Tissue Organization Field Theory

It’s been a while since I brought everyone up to date on the progress of my Ecological Development course, because I’ve been busy. So have the students. After our spring break I subjected them to the dreaded oral exam, which actually isn’t so bad. I tried to engage them less in an adversarial role and more as a quiet conversation between two people on science. Some students took to it easily — the more outgoing ones — others were noticeably nervous, which was OK, and I hope they learned that it isn’t that terrifying to have a discussion with a mentor.

Then the next few weeks were a mad whirl of horrible things done to babies: teratogens, endocrine disruptors, multi-generational epigenetic inheritance, all that fun stuff. We wrapped up with the depressing stuff for me, although the young’uns were more sanguine, I think. We talked about adult onset developmental diseases (it’s good to look at heart disease through the lens of developmental biology), aging, and cancer. Next week they get some time off, because I’m being drawn away to a conference on the east coast, but they’re supposed to spend it preparing for their final presentations, which will consume the last two weeks of class. And then we’re all done. School’s out for summer!

I’m going to say a bit about our last class discussion, because it got into some interesting territory and reflects the theme of the course well. We talked about that theory mentioned in the title of this article, and the origins of cancer, and to do that I have to give you all a little background.

Tissue Organization Field Theory (TOFT) is an alternative to what is sort of the dominant paradigm in cancer biology, the Somatic Mutation Theory (SMT). I have to say “sort of” because what I get from the literature is that SMT is more of a working assumption, and that cancer biologists are open to new ideas. The SMT is a useful molecular perspective on carcinogenesis. It postulates that cancer is a cellular disorder in which the genetic material has been perturbed to produce a lineage of cells with aberrant characteristics, that if we want to figure out what the primary cause of a cancer was, we can trace it back to a somatic mutation, or a change in a critical gene or, more likely, multiple genes, that lead to uncontrolled proliferation. So we pursue oncogenes, genes that have the potential to acquire mutations that trigger cell division or bypass control points, and tumor suppressor genes, protective genes that, when damaged, remove essential regulators of growth.

So, under the SMT, cancer is a disease caused by the progressive accumulation of mutations in cells of the body, as they divide. These mutations gradually strip away the normal restraints on cell division, and on immune system recognition, and on cell death activation, etc., etc., etc. until you have a rogue cell that can seed the growth of a massively disruptive tumor.

And it’s not wrong! Cancer biology has been immensely productive in identifying the enabling mutations, and even developing treatments that specifically target molecular agents of cancer. We know that somatic mutations are a routine part of the progression of cancer, and we also know that there heritable alleles that can affect the likelihood of the disease. The SMT is a tool to explain many of the phenomena of cancer, and it’s not going to just go away. It’s also a tool that is amenable to a reductionist approach to cancer biology, and is well-adapted to the utility of molecular biology.

Tissue Organization Field Theory is an alternative explanation for the origins of cancer.

TOFT argues that the focus of the SMT on single cell events is inappropriate and misses a whole range of effects at the level of tissue organization, effects which are more important in creating a pathological environment in which those mutations can accumulate. Further, it gets into field theory, which is important in developmental biology but isn’t exactly the subject of common conversation. Here’s one standard definition of a field: “a morphogenetic (or developmental) field is a region or a part of the embryo which responds as a coordinated unit to embryonic induction and results in complex or multiple anatomic structures.” If that’s not helpful — and it probably isn’t, we’d have to go over a textbook if we wanted to explain developmental field theory — here’s a diagramatic metaphor. Do you see the field in this picture?

There’s something special about part of that image, but it’s not that the individual subunits are intrinsically different — it’s tied up in the relationships between the central set of blocks and the blocks outside of it. There’s something different going on with a subset of the blocks, but it’s not necessarily best described by explaining the details of single blocks, but is more easily explained at a higher level, as properties of a tissue within a tissue. Of course, what will eventually happen in a developing organism is that those central blocks will express a unique pattern of genes, so eventually it’s identifiable by molecular markers, but the field first arises in a sea of genetically and epigenetically uniform cells.

Another important property of a field is that it is not itself uniform. It’s going to acquire complex spatial properties over time. Insect limbs, for instance, arise from a disc-shaped field with extensive patterning information within them, so the central region will become the distal tip of the limb, and there is information that is interpreted as polar coordinates that specifies what portion of the limb is anterior, posterior, medial, and lateral (the limb is not a uniform cylinder). Similarly, vertebrates have a limb field represented in the limb bud, with gradients of morphogens specifying the orientation of the limb, and with re-expression of Hox genes used to specify longitudinal positions. Hox genes in a limb field are interpreted in different ways than Hox genes along the body axis, obviously.

The key factor here is that in field theory cells are not simply independent units — they are part of a larger assemblage, a tissue, that has complex fates that are not easily summarized by individual gene expression. They have to be understood as a network.

That’s the first thing to remember: TOFT is treating a cancer as a field, with field properties, which are not adequately described if you only look at cancer as a collection of autonomous cells all doing their own thing at the command of their broken genes. Aberrant disruption of the field can produce aberrant structures without requiring any genetic changes.

This is the difference between a mutagen and a teratogen. The effects of a mutagen are caused directly by damage to the structure or sequence of DNA; they produce heritable changes to the cells of an organism. Teratogens, on the other hand, are not necessarily mutagenic at all — they disrupt the normal pattern of development without changing genes at all. Thalidomide babies, for example, had some extreme morphological changes, like phocomelia or truncated limb development, but those are not heritable, and the people affected by thalidomide can grow up to have normal, healthy children.

TOFT argues something similar, that there is a disruption of a tissue that initializes aberrant growth, that may then be an enabling precondition for the accumulation of mutations. One piece of evidence for this is a set of experiments on tissues, illustrated below.

Most cancers arise in epithelial tissues, like the sheets of cells that line glands or your organs, in large part because those are the cells that divide most frequently. These epithelial cells, also called parenchyma, do not typically grow in isolation, but on a substrated of connective tissue, extracellular matrix, and other cell types, called stroma. The stroma supports and signals the overlying epithelium, and vice versa, and together they make a coherent functional tissue.

The theory suggests that cancers can arise in epithelia by way of disruptions in signaling in the stroma. A carcinogen could distort the interactions between stroma and epithelium at the level of the stroma, and the epithelium then goes nuts and proliferates to produce a pre-cancerous mass.

One test of the theory would be to separate stroma and epithelium, expose the stroma to a short-lived teratogen, and then after the teratogen was washed out, re-associate the two and determine whether there was an increase in the frequency of cancers in the epithelium, which has not been exposed to teratogens.

The experiment has been done. Here are the results for rat mammary gland tissue in which the epithelium was exposed to the solvent vehicle but no N-methyl nitorsourea (a potent mutagen), while the stroma was soaked in NMu, labeled VEH/NMu. The numerator describes the epithelial condition, and the denominator is the stroma condition, so NMu/NMu means both were hit with the mutagen, VEH/VEH means both were exposed only to the vehicle, and NMu/VEH means the epithelium was poisoned with NMu, while the stroma was not.

There’s an awfully strong positive correlation between exposing the stroma to mutagens and getting tumors, and a negative correlation with exposing epithelia to mutagens and tumors.

You want more evidence? Here’s a very interesting experiment. Start with aggressively metastatic melanoma cells from a human patient (labeled in green, below). Inject them into a completely different environment, the neural crest pathway in a developing chick embryo. Surprisingly, if you accept the SMT, the cancer cells calm right down and are conditioned by their environment to participate in normal development in the chick and get incorporated into the facial cartilages and sympathetic ganglia.

I suspect those melanoma cells do carry somatic mutations, and are not actually “cured” of a predisposition to cancer. What the experiment says, though, is that environmental influences are extremely important in regulating the behavior of these cells, and that modifying the cells communicating with the cancerous cells can have a profound effect on how they act.

Note that this is not a pathway to a cure. It’s all well and good to say that if we could break up a tumor, separate the individual cells and put them in a more nurturing, embryo-like environment, they’ll stop acting up and resume normal, regulated growth, but if we could do that, slicing out the tumor and tossing it in an incinerator would also be effective. The problem is that in a human patient we do not and cannot have such precise control of the micro-environment of the cancer, and in fact, the tumor itself is a kind of bubble of micro-environment that actively reinforces cancer growth.

My students and I read a paper from Carlos Sonnenschein, who is a major proponent of TOFT, as well as our textbook summary. The paper was titled The tissue organization field theory of cancer: a testable replacement for the somatic mutation theory. They’re a smart bunch, and they see the promise of the idea, in part because this whole course is about thinking a level above reductionist cell biology, but they also found the word “replacement” off-putting. It doesn’t invalidate everything about the SMT, but it does support an important alternative route for carcinogenesis. They also weren’t impressed by the rather aggressive insistence by some TOFT proponents that they have the One True Explanation, and that their observations are sufficent to explain cancer — we came up with a few alternative interpretations of their own favorite experiments that they haven’t nailed down completely just yet.

One thing that amused me is that the class consensus actually converged on the views of another paper by Bedessem and Ruphy, which I did not assign them to read, largely because of its more philosophical argument (I’ve focused on empirical/experimental papers in the class). This is how I feel about it, too.

The building of a global model of carcinogenesis is one of modern biology’s greatest challenges. The traditional somatic mutation theory (SMT) is now supplemented by a new approach, called the Tissue Organization Field Theory (TOFT). According to TOFT, the original source of cancer is loss of tissue organization rather than genetic mutations. In this paper, we study the argumentative strategy used by the advocates of TOFT to impose their view. In particular, we criticize their claim of incompatibility used to justify the necessity to definitively reject SMT. First, we note that since it is difficult to build a non-ambiguous experimental demonstration of the superiority of TOFT, its partisans add epistemological and metaphysical arguments to the debate. This argumentative strategy allows them to defend the necessity of a paradigm shift, with TOFT superseding SMT. To do so, they introduce a notion of incompatibility, which they actually use as the Kuhnian notion of incommensurability. To justify this so-called incompatibility between the two theories of cancer, they move the debate to a metaphysical ground by assimilating the controversy to a fundamental opposition between reductionism and organicism. We show here that this argumentative strategy is specious, because it does not demonstrate clearly that TOFT is an organicist theory. Since it shares with SMT its vocabulary, its ontology and its methodology, it appears that a claim of incompatibility based on this metaphysical plan is not fully justified in the present state of the debate. We conclude that it is more cogent to argue that the two theories are compatible, both biologically and metaphysically. We propose to consider that TOFT and SMT describe two distinct and compatible causal pathways to carcinogenesis. This view is coherent with the existence of integrative approaches, and suggests that they have a higher epistemic value than the two theories taken separately.

Anyway, keep an eye open for more on the tissue organization field theory — there seems to be a fair bit of ongoing debate in the scientific literature about it. I’ll keep telling everyone cancer is a developmental disease, so you need more developmental biologists to study it. Or, alternatively, every cancer biologist is already a developmental biologist.

Bedessem B, Ruphy S. (2015) SMT or TOFT? How the two main theories of carcinogenesis are made (artificially) incompatible. Acta Biotheor. 63(3):257-67.

Soto AM, Sonnenschein C (2011) The tissue organization field theory of cancer: a testable replacement for the somatic mutation theory. Bioessays. 33(5):332-40.

Steve Pinker’s hair and the muscles of worms

I’ve been guilty of teaching bean-bag genetics this semester. Bean-bag genetics treats individuals as a bag of irrelevant shape containing a collection of alleles (the “beans”) that are sorted and disseminated by the rules of Mendel, and at its worst, assigns one trait to one allele; it’s highly unrealistic. In my defense, it was necessary — first-year students struggle enough with the basic logic of elementary transmission genetics without adding great complications — and of course, in some contexts, such as population genetics, it is a useful simplification. It’s just anathema to anyone more interested in the physiological and developmental side of genetics.

The heart of the problem is that it ignores the issue of translating genotype into phenotype. If you’ve ever had a basic genetics course, it’s quite common to have been taught only one concept about the phenotype problem: that an allele is either dominant, in which case it is expressed as the phenotype, or it’s recessive, in which case it is completely ignored unless it’s the only allele present. This idea is so 19th century — it’s an approximation made in the complete absence of any knowledge of the nature of genes.

And the “one gene, one trait” model violates everything we do know about the phenotype and genotype. Every gene is pleiotropic — it influences multiple traits to varying degrees. Every trait is multigenic — multiple genes contribute to the expression of every phenotypic detail. The bean-bag model is totally inadequate for describing the relationship of genes to physiology and morphology. Instead of a bean-bag, I prefer to think of the genome as comparable to a power spectrum, an expression of the organism in a completely different domain. But I wrote about that previously, and I’ll make this explanation a little simpler.

Here’s the problem: you can’t always reliably predict the phenotype from the genotype. We have a skewed perspective on the problem, because historically, genetics has first searched for strong phenotypes, and then gone looking for the genetic cause. We’ve been effectively blind to many subtle phenotypic effects, simply because we don’t know how to find them. When we go the other way, and start by mutating known genes and then looking for changes in the phenotype, we’re often surprised to discover no detectable change. One of the classic examples is the work of Elkins (1990), who found that mutating a neural cell adhesion gene, Fasciclin I, did not generate any gross defects. Mutating another gene, a signal transduction gene called Abelson tyrosine kinase, similarly had no visible effects. Mutating the two together, though — and this is a major clue to how these strange absences of effect could work — did produce gross and obvious effects on nervous system development.

Providing another great example, Steve Pinker examined his own genome, and discovered that his genes said he was predisposed to be red-haired and at high risk for baldness. If you’ve seen Steve Pinker, you know he’s neither.

How can this be? As any geneticist will tell you, the background — the other alleles present in the organism — are important in defining the pattern of expression of a specific gene of interest. One simple possibility is that the genome contains redundancy: that a trait such as adhesion of axons in the nervous system or the amount of hair on the head can be the product of multiple genes, each doing pretty much the same thing, so knocking out one doesn’t have a strong effect, because there is a backup present.

Genetic interactions provide a general model for incomplete penetrance. Representation of a negative (synergistic) genetic interaction between two genes A and B.

So Steve Pinker could have seen that he has a defective Gene A, which is important in regulating hair, but maybe there’s another Gene B lurking in the system that we haven’t characterized yet, and which can compensate for a missing Gene A, and he has a particularly strong form of it. One explanation for a variable association between an allele and the phenotype, then, is that we simply don’t have all the information about the multigenic cause of the phenotype, and there are other genes that can contribute.

This doesn’t explain all of the observed phenomena, however. Identical twins who share the same complement of alleles also exhibit variability in the phenotype; we also have isogenic animal lines, where every individual has the same genetic complement, and they also show variability in phenotype. This is the problem of penetrance; penetrance is a genetics term that refers to the likelihood that an individual carrying an allele will actually express the phenotype associated with that allele…and it’s not always 100%.

Again, the explanation lies in the other genes present in the organism. No gene functions all by itself; its expression is dependent on a cloud of other proteins — transcription factors, enhancers, chaperones — all of which modulate the gene of interest. We also have to deal with statistical variation in the degree of expression of all those modulatory factors, which vary by chance from cell to cell, and so the actual degree of activation of a gene may follow a kind of bell curve distribution. In the cartoon below, the little diamonds represent these partners; sometimes, just by chance, they’ll be present in sufficiently high numbers to boost Gene B’s output enough to fully compensate for a defective Gene A; in other cases, just by chance, they’re too low in concentration to adequately compensate for the absence.

Genetic interactions provide a general model for incomplete penetrance. A model for incomplete penetrance based on variation in the activity of genetic interaction partners.

What the above cartoon illustrates is the concept of developmental noise, the idea that the cumulative total of statistical variation in gene expression during development can produce significant phenotypic variation in the absence of any differences in the genotype. Developmental noise is a phrase bruited about quite a bit, and there’s good reason to think it’s valid: we can see quantitative variation in gene expression with molecular techniques, for instance. But at the same time we have other concepts, like redundancy and canalization, that work to buffer variation and produce reliable outputs from developmental processes, so we don’t have many good examples where we can directly correlate subtle variation at the molecular level with clear morphological differences.

To test that, we have to go to simple animal models (it turns out that Steve Pinker is a rather intractable experimental animal). And here we have a very nice example in the nematode worm, C. elegans. In these experiments, the investigators were dealing with an isogenic strain — the genetic background was identical in all of the animals — raised in a uniform environment. They were looking at a mutant in the gene tbf9, which causes defects in muscle formation, but only 50% penetrance; that is, half the time, the mutants appeared completely normal, and the other half of the time they had grossly abnormal muscle development.

Genetic interactions provide a general model for incomplete penetrance. Inactivation of the gene tbx-9 in C. elegans results in an incompletely penetrant defect, with approximately half of embryos hatching with abnormal morphology (small arrow).

See the big red question mark? That’s the big question: can we trace the abnormal phenotype all the way back to random fluctuations in the expression of other genes in the animal? Yes, they can, otherwise it would never have been published in Nature and I wouldn’t be writing about it now.

In this case, they have a situation analogous to the Gene A/Gene B cartoons above. Gene B is tbx-9; Gene B is a related gene, a duplicate called tbx-8 which acts as a redundant copy. In the experiments below, they knock out tbx-9 with a mutation, and then measure the quantity of other genes in the system using a very precise technique of quantitative fluorescence. Below, I’ve reproduced the entirety of their summary figure, because it is awesome — I just love the idea of being able to count the number of molecules expressed in a developing system. In order to avoid overwhelming everyone, though, I’ll just describe a couple of the panels to give you the gist of the work.

First, just look at the top left panel, a. It’s a plot of the level of expression of the tbx-8 gene over time, where each line in the plot is a different animal. The lines in black are in the wild type animal, with fully functional copies of bothe tbx-8 and tbx-9, and you should be able to see that there’s a fair amount of variation in expression, about two-fold, in different individuals. The lines in green are from animals mutant for tbx-9; it’s messy, but statistically what happens when tbx-9 is knocked out, more tbx-8 gene product is produced.

Panel e, just below it, shows the complementary experiment: the expression of tbx-9 is shown for both wild type (black) and animals with tbx-8 knocked out. Here, the difference is very clear: tbx-9 levels are greatly elevated in the absence of tbx-8. This shows that tbx-8 and tbx-9 are actually tied together in a regulatory relationship where levels of one rise in response to reduced levels of the other, and vice versa.

(Click for larger image)

Early inter-individual variation in the induction of ancestral gene duplicates predicts the outcome of inherited mutations. a, Quantification of total green fluorescent protein (GFP) expression from a tbx-8 reporter during embryonic development in WT (black) and tbx-9(ok2473) (green) individuals. Each individual is a separate line. a.u., Arbitrary units. b, Boxplot of tbx-8 reporter expression (a) showing 1.2-fold upregulation in a tbx-9 mutant at comma stage (~290 min, P=1.6×3 10-3, Wilcoxon rank test). c, Expression of tbx-8 reporter in a tbx-9(ok2473) background for embryos that hatch with (red) or without (blue, WT) a morphological defect. d, Boxplot of c showing tbx-8 expression is higher in tbx-9 embryos that develop a WT phenotype (blue) compared with those that develop an abnormal (red) phenotype at comma stage (P= 6.1×10-3). e, Expression of a ptbx-9::GFP reporter in WT (black) and tbx-8(ok656) mutant (green). f, Boxplot of tbx-9 reporter showing 4.3-fold upregulation at comma stage (~375 min, P=3.6×10-16). g, Expression of tbx-9 reporter in a tbx-8(ok656) mutant background, colour code as in
c. h, Boxplot of g showing tbx-9 expression is higher in tbx-8 embryos that develop a WT phenotype (P=0.033). i, Expression of a pflh-2::GFP reporter in WT (black) and flh-1(bc374) mutant (green). j, Boxplot of flh-2 reporter expression (i) showing 1.8-fold upregulation in a flh-1 mutant at comma stage (~180 min, P=2.2×10-16). k, Bright-field and fluorescence image of an approximate 100-cell flh-1; pflh-2::GFP embryo. Red arrow indicates the local expression of flh-2 reporter quantified for flh-1 phenotypic prediction.
l, Boxplot showing higher flh-2 reporter expression at approximate 100 cells for WT (blue) compared with abnormal (red) phenotypes (P=0.014). Boxplots show the median, quartiles, maximum and minimum expression in each data set.

Now skip over to the right, to panel c. All of the lines in this plot are of tbx-8 expression in tbx-9 mutants, and again you see a wide variation in levels of gene expression. In addition, the lines are color-coded by whether the worm developed normally (blue), or had the mutant phenotype (red). The answer: worms with low tbx-8 levels were more likely to have the abnormal phenotype than those with high levels.

Panel g, just below it, is the complementary analysis of tbx-9 levels in tbx-8 mutants, and it gives the same answer.

Obviously, though, there is still a lot of variability unaccounted for; having relatively high levels of one or the other of the tbx genes didn’t automatically mean the worm developed a wild-type phenotype. There’s got to be something more that is varying. Look way back to the second cartoon I showed, with the little diamonds representing the cloud of transcription factors and chaperone proteins that modulate gene expression. Could there also be correlated variation there? And yes, there is. The authors looked at a chaperone protein called daf-21 that is associated with the tbx system, and found, in mutants for tbx-9, that elevated levels of daf-21 were associated with wildtype morphology (in blue), while lowered levels of daf-21 were associated with the mutant phenotype.

(Click for larger image)

Expression of daf-21 reporter in a tbx-9(ok2473) mutant background. Embryos that hatch into phenotypically WT worms (blue) have higher expression than those hatching with a morphological defect (red) at the comma stage (P=1.9×10-3).

I know what you’re thinking: there isn’t a perfect correlation between high daf-21 levels and wildtype morphology either. But when they do double-label experiments, and take into account both daf-21 and tbx-8 levels in tbx-9 mutants, they found that 92% of the animals with greater than median levels of expression of both daf-21 and tbx-8 had wildtype morphology. It’s still not perfect, but it’s pretty darned good, and besides, it’s no surprise that there are probably other modulatory factors with statistical variation lurking in the system.

What should you learn from this? Developmental noise is real, and is a product of statistical variation in the degree of expression of multiple genetic components that contribute to a phenotype. We can measure that molecular variation in living, developing systems and correlate it phenotypic outcomes. None of this is surprising; we expect that the process of gene expression is going to be a bit noisy, especially in these transcriptional regulators that are present in low concentration in the cell, anyway. But the other cool thing we can observe here is that having multiple noisy systems that interact with each other can produce a more reliable, robust signal and contribute to the fidelity of developmental outcomes.

Burga A, Casanueva MO, Lehner B (2011)
Predicting mutation outcome from early stochastic variation in genetic interaction partners. Nature 480(7376):250-3.

Elkins T, Zinn K, McAllister L, Hoffmann FM, Goodman CS (1990)
Genetic analysis of a Drosophila neural cell adhesion molecule: interaction of fasciclin I and Abelson tyrosine kinase mutations. Cell 60(4):565-75.

(Also on FtB)

Science overwhelmed by self-defeating awe

This video by Alexander Tsiaras is simultaneously lovely and infuriating; it’s a product of technology and science, and the narration is profoundly anti-science.

There are some technical issues that annoy me about the video — it’s a mix of real imagery and computer animation, and it doesn’t draw a line between what is observed and what is fabricated — but it’s visually stunning and otherwise fairly accurate.

But Tsiaras’s running commentary…it’s mystical airy-fairy glop. It takes awe and turns it into a celebration of ignorance.

Even though I am a mathematician, I look at this with marvel of how do these instruction sets not make these mistakes as they build what is us? It’s a mystery, it’s magic, it’s divinity. Then you start to take a look at adult life. Take a look at this little tuft of capillaries. It’s just a tiny sub-substructure, microscopic. But basically by the time you’re nine months and you’re given birth, you have almost 60,000 miles of vessels inside your body. I mean, and only one mile is visible. 59,999 miles that are basically bringing nutrients and taking waste away. The complexity of building that within a single system is, again, beyond any comprehension or any existing mathematics today.

And that instruction set, from the brain to every other part of the body — look at the complexity of the folding. Where does this intelligence of knowing that a fold can actually hold more information, so as you actually watch the baby’s brain grow — and this is one of the things that we’re doing right now. We’re actually doing the launch of two new studies of actually scanning babies’ brains from the moment they’re born. Every six months until they’re six years old — we’re going to be doing actually to about 250 children — watching exactly how the gyri and the sulci of the brains fold to see how this magnificent development actually turns into memories and the marvel that is us.

And it’s not just our own existence, but how does the woman’s body understand to have genetic structure that not only builds her own, but then has the understanding that allows her to become a walking immunological, cardiovascular system that basically is a mobile system that can actually nurture, treat this child with a kind of marvel that is beyond, again, our comprehension — the magic that is existence, that is us?

It’s not magic, and it’s sure as hell not divinity — it’s chemistry. And it certainly does make mistakes: half of all conceptions end in a spontaneous abortion, and about 15% of all pregnancies where the mother knows she is pregnant spontaneously terminate.

I genuinely despise the tactic so widely used by intelligent design creationists, and here by Tsiaris, of reciting really big numbers and babbling about complexity, complexity, complexity. Yes, it’s complicated. But you can build complicated structures with simple rules, and if you look at these systems, what you find are iterative properties and variation induced by local conditions. And if it’s beyond mathematics today, what are all those mathematicians and biologists doing modeling angiogensis?

And then there’s the rampant assignment of agency to everything. “Where does this intelligence of knowing that a fold can actually hold more information” in the brain come from? It doesn’t. The expansion of the cortex is a consequence of selected variation in mitotic regulators for that region of the brain — it expands like bread dough because the cells are replicating to large numbers, and the confines of the skull cause it to buckle and fold. It’s neurogenesis; there aren’t little angels folding pastry in there.

That entire last paragraph beginning from “how does the woman’s body understand to have genetic structure” is total nonsense. The answer is no, the woman’s body does not “understand”. There is no “knowing” there. There are physical/chemical processes guided by a molecular biology that has been shaped by a few billion years of variation and selection to produce a functional outcome. It’s not magic. It’s not guided by intelligence and intent.


Yet here is this intelligent, accomplished, technically skilled loon painting it with useless, mystical, misleading bullshit.

That kind of delusion has consequences. Right now, that video is getting featured on anti-maternal-life websites all over the internet. Here’s a self-selected sample of responses to Tsiaras’s work:

“For you created my inmost being; you knit me together in my mother’s womb.”

“Pro-choicers vanquished by Science.”

“This truly is amazing.”

“How could anyone get an abortion after watching this?”

“To say that this is a must see or fantastic is an understatement of the truth.”

I am most amused by the claim “Pro-choicers vanquished by Science.” I’ve been familiar with the developmental series shown in that video for about 30 years, and it confirms to me that there is nothing magical or special about human development that demands that we privilege the human embryo as deserving the full rights of an adult, aware, thinking person. It is meat in motion, driven by unthinking processes. Cow embryos go through the same events, and through the first month or so would be indistinguishable from a human embryo; does this somehow compel the anti-woman brigade to shun steaks?

Here, I have a video of zebrafish development. I don’t have all the gadgets and animation tools that Tsiaras has at his disposal, just a microscope, a video camera, and Quicktime software, but still…this truly is amazing. It’s a must see or fantastic.

Wow. How did a fish embryo know how to do that?

The answer is that it doesn’t. We don’t grant human beings a privileged place in our cultural ethics because they develop from embryos, or because they have a heart that beats with many miles of capillaries, or because we don’t understand every minuscule detail of their formation. If that were the case, the anti-choicers would have to be rushing to protect the fruit flies growing on the bananas in their kitchen and be picketing the battery farms producing chicken eggs. Witnessing development shouldn’t turn rational people into irrational knee-jerk defenders of embryos…it should turn them into developmental biologists who are awed at the grandeur of growth and differentiation, who will spend their lives working to figure out how it all works.

Where Tsiaras sees ineffable unapproachable mystery, I see interesting problems to be solved.

(Also on FtB)

Hamza Tzortzis on the Intellectual Dishonesty of Professor Myers SHOCKING!

That’s what he titles his latest youtube video, anyway. I laughed, just like I laughed when Eric Hovind called to complain about the misinformation on my website. He also claims I “accept defeat”

Myers accepts defeat see below:

Myers changes his stance from Ireland, In Ireland Myers says the ‘Quran is Wrong’. After reviewing the iERA Research Paper he now believes its the Quran has ‘ very little opportunity for disproof, and they can be made to fit just about any reasonable observation.’

I am surprised to learn that I accepted defeat. Doesn’t he know I’m indomitable? Anyway, here’s the video where Tzortzis crushes me.

I will give him credit — he does link to my article debunking Islamic embryology, which is more than most creationists would do. But still, he’s got it all wrong.

During our encounter in Ireland, I pointed out that their specific claim of a discrete sequence of development in the embryo, from bones to muscles being added to bones, was false. In the article I wrote on Tzortzis’s strained exegesis of two verses from the Quran, I explained that you can’t make concrete claims about embryology from such a vague, cursory, and intentionally poetic source, such as those two verses. These are not incompatible arguments. The second point is not a softening of the views made in the first point.

If anything, Tzortzis has backed down. In Ireland, he and his friends were trying desperately to argue that Mohammed knew things that no man in his position could possibly have known without a divine source of information; my argument was that no, what’s in the Quran is very much in line with the knowledge of his day, derived from Aristotle and Galen. No miracles were required to write those two verses.

Now Tzortzis’s claim is greatly reduced; it is that the Quran does not “negate reality”, or does not make claims that contradict known science. That’s fine; as I said, it’s the most minuscule of verses saying the wobbliest things, and it’s derived from observations of embryos made by Greek and Roman predecessors, so it’s not surprising that it can be retrofitted to fit modern science by playing enough word games.

Tzortzis relies on what he calls “lexical analysis”, but it’s little more than compiling the equivalent of thesaurus entries for words in the verses, and then picking and choosing the ones that fit the point he’s trying to make. That’s not analysis, it’s cherry-picking.

Amusingly, he does the same thing to modern developmental biology. He’s gone rifling through legitimate embryology texts, trying to prove that I don’t know what I’m talking about, and he found one sentence in a textbook — “after the cartilaginous models of the bone have been established, the myogenic cells, which have now become myoblasts, aggregate to form the muscle masses” — that he thinks shows I was wrong and that his interpretation of the Quran phrase — “bones were clothed with flesh” — is correct.

Wrong. See, this is the problem with his “lexical analysis” approach — it means he tries to conform what he reads to what he already thinks he knows. I know what a developing limb looks like; mesodermal masses condense gradually into organized clusters of cells that differentiate in parallel. Centers of what will become bones aggregate and form cartilage (not bone, notice) as centers of what will become muscle (the myogenic cells in that description) aggregate and begin differentiation into myoblasts and myotubes and eventually muscle fibers.

Here’s what we actually see in the developing limb: branching patterns of cell fate decisions by tissue precursors, and parallel differentiation of the cellular components of those tissues.


The simplistic and discrete idea of “bones, then flesh” doesn’t even recognize that “bones” and “flesh” aren’t simple binaries, and the sequence isn’t a simple temporal switch. What you had instead was the early segregation of cells into differing mucopolysaccharide matrices, within which cells began complex sequences of shifting patterns of gene expression and differentiation into mesodermally-derived tissues.

Or more poetically, bones and flesh congealed together out of balls of snot. There are sequences within that pattern, but chondrocytes aren’t bones and myoblasts are not muscles. Tzortzis is trying too hard to fit the Quran to science, because he can’t appreciate that it’s just a book written by men trying to make sense of the world, and also unfortunately trying to add extra weight to their opinions by claiming the authority of a god behind them. A sad state of affairs that I’m afraid their modern descendants continue to perpetrate.

(Also on FtB)

Islamic embryology: overblown balderdash

I have read the entirety of Hamza Andreas Tzortzis’ paper, Embryology in the Qur’an: A scientific-linguistic analysis of chapter 23: With responses to historical, scientific & popular contentions, all 58 pages of it (although, admittedly, it does use very large print). It is quite possibly the most overwrought, absurdly contrived, pretentious expansion of feeble post hoc rationalizations I’ve ever read. As an exercise in agonizing data fitting, it’s a masterpiece.

Here, let me give you the short version…and I do mean short. This is a paper that focuses with obsessive detail on all of two verses from the Quran. You heard me right: the entirety of the embryology in that book, the subject of this lengthy paper, is two goddamned sentences, once translated into English.

We created man from an essence of clay, then We placed him as a drop of fluid in a safe place. Then We made that drop of fluid into a clinging form, and then We made that form into a lump of flesh, and We made that lump into bones, and We clothed those bones with flesh, and later We made him into other forms. Glory be to God the best of creators.

Seriously, that’s it. You have just mastered all of developmental biology, as taught by Mohammed.

Tzortzis bloats this scrap into a long, tedious potboiler by doing a phrase by phrase analysis, and by comparing it to the work of Aristotle and Galen, who got lots of things wrong. How, he wonders many times, could Mohammed have written down only the correct parts of the Greek and Roman embryological tradition, and avoided their errors, if he weren’t divinely inspired? My answer is easy: because Mohammed only made a vague and fleeting reference to the science of the time, boiling down Aristotle’s key concept of an epigenetic transformation into a few non-specific lines of poetry. Aristotle and Galen got a lot wrong because they tried to be specific and wrote whole books on the subject; you can read the entirety of Aristotle’s On the Generation of Animals. Galen was prolific and left us about 20,000 pages on physiology and medicine.

So, yes, you can find lots of examples in their work where they got the biology completely wrong, and it’s harder to do that in the Quran…because the Quran contains negligible embryological content, and what there is is so sketchy and hazy that it allows his defenders to make spectacular leaps of interpretation. Mohammed avoided the trap of being caught in an overt error here by blathering generalized bullshit, and saying next to nothing. This is neither an accomplishment nor a miracle.

I’ll go through his argument piece by piece, but at nowhere near the length. It’s hard to believe anyone is using this feeble fragment to claim proof of divinity, but then, Christians do exactly the same thing.

  1. “essence of clay”. Tzortzis happily announces that clay contains “Oxygen, Carbon, Hydrogen, Nitrogen, Calcium, Phosphorus, Potassium, Sulfur, Chlorine, Sodium, Magnesium and Silicon; all of which are required for human functioning and development”. These are irrelevant factlets. Clay is a fine-grained hydrous aluminum phyllosilicate; carbon, which is the element to consider in organic chemistry, is present as a contaminant, but the primary elements are aluminum and silicon. It’s nothing like the composition of the human body. This part of Tzortzis case is simply a lie.

  2. “drop of fluid”. Tzortzis tells us that the Arabic word here is “nutfah”, which has a number of meanings, but he likes the interpretation that it implies mingled fluids. Then he babbles on about oocytes and spermatazoa and secretions of the oviduct, none of which are mentioned in the Quran and are completely irrelevant. Bottom line: Arabs noticed long ago that sex involves a mingling of fluids. Brilliant. I think most of us could figure that out without divine inspiration.

    He spends a fair amount of time pointing out that both Aristotle and Galen had a male-centric view of procreation, where the man’s contribution was the dynamic agent and the woman was a passive vessel. They were wrong. In order to rescue the Quran, though, Tzortzis has to bring in Ibn Qayyim, a 13th century Islamic scholar, who pointed out that women have to provide a significant contribution to inheritance, since their traits are also present in the children. This, again, is an obvious and observable property, and the Greeks also argued over the relative contributions of male and female. There is nothing in the Quran that is beyond casual observation or non-existent in the scholarly works of the time.

  3. “in a safe place”. Tzortzis quotes modern embryologists and throws around the terms endometrium, syntrophoblast, implantation, uterine mucosa, proteolytic enzymes, etc., etc., etc. I ask you, is any of that in the quoted verse from the Quran? No. Total bullshit from the apologists. That the embryo grows in a “safe place” — the woman’s belly — is another obvious property.

  4. “a clinging form”. It seems that the word used here means just about anything.

    The Qur’an describes the next stage of the developing human embryo with the word `alaqah. This word carries various meanings including: to hang, to be suspended, to be dangled, to stick, to cling, to cleave and to adhere. It can also mean to catch, to get caught, to be affixed or subjoined. Other connotations of the word `alaqah include a leech-like substance, having the resemblance of a worm; or being of a ‘creeping’ disposition inclined to the sucking of blood. Finally, its meaning includes clay that clings to the hand and thick, clotted blood – because of its clinging together.

    I could call the embryo a sticky blob, too, and stretch and twist the words to match it in the vaguest possible way to a technical description, too…but it doesn’t make it a technical description, and it doesn’t make it informative.

    This section concludes by claiming that the “leech” interpretation of ‘alaqah is accurate, because later in development it looks, he claims, like a leech. Only to a blind man. And further, he applies this term “like a leech” to every stage in the first month of development; the accuracy of the comparison seems irrelevant.

  5. “a lump of flesh”. More of the same. Take the Arabic word (“mudghah”), throw out a bunch of definitions for the word, then force-fit them all into the actual science.

    The next stage of human development defined in the Qur’an is mudghah. This term means to chew, mastication, chewing, to be chewed, and a small piece of meat. It also describes the embryo after it passes to another stage and becomes flesh. Other meanings include something that teeth have chewed and left visible marks on; and marks that change in the process of chewing due to the repetitive act.

    No. I refuse. I’m sorry, but this is patently ridiculous. You do not get to quote the Quran talking about a chawed on scrap o’ meat, and then go on with four pages of windy exegesis claiming that corresponds to the 4th week of human development, the pharyngula stage, as if it is an insightful and detailed and specific description of an embryo. It is not. It is the incomprehending grunt of an ignorant philistine.

  6. “into bones”. Yeah. There is a mingling of fluids in sex, and at birth you have a baby with bones. Somewhere in between, bones must have formed. You do not get credit for noting the obvious without any specifics. Furthermore, turning the phrase “into bones” (‘idhaam) into this:

    There are clear parallels between the qur’anic `idhaam stage and the view modern embryology takes i.e. the development of the axial, limb and appendicular skeleton.

    is pure hyperbole and bunkum. But then, that’s all we get from Tzortzis.

  7. “clothed the bones with flesh”. Tzortzis now talks about myoblasts aggretating and migrating distally, formation of dorsal and ventral muscle masses, innervation of the tissue, and specification of muscle groups. Good god, just stop. The Quran says nothing about any of this. And then to complain that This level of detail is not, however, included in Aristotle’s description, is absurd and ironic. It’s not in Mohammed’s description, either.

    It must be noted that the migration of the myoblasts surrounding the bones cannot be seen with the naked eye. This fact creates an impression of the Divine nature of the Qur’an and reiterates its role as a signpost to the transcendent.

    Crap. The Quran doesn’t describe myoblast migration. There isn’t even a hint that Mohammed saw something you need a microscope to see.

  8. “made him into other forms”. Then Allah did all the other stuff that he needed to do to turn a chunk of chewed meat made of bone and flesh into a person. Presto, alakazam, abracadabra. Oooh, I am dazzled with the scrupulous particularity of that scientific description.

There’s absolutely nothing novel or unexplainable in the Quran’s account of development. It is a vague and poetic pair of verses about progressive development, expressed in the most general terms, so nebulous that there is very little opportunity for disproof, and they can be made to fit just about any reasonable observation. They can be entirely derived from Aristotle’s well-known statement about epigenesis, “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?”, which is also a very broad statement about the gradual emergence of differentiated tissues from an amorphous fluid.

Only a blinkered fanatic could turn that mush into an overwrought, overextended, overblown, strained comparison with legitimate modern science. Tzortzis’s paper is risible crackpottery.

(Also on FtB)

William Lane Craig and the problem of pain

Kitties experience pain and suffering, which turns out to be a theological problem. If a god introduced pain and death into the world because wicked ol’ Eve was disobedient, why is god punishing innocent animals? It seems like a bit of a rotten move to afflict the obedient along with the disobedient — shouldn’t god have just stricken humanity with the wages of sin (or better yet, just womankind)?

William Lane Craig has an answer. His answer involves simply waving the problem away — animals don’t really feel pain — and he drags in science to prop up his claim. Basically, Craig is playing the creationist gambit of abusing the authority of science falsely to support his peculiar theology.

So Christian theologians of all stripes have to face the challenge posed by animal pain. Here recent studies in biology have provided surprising, new insights into this old problem. In his book Nature Red in Tooth and Claw: Theism and the Problem of Animal Suffering, Michael Murray distinguishes three levels in an ascending pain hierarchy (read from the bottom up):

Level 3: a second order awareness that one is oneself experiencing (2).

Level 2: a first order, subjective experience of pain.

Level 1: information-bearing neural states produced by noxious stimuli resulting in aversive behavior.

Spiders and insects–the sort of creatures most exhibiting the kinds of behavior mentioned by Ayala–experience (1). But there’s no reason at all to attribute (2) to such creatures. It’s plausible that they aren’t sentient beings at all with some sort of subjective, interior life. That sort of experience plausibly does not arise until one gets to the level of vertebrates in the animal kingdom. But even though animals like dogs, cats, and horses experience pain, nevertheless the evidence is that they do not experience level (3), the awareness that they are in pain. For the awareness that one is oneself in pain requires self-awareness, which is centered in the pre-frontal cortex of the brain–a section of the brain which is missing in all animals except for the humanoid primates. Thus, amazingly, even though animals may experience pain, they are not aware of being in pain. God in His mercy has apparently spared animals the awareness of pain. This is a tremendous comfort to us pet owners. For even though your dog or cat may be in pain, it really isn’t aware of it and so doesn’t suffer as you would if you were in pain.

As is usual upon reading any argument by William Lane Craig, I find myself wondering if we shouldn’t, in the name of common decency, have him locked up or in some way isolated from the sane human population. He makes bad arguments, he makes dishonest arguments, and he seems opportunistically willing to sacrifice moral reasoning on the altar of his barbarian god. Or at least, maybe we should confiscate his pets and put them in a safer home.

A few objections popped instantly into my head when I read his essay.

  • An assertion built on a false premise is likely to be false itself. Craig (or possibly his source, Murray), misrepresent the science. They claim that the prefrontal cortex “is missing in all animals except for the humanoid primates.” This is simply false! I’ve personally done histological work and surgery on the prefrontal cortex of cats, many years ago, and you can find papers describing the prefrontal cortex of opossums, and just about any common mammal you can think of. Craig has made a truly bizarre claim, like declaring that only people have noses or something.

    Primates do have a unique histologic feature of their primary cortices, an internal granule layer that is developed to varying degrees. But it’s also present in prosimians as well as all primates, so you can’t argue that it is unique to ‘humanoid primates’, and you can’t claim that it’s necessary and sufficient for self-awareness. If a bushbaby is going to be declared self-aware because it has an internal granule layer, it seems ridiculous to argue that other mammals with a similar or greater degree of cortical development are excluded from the club on the basis of this one detail.

    Scientists are supposed to talk about the evidence. Theologians are apparently not only exempt, but they get to fabricate their evidence. Also, I’m used to hearing theologians babble about the nonexistent as if it were real, but this is the first time I’ve heard one argue that a real structure is nonexistent.

  • There is a real issue here: we can identify pain neurons in insects and fish and all kinds of animals — they’re ubiquitous. But you could ask about the slippery problem of consciousness, and wonder whether there is a real difference between reflexive aversion to a noxious stimulus and a more substantial awareness of pain. There are people who argue that non-human animals are not thinking and self-aware like we are, and so their perception of pain is qualitatively different.

    Unfortunately, you can’t make a binary distinction here. If we accept that humans are all aware of pain (there have been people who don’t accept that: Nazi-types and racists have argued that Jews and blacks, for instance, are subhumans who have blunted sensitivities), it’s hard to argue that chimpanzees aren’t also aware — they exhibit all the signs of stress, of learning aversion, of memory and recall of unpleasant experiences, and their behavior is identical to ours: they make it known that they don’t like needles or fear snakes or suffer pain and distress at their discomfort and the discomfort of others. And if you admit chimps, where do you draw the line? Dogs also exhibit all of those behaviors; they even show empathy when people are injured or unhappy.

    How can anyone who has known a dog deny that they are capable of perceiving pain in fairly complex ways?

    But it really is a continuum. I haven’t been able to tell if cats feel much empathy — they don’t show it, but I have no way to see what interesting (or terrifying) cognitive wheels are spinning in a cat’s brain. I know they react to their own pain in very emotional ways, and I’ve seen mother cats respond with what looks like affection and protectiveness to their kittens…and I would not assume that a cat’s aversive reaction to getting cut is all a superficial reflex, and therefore anesthesia is unnecessary in operating on them. That is the road of the psychopath.

    Again, scientists rely on the evidence: if I see an animal struggling and making frightened noises and fighting to avoid a painful experience, and if it shows recognition of the circumstances of that pain in the future, I’m going to assume that it feels pain and is in some sense aware of its situation. Theologians are apparently able to see a cat or dog in the throes of agony and declare that it isn’t really suffering, no, not like you or me. Hey, theologians and psychopaths have something in common!

  • Let us consider the implications of Craig’s worldview. If this property of awareness sets humans apart from animals, making our suffering have a greater moral significance than that of animals, and if that awareness is a product of a specific neuroanatomical structure, the prefrontal cortex (or more specifically, a well-developed internal granule cell layer in that cortex), then what is the status of a human that lacks that all-important, very specific pattern of neuronal connectivity?

    I’m thinking, of course, of the embryo. The internal granule cell layer does not pop into existence at the moment of fertilization — it arises much later, gradually, as the brain matures. Cortical wiring is an ongoing process after birth, as well — the microstructure of the human brain changes amazingly during the first couple of years of life. If we’re going to claim that an adult dog, despite appearances, isn’t really aware of pain, shouldn’t we be saying the same thing about the embryo?

    I mean, sure, babies squall and scream and flail about at the slightest discomfort, but how do you really know that they’re actually conscious? Maybe they’re just bio-reflexive hunks of meat until the final bits of their cortical cytoarchitecture snap into place, and we should be unperturbed by their struggles. They’re not really human yet, after all — god hasn’t given them that second-order awareness that they need in order to be conscious of their deontological status as the product of original sin, you know.

    I don’t know of any scientist — or sane human being — who could make that argument seriously. Again, it’s about the evidence; they exhibit the symptoms of feeling pain, they have some complex cerebral machinery that we think is likely capable of processing experiences in complex ways (but we don’t know for sure — we don’t have a parts list of neuroanatomical correlates that are sufficient to generate consciousness), so the humane assumption is that yes, babies perceive pain. Apparently, this is a much more ambiguous issue for theologians, if they had any consistency in their views. Oh, but wait — theologians. Evidence, consistency, reason are not highly valued properties of theological arguments. If they were, it would suggest that Craig ought to rethink his dogmatic anti-abortion stance.

Sorry, Mr Craig, but pain is still a big problem for your religion, and you don’t get to shoo it away or drag in the mangled, bleeding body of a butchered science in agony to act as a scarecrow and distract people from your absence of evidence.

(Also on FtB)

How many genes does it take to make a squid eye?

This is an article about cephalopods and eye evolution, but I have to confess at the beginning that the paper it describes isn’t all that interesting. I don’t want you to have excessive expectations! I wanted to say a few words about it, though, because it addresses a basic question I get all the time, and while I was at it, I thought I’d mention a few results that set the stage for future studies.

I’m often asked to resolve some confusion: the scientific literature claims that eyes evolved multiple times, but I keep saying that eyes show evidence of common origin. Who is right? Why are you lying to me, Myers? And the answer is that we’re both right.

Eyes evolved independently multiple times: the cephalopod eye evolved about 480 million years ago, and the vertebrate eye is even older (490 to 600 million years), but both evolved long after the last common ancestor of molluscs and chordates, which lived about 750 million years ago. The LCA probably did not have an image-forming eye at all.

And that’s the key point: a true eye is a structure that has an image forming element, a retina, and some kind of morphological organization that allows a distant object to form a pattern of light on that retina. That organization can be something as simple as a cup-shaped depression or pinhole lens, or as elaborate as our camera eye, or an insect’s compound eye, or the mirror eyes of a scallop. An eye is photoreceptors + structure. Eyes have evolved multiple times; they’ve even evolved multiple times within the phylum Mollusca, and different lineages have adopted different strategies for forming images.

(Click for larger image)

Phylogenetic view of molluscan eye diversification. Camera eyes were independently acquired in the coleoid cephalopod (squids and octopuses) and vertebrate lineages.

The LCA probably didn’t have an eye, but it did have photoreceptors, and the light sensitive cells were localized to patches on the side of the head. It even had two different classes of photoreceptors, ciliary and rhabdomeric. That’s how I can say that eyes demonstrate a pattern of common descent: animals share the same building block for an eye, these photoreceptor cells, but different lineages have assembled those building blocks into different kinds of eyes.

Photoreceptors are fundamental and relatively easy to understand; we’ve worked out the full pathways in photoreceptors that take an incoming photon of light and convert it into a change in the cell’s membrane properties, producing an electrical signal. Making an eye, though, is a whole different matter, involving many kinds of cells organized in very specific ways. The big question is how you evolve an eye from a photoreceptor patch, and that’s going to involve a whole lot of genes. How many?

This is where I turn to the paper by Yoshida and Ogura, which I’ve accused of being a bit boring. It’s an exercise in accounting, trying to identify the number and isolate genes that are associated with building a camera eye in cephalopods. The approach is to take advantage of molluscan phylogeny.

As shown in the diagram above, molluscs are diverse: it’s just the coleoid cephalopods, squid and octopus, that have evolved a camera eye, while other molluscs have mirror, pinhole, or compound eyes. So one immediate way to narrow the range of relevant genes is a homology search: what genes are found in molluscs with camera eyes that are not present in molluscs without such eyes. That narrows the field, stripping out housekeeping genes and generic genes involved in basic cellular processes, even photoreception. Unfortunately, it doesn’t narrow the field very much: they identified 5,707 candidate genes that might be evolved in camera eye evolution.

To filter it further, the authors then looked at just those genes among the 5,707 that were expressed in embryos. Eye formation is a developmental process, after all, so the interesting genes will be expressed in embryos, not adults (a sentiment with which I always concur). Unfortunately, development is a damnably complicated and interesting process, so this doesn’t narrow the field much, either: we’re down to 3,075 candidate genes.

Their final filter does have a dramatic effect, though. They looked at the ratio of non-synonymous to synonymous nucleotide changes in the candidate genes, a common technique for identifying genes that have been the target of selection, and found a grand total of 156 genes that showed a strong signal for selection. That’s 156 total genes that are different between coleoids and other molluscs, are expressed in the embryonic eye, and that show signs of adaptive evolution. That’s manageable and interesting.

They also looked for homologs between cephalopod camera eyes and vertebrate camera eyes, and found 1,571 of them; this analysis would have been more useful if it were also cross-checked against other non-camera-eye molluscs. As it is, that number just tells us some genes are shared, but they could have been genes involved in photoreceptor signalling (among others), which we already expect to be similar. I’d like to know if certain genes have been convergently adopted in both lineages to build a camera eye, and it’s not possible to tell from this preliminary examination.

And that’s where the paper more or less stops (I told you not to get your hopes up too high!) We have a small number of genes identified in cephalopods that are probably important in the evolution of their vision, but we have no idea what they do, precisely, yet. The authors have done some preliminary investigations of a few of the genes, and one important (and with hindsight, rather obvious) observation is that some of the genes are expressed not just in the retina, but in the brain and optic lobes. Building an eye involved not just constructing an image-forming sensor, but expanding central tissues involved in processing visual information.

Fernald RD (2006) Casting a genetic light on the evolution of eyes. Science 313(5795):1914-8.

Yoshida MA, Ogura A (2011) Genetic mechanisms involved in the evolution of the cephalopod camera eye revealed by transcriptomic and developmental studies.. BMC Evol Biol 11:180.

(Also on FtB)

I wish I could go

It’s a conference, in Oregon, and it’s about The Future of Evo-Devo, all wonderful things, and it’s on 10-12 February — right in the thick of the traditional Darwin Day hoopla, the days when I’m like a big egg-laying bunny at Easter. I’m already booked for Pullman, Washington, then Florida, then Las Vegas in that week.

You’ll just have to go in my place and report back. Yes, you — the one looking around quizzically and wondering “why me?” Because I said so. Book it now. Portland, 10 February, the Nines Hotel.

Coincidentally, I’m giving a talk at UNLV that is kind of about the future of evo-devo: I’m going to be both pessimistic and optimistic, and talk about the mainstreaming of evo-devo into the discourse of evolution and development, and propose that it isn’t so much a revolution in evolution as it is developmental biologists finally adopting views much more copacetic with standard model evolutionary thinking. There may be a lynching afterwards.

(Also on FtB)

The epigenetics miracle?

Jerry Coyne is mildly incensed — once again, there’s a lot of recent hype about epigenetics, and he doesn’t believe it’s at all revolutionary. Well, I’ve written about epigenetics before, I think it’s an extremely important subject central to our understanding of development, and…I agree with him completely. It’s important, we ought to spend more time discussing it in our classes, but it’s all about the process of gene expression, not about radically changing our concepts of evolution. I like to argue that what multigenerational epigenetic effects do is blur out or modulate the effects of genetic change over time, and it might mask out or highlight allelic variation, but ultimately, it’s all about the underlying genetic differences.

Coyne mentions one journalist who claims that new discoveries in epigenetics would “make Darwin swoon,” which is a bizarre standard. Darwin knew next-to-nothing about genetics — he had his own weird version of Lamarckian inheritance — and wasn’t even equipped to imagine molecular biology, so yes, just about anything in this field would dazzle him. My freshman introductory biology course would blow Charles Darwin away — he’d have to struggle to keep up with the products of American public education.

(Also on FtB)

Simple rules for folding a gut

I learned something new today, and something surprising. I’ve opened up my fair share of bellies and seen intestines doing their slow peristaltic dance in there, and I knew in an abstract way that guts were very long and had to coil to fit into the confined space of the abdominal cavity, but I’d always just assumed it was simply a random packing — that as the gut tube elongated, it slopped and slithered about and fit in whatever way it could. But no! I was reading this new paper today, and that’s not the case at all: there is a generally predictable pattern of coiling in the developing gut, and it’s species-specific.

The midgut forms as a simple linear tube of circular cross-section running down the midline of the embryo, and grows at a greater rate than the surrounding tissue, eventually becoming significantly longer than the trunk. As the size of the developing mid- and hindgut exceeds the capacity of the embryonic body cavity, a primary loop is forced ventrally into the umbilicus (in mammals) or yolk stalk (in birds). This loop first rotates anticlockwise by 90° and then by another 180° during the subsequent retraction into the body cavity. Eventually, the rostral half of the loop forms the midgut (small intestine) and the caudal half forms the upper half of the hindgut (the ascending colon).

The chirality of this gut rotation is directed by left-right asymmetries in cellular architecture that arise within the dorsal mesentery, an initially thick and short structure along the dorsal-ventral axis through which the gut tube is attached to the abdominal wall. This leads the mesentery to tilt the gut tube leftwards with a resulting anticlockwise corkscrewing of the gut as it herniates. However, the gut rotation is insufficient to pack the entire small intestine into the body cavity, and additional loops are formed as the intestine bends and twists even as it elongates. Once the gut attains its final form, which is highly stereotypical in a given species, the loops retract into the body cavity. During further growth of the juvenile, no additional loops are formed, as they are tacked down by fascia, which restrict movement and additional morphogenesis without inhibiting globally uniform growth.

That is just plain awesome. Now I want to open up a zebrafish and look at the curling of its intestines, or better yet, peer into a larva and see if there are any predictable rules of formation. Oh, jeez, I want to look inside my own belly, although that would be a kind of self-defeating experiment.

Morphology of loops in the chick gut. a, Chick gut at embryonic day 5 (E5), E8, E12 and E16 shows stereotypical looping pattern.
b, Proliferation in the E5 (left) and E12 (right) gut tubes (blue) and mesentery (red). Each blue bar represents the average number of phospho-H3-positive cells per unit surface in 40 (E5) or 50 (E12) 10-mm sections. Each red bar represents the average number of phospho-H3-positive cells per unit surface over six 10-mm sections (E5) or in specific regions demarcated by vasculature along the mesentery (E12). The inset images of the chick guts align the proliferation data with the locations of loops (all measurements were made in three or more chick samples). Ant., anterior; post., posterior. Error bars, s.d. c, The gut and mesentery before and after surgical separation at E14 show that the mesentery shrinks while the gut tube straightens out almost completely. d, The E12 chick gut under normal development with the mesentery (left) and after in ovo surgical separation of the mesentery at E4 (right). The gut and mesentery repair their attachment, leading to some regions of normal looping (green). However, a portion of the gut lacks normal loops as a result of disrupting the gut-mesentery interaction over the time these loops would otherwise have developed.

So how do species-specific coiling patterns emerge? A naive expectation might be that there are specific genes associated with the process that selectively impose bends at specific locations along the length of the intestine — that there is genetically determined spatial information along the tube that defines how it should coil. This is not the case. Instead, the reproducible pattern of coiling is an emergent property of some general parameters of the tissues.

You do need to know some very elementary anatomy to know what’s going on here. The gut begins embryonically as a simple, straight tube, fixed at both ends at the mouth and anus. Initially, the gut is the same length as the body, and is suspended from the back of the body cavity by a continuous sheet of tissue, the mesentery, that is also the same length as the gut. But then what happens is that the gut elongates, while the mesentery grows much more slowly. This difference in growth rates means that the gut is under compression along its length, restrained by the mesenteries, which causes it to periodically buckle.

One way to test the role of the mesentery is to remove it. If you carefully cut it away from the gut, as is shown in (c) and (d) of the figure above, it straightens out — in a fully relaxed state, without the compression of the mesenteries, the gut is straight and linear. You can do partial cuts, too, and wherever a stretch of gut is released from the mesentery constraint, it uncoils.

Take it another step. Is this how generic tubes and sheets interact? The authors took a rubber tube of length Lt, and a rubber sheet of length Lm, where Lm is less than Lt. They stretched the rubber sheet to length Lt, stitched it to the rubber tube, and then let it go. Voila, it spontaneously coiled into a configuration (b) that closely resembles the chicken gut (c).

Rubber simulacrum of gut looping morphogenesis. a, To construct the rubber model of looping, a thin rubber sheet (mesentery) was stretched uniformly along its length and then stitched to a straight, unstretched rubber tube (gut) along its boundary; the differential strain mimics the differential growth of the two tissues. The system was then allowed to relax, free of any external forces. b, On relaxation, the composite rubber model deformed into a structure very similar to the chick gut (here the thickness of the sheet is 1.3 mm and its Young’s modulus is 1.3 MPa, and the radius of the tube is
4.8 mm, its thickness is 2.4 mm and its Young’s modulus is 1.1 MPa. c, Chick gut at E12. The superior mesenteric artery has been cut out (but not the mesentery), allowing the gut to be displayed aligned without altering its loop pattern.

This is qualitatively convincing — they do look very similar, and at this point I’m willing to believe that mechanical forces are sufficient to explain the coiling pattern. The authors take another step, though: they bring out the math and get all quantitative. This is a reasonable idea; from the model above, it does look like the shape is reducible to a small number of parameters, so it’s a manageable problem. So brace yourself: a little math coming right up.

We now quantify the simple physical picture for looping sketched above to derive expressions for the size of a loop, characterized by the contour length, λ, and mean radius of curvature, R, of a single period. The geometry of the growing gut is characterized by the gut’s inner and outer radii, ri and ro, which are much smaller than its increasing length, whereas that of the mesentery is described by its homogeneous thickness, h, which is much smaller than its other two dimensions. Because the gut tube and mesentery relax to nearly straight, flat states once they are surgically separated, we can model the gut as a one-dimensional elastic filament growing relative to a thin two-dimensional elastic sheet (the mesentery). As the gut length becomes longer than the perimeter of the mesentery to which it is attached, there is a differential strain, ε, that compresses the tube axially while extending the periphery of the sheet. When the growth strain is larger than a critical value, ε* the straight tube buckles, taking on a wavy shape of characteristic amplitude A and period λ>A. At the onset of buckling, the extensional strain energy of the sheet per wave- length of the pattern is Um∝Emε22, where Em is the Young’s modulus of the mesentery sheet. The bending energy of the tube per wavelength is Ut∝EtItκ2λ, where κ ∝ A/λ2 is the tube curvature, It ∝ ro4-ri4 is the moment of inertia of the tube and Et is the Young’s modulus of the tube. Using the condition that the in-plane strain in the sheet is ε* ∝ A/λ and minimizing the sum of the two energies with respect to λ then yields a scaling law for the wavelength of the loop:


Did you get all that? If not, don’t worry about it. What it all means is that we can measure general properties of gut tissues, plug the parameters into these formulas, and ask a computer to predict what the gut should look like in a numerical simulation. And it works!

Predictions for loop shape, size and number at three stages in chick gut development. a, Comparisons of the chick gut at E16 (top) with its simulated counterpart (bottom). b, Scaled loop contour length, λ/ro, plotted versus the equivalently scaled expression from equation (3) for the chick gut (black squares), the rubber model (green triangles) and numerical simulations (blue circles). The results are consistent with the scaling law in equation (1). c, Scaled loop radius, R/ro, plotted versus the equivalently scaled expression from equation (4) for the chick gut, the rubber model, and numerical simulations (symbols are as in b). The results are consistent with the scaling law in equation (2). Error bars, s.d.

At this point, you should be saying enough — that’s more than enough awesome to convince you that they’ve determined the rules that shape the gut. But no, they go further: all the above work is in chickens, so they reach out and start disemboweling other species, and ask if their formulas work to describe their gut coiling, too. Would you be surprised to learn that it does?

Comparative predictions for looping parameters across species. a, Gut looping patterns in the chick, quail, finch and mouse (to scale) show qualitative similarities in the shape of the loops, although the size and number of loops vary substantially. b, Comparison of the scaled loop contour length, λ/ro, with the equivalently scaled expression from equation (3) shows that our results are consistent with the scaling law in equation (1) across species. Black symbols are for the animals shown in a, other symbols are the same as in Fig. 4b. c, Comparison of the scaled loop radius, R/ro, with the equivalently scaled expression from equation (4) shows that our results are consistent with the scaling law in equation (2) across species (symbols are as in b). In b and c, points are reported for chick at E8, E12 and E16; quail at E12 and E15; finch at E10 and E13; and mouse at E14.5 and E16.5. Error bars, s.d.

What makes this a beautiful result is that it’s a perfect illustration of the principles D’Arcy Wentworth Thompson laid out in his book, On Growth and Form (and even the title of the paper is a nod to that classic of developmental biology). Sometimes, simple mathematical rules govern the patterns we see in developing systems, whether it’s the Fibonacci spirals we see in the head of a sunflower or the coils of a nautilus shell, or tangled loops of our intestines. The form is not laid out in tightly-coded, case-by-case specification in the genome, but by the genetic definition of only a few parameters, in this case the relative rates of growth of two adherent tissues and the compression they impose on an elongating tube, from which a lovely arrangement flowers elegantly.

Savin T, Kurpios NA, Shyer AE, Florescu P, Liang H, Mahadevan L, Tabin CJ (2011) On the growth and form of the gut. Nature 476:57-63.

(Also on FtB)