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.

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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.

i-4e599384fc1ad3453f1e71306459fde4-penetrance.jpeg
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.

i-2265898264c55ebafe7177e5f8b47d97-devnoise.jpeg
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.

i-b9e909958ec9f54fcafe88463aec893a-quanttbx-thumb-500x412-71413.jpeg
(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.

i-d7b413047f2767e92cdc267d44f8830a-daf21-thumb-500x259-71416.jpeg
(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)

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.

[Read more…]

von Däniken poisons everything

Gah, the stupid, it burns. Ridley Scott is making a kind of prequel to Alien called Prometheus, which sounds fun; I liked the first two movies in the Alien franchise. But his rationale dismays me, and makes me regard Scott as a bit dim.

"The (space) journey, metaphorically, is about a challenge to the gods," Scott said. But Scott’s ambitions with Prometheus go far beyond simply restarting a hit franchise. The British director said the film’s storyline, and script by David Lindelof, was partially inspired by the writings of legendary Swiss sci-fi writer Eric van Daniken.

Van Daniken, author of 1968 bestseller Chariot of the Gods, is best known as the first proponent of the so-called ancient astronaut theory, which holds that aliens kick-started civilization on earth. "NASA and the Vatican agree that is almost mathematically impossible that we can be where we are today without there being a little help along the way," Scott said. "That’s what we’re looking at (in the film), at some of Eric van Daniken’s ideas of how did we humans come about."

I had to laugh at the claim that von Däniken was a “sci-fi writer”. He wasn’t. He was a pseudo-science writer who believed that his nonsense about aliens helping the Egyptians construct the pyramids (and other belittlings of human abilities) was actual history. I’ve read a couple of his books, many years ago, and they were so hopelessly inane and incompetently supported that I rejected them as a high school student. It doesn’t say much about Scott’s scientific discrimination that he can be inspired by that drivel, and it is just about as damning to his competence at recognizing a good story that he mistook it for a sci-fi novel.

I also don’t consider the opinion of a bunch of engineers or a gang of theological thugs to be of much value in assessing the likelihood of evolutionary events — the authorities he cites are not authorities in the subject he’s discussing. I have a strong suspicion that Scott is making crap up, doesn’t know much about what either NASA or the Vatican has said, and probably hasn’t even read any of von Däniken’s books, but is only vaguely echoing the ‘common knowledge’ of blithering Hollywood celebrities.

My expectations for this movie have plummeted, though. Those Hollywood celebrities should never ever speak, because they always seem to confirm that they’re vacuous and credulous.

Post-season scam

A few years ago, the University of Minnesota football teams went to the Insight Bowl. Aren’t you thrilled? If you’re like me, though, you might be wondering what the heck the “Insight Bowl” is: the team had a 6-6 record, which isn’t anything to get excited about, and the bowl doesn’t seem to have any connection to Minnesota or any kind of regional association.

If you’ve also been wondering about the mysterious proliferation of post-season bowl games, you need to read about the economics of the college football bowl system. They’re a big scam, and our athletics administration gets sucked right in.

The racket works like this: Through required purchases of anywhere from 10,000 to 17,500 tickets, schools essentially pay for the right to appear in a bowl. The bowls keep the ticket and sponsorship money. Bowl execs also negotiate their own TV contracts.

After taking 50 to 60 percent off the top, the bowls then write checks to the teams’ conferences. The conferences, in turn, split that money among their schools. (Profits from the five Bowl Championship Series games are spread to varying degrees among all conferences.)

But only about half of the 35 bowls offer payouts large enough to cover team expenses. So the conferences use money from more lucrative bowl games to cover losses from the barkers.

“You don’t lose money going to bowl games, at least not in the Big 10,” says Minnesota football spokesman Andy Seeley.

But that’s true only in a technical sense. In the Gophers’ case, the Big 10 covered the university’s $1.3 million blemish from the 2009 Insight Bowl. What insiders don’t mention is the humungous pyramid of cash schools are leaving on the table.

“They should go take economics 101,” says Dan Wetzel, a Yahoo sports columnist and co-author of Death to the BCS. “Lost profit is lost money to any other business in the world.”

And these losses are staggering.

Last year, the nation’s bowls paid schools roughly $270 million. Just for playing middlemen and providing 70-degree temperatures, bowl execs grabbed a larger cut, north of $300 million.

Why does this continue to happen? Because the people who make the choices about participation in these events are basically bribed: they get week-long vacations in places like Arizona, and no long term investment in the health of the institution.

College presidents could easily put a stop to the shell game—if they had the will, which they don’t. They tend to be a lot like coaches, a job-jumping species forever on the hunt for more prestigious posts. This march to greater altitudes requires staying within the good graces of trustees and big donors, who enjoy free bowl vacations as much as everyone else. Besides, many presidents wield less institutional power than their own coaches, as Penn State’s pedophilia scandal revealed.

So they behave like congressmen, allowing their schools to be pillaged to preserve their political capital. Better to kick these decisions to athletic directors and conference commissioners.

Faculty at universities often have an adversarial relationship with the administrators. Now you know why.

The children of Polk County must be especially sexy and delectable

That must be it. How else to explain how four pastors in one week were arrested on child rape charges? Those tempting little minxes! To tempt even saintly men of God!

As an extra special bonus, the George Jenkins High School football coach and the St. Petersburg baseball coach were arrested for sex with minors this month, too.

It couldn’t possibly be that the culture grants churches and athletics excessive privileges that draw in cocky parasites, could it? Nasty little men who believe their calling gives them special dispensation to abuse?

Bad Atheist Tropes

The Cuttlefish is asking what Atheist Tropes We Can Do Without. He’s got a bunch of good ones listed, but misses the obvious one despite noting their existence: the media, when confronted with the need to write something about those awful atheists, always turn to a simpering godbotherers like Barbara Bradly Hagerty or certifiable morons like Dinesh D’Souza for commentary. Hey, how about next time a pope dies or someone organizes a prayer rally, call me for an opinion? I’ll give you pith and sound bite.

Another one that infuriates me is the smug theist who wants to prove that I actually have faith in something, and the one thing they always choose is “love”. It’s invisible, isn’t it, just like god, so if you can believe in love, you must believe in god. Nope, sorry: I see evidence of love every day, and I can show it to you — and I don’t accept the existence of love that doesn’t demonstrate itself.