2 with the Mother #1-derived sperm. Any sons produced by this procedure would have three parents, Mother #1, Mother #2, and the Male Donor who provided the Y chromosome, and only the Y chromosome. Any daughters, though, would only have two parents: Mother #1 and Mother #2.

Isn’t reproductive biology fun? It’s the combination of exciting science with terrifyingly deep social implications.

Deng JM, Satoh K, Chang H, Zhang Z, Stewart MD, Wang H, Cooney AJ, Behringer RR (2010) Generation of viable male and female mice from two fathers. Biology of Reproduction DOI:10.1095/biolreprod.110.088831.