The secret life of babies

Years ago, when the Trophy Wife™ was a psychology grad student, she participated in research on what babies think. It was interesting stuff because it was methodologically tricky — they can’t talk, they barely respond in comprehensible way to the world, but as it turns out you can get surprisingly consistent, robust results from techniques like tracking their gaze, observing how long they stare at something, or even the rate at which they suck on a pacifier (Maggie, on The Simpsons, is known to communicate quite a bit with simple pauses in sucking.)

There is a fascinating article in the NY Time magazine on infant morality. Set babies to watching puppet shows with nonverbal moral messages acted out, and their responses afterward indicate a preference for helpful agents and an avoidance of hindering agents, and they can express surprise and puzzlement when puppet actors make bad or unexpected choices. There are rudiments of moral foundations churning about in infant brains, things like empathy and likes and dislikes, and they acquire these abilities untaught.

This, of course, plays into a common argument from morality for religion. It’s unfortunate that the article cites deranged dullard Dinesh D’Souza as a source — is there no more credible proponent of this idea? That would say volumes right there — but at least the author is tearing him down.

A few years ago, in his book “What’s So Great About Christianity,” the social and cultural critic Dinesh D’Souza revived this argument [that a godly force must intervene to create morality]. He conceded that evolution can explain our niceness in instances like kindness to kin, where the niceness has a clear genetic payoff, but he drew the line at “high altruism,” acts of entirely disinterested kindness. For D’Souza, “there is no Darwinian rationale” for why you would give up your seat for an old lady on a bus, an act of nice-guyness that does nothing for your genes. And what about those who donate blood to strangers or sacrifice their lives for a worthy cause? D’Souza reasoned that these stirrings of conscience are best explained not by evolution or psychology but by “the voice of God within our souls.”

The evolutionary psychologist has a quick response to this: To say that a biological trait evolves for a purpose doesn’t mean that it always functions, in the here and now, for that purpose. Sexual arousal, for instance, presumably evolved because of its connection to making babies; but of course we can get aroused in all sorts of situations in which baby-making just isn’t an option — for instance, while looking at pornography. Similarly, our impulse to help others has likely evolved because of the reproductive benefit that it gives us in certain contexts — and it’s not a problem for this argument that some acts of niceness that people perform don’t provide this sort of benefit. (And for what it’s worth, giving up a bus seat for an old lady, although the motives might be psychologically pure, turns out to be a coldbloodedly smart move from a Darwinian standpoint, an easy way to show off yourself as an attractively good person.)

So far, so good. I think this next bit gives far too much credit to Alfred Russel Wallace and D’Souza, though, but don’t worry — he’ll eventually get around to showing how they’re wrong again.

The general argument that critics like Wallace and D’Souza put forward, however, still needs to be taken seriously. The morality of contemporary humans really does outstrip what evolution could possibly have endowed us with; moral actions are often of a sort that have no plausible relation to our reproductive success and don’t appear to be accidental byproducts of evolved adaptations. Many of us care about strangers in faraway lands, sometimes to the extent that we give up resources that could be used for our friends and family; many of us care about the fates of nonhuman animals, so much so that we deprive ourselves of pleasures like rib-eye steak and veal scaloppine. We possess abstract moral notions of equality and freedom for all; we see racism and sexism as evil; we reject slavery and genocide; we try to love our enemies. Of course, our actions typically fall short, often far short, of our moral principles, but these principles do shape, in a substantial way, the world that we live in. It makes sense then to marvel at the extent of our moral insight and to reject the notion that it can be explained in the language of natural selection. If this higher morality or higher altruism were found in babies, the case for divine creation would get just a bit stronger.

No, I disagree with the rationale here. It is not a problem for evolution at all to find that humans exhibit an excessive altruism. Chance plays a role; our ancestors did not necessarily get a choice of a fine-tuned altruism that works exclusively to the benefit of our kin — we may well have acquired a sloppy and indiscriminate innate tendency towards altruism because that’s all chance variation in a protein or two can give us. There’s no reason to suppose that a mutation could even exist that would enable us to feel empathy for cousins but completely abolish empathy by Americans for Lithuanians, for instance, or that is neatly coupled to kin recognition modules in the brain. It could be that a broad genetic predisposition to be nice to fellow human beings could have been good enough to favored by selection, even if its execution caused benefits to splash onto other individuals who did not contribute to the well-being of the possessor.

But that idea may be entirely moot, because there is some evidence that babies are born (or soon become) bigoted little bastards who do quickly cobble up a kind of biased preferential morality. Evolution has granted us a general “Be nice!” brain, and also that we acquire capacities that put up boundaries and foster a kind of primitive tribalism.

But it is not present in babies. In fact, our initial moral sense appears to be biased toward our own kind. There’s plenty of research showing that babies have within-group preferences: 3-month-olds prefer the faces of the race that is most familiar to them to those of other races; 11-month-olds prefer individuals who share their own taste in food and expect these individuals to be nicer than those with different tastes; 12-month-olds prefer to learn from someone who speaks their own language over someone who speaks a foreign language. And studies with young children have found that once they are segregated into different groups — even under the most arbitrary of schemes, like wearing different colored T-shirts — they eagerly favor their own groups in their attitudes and their actions.

That’s kind of cool, if horrifying. It also, though, points out that you can’t separate culture from biological predispositions. Babies can’t learn who their own kind is without some kind of socialization first, so part of this is all about learned identity. And also, we can understand why people become vegetarians as adults, or join the Peace Corps to help strangers in far away lands — it’s because human beings have a capacity for rational thought that they can use to override the more selfish, piggy biases of our infancy.

Again, no gods or spirits or souls are required to understand how any of this works.

Although, if they did a study in which babies were given crackers and the little Catholic babies all made the sign of the cross before eating them, while all the little Lutheran babies would crawl off to make coffee and babble about the weather, then I might reconsider whether we’re born religious. I don’t expect that result, though.

Sam Harris v. Sean Carroll

The discussion is interesting. Sam Harris recently and infamously proposed that, contra Hume, you can derive an ‘ought’ from an ‘is’, and that science can therefore provide reasonable guidance towards a moral life. Sean Carroll disagrees at length.

I’m afraid that so far I’m in the Carroll camp. I think Harris is following a provocative and potentially useful track, but I’m not convinced. I think he’s right in some of the examples he gives: science can trivially tell you that psychopaths and violent criminals and the pathologies produced by failed states in political and economic collapse are not good models on which to base a successful human society (although I also think that the desire for a successful society is not a scientific premise…it’s a kind of Darwinian criterion, because unsuccessful societies don’t survive). However, I don’t think Harris’s criterion — that we can use science to justify maximizing the well-being of individuals — is valid. We can’t. We can certainly use science to say how we can maximize well-being, once we define well-being…although even that might be a bit more slippery than he portrays it. Harris is smuggling in an unscientific prior in his category of well-being.

One good example Harris uses is the oppression of women and raging misogyny of the Taliban. Can we use science to determine whether that is a good strategy for human success? I think we can, but not in the way Harris is trying to do so: we could ask empirically, after the fact, whether the Taliban was successful in expanding, maintaining its population, and responding to its environment in a productive way. We cannot, though, say a priori that it is wrong because abusing and denigrating half the population is unconscionable and vile, because that is not a scientific foundation for the conclusion. It’s an emotional one; it’s also a rational one, given the premise that we should treat all people equitably…but that premise can’t claim scientific justification. That’s what Harris has to show!

That is different from saying is is an unjustified premise, though — I agree with Harris entirely that the oppression of women is an evil, a wrong, a violation of a social contract that all members of a society should share. I just don’t see a scientific reason for that — I see reasons of biological predisposition (we are empathic, social animals), of culture (this is a conclusion of Enlightenment history), and personal values, but not science. Science is an amoral judge: science could find that a slave culture of ant-like servility was a species optimum, or that a strong behavioral sexual dimorphism, where men and women had radically different statuses in society, was an excellent working solution. We bring in emotional and personal beliefs when we say that we’d rather not live in those kinds of cultures, and want to work towards building a just society.

And that’s OK. I think that deciding that my sisters and female friends and women all around the world ought to have just as good a chance to thrive as I do is justified given a desire to improve the well-being and happiness of all people. I am not endorsing moral relativism at all — we should work towards liberating everyone, and the Taliban are contemptible scum — I’m just not going to pretend that that goal is built on an entirely objective, scientific framework.

Carroll brings up another set of problems. Harris is building his arguments around a notion that we ought to maximize well-being; Caroll points out that “well-being” is an awfully fuzzy concept that means different things to different people, and that it isn’t clear that “well-being” isn’t necessarily a goal of morality. Harris does have an answer to those arguments, sort of.

Those who assumed that any emphasis on human “wellbeing” would lead us to enslave half of humanity, or harvest the organs of the bottom ten percent, or nuke the developing world, or nurture our children a continuous drip of heroin are, it seems to me, not really thinking about these issues seriously. It seems rather obvious that fairness, justice, compassion, and a general awareness of terrestrial reality have rather a lot to do with our creating a thriving global civilization–and, therefore, with the greater wellbeing of humanity. And, as I emphasized in my talk, there may be many different ways for individuals and communities to thrive–many peaks on the moral landscape–so if there is real diversity in how people can be deeply fulfilled in life, this diversity can be accounted for and honored in the context of science. As I said in my talk, the concept of “wellbeing,” like the concept of “health,” is truly open for revision and discovery. Just how happy is it possible for us to be, personally and collectively? What are the conditions–ranging from changes in the genome to changes in economic systems–that will produce such happiness? We simply do not know.

The phrase beginning “It seems rather obvious…” is an unfortunate give-away. Don’t tell me it’s obvious, tell me how you can derive your conclusion from the simple facts of the world. He also slips in a new goal: “creating a thriving global civilization.” I like that goal; I think that is an entirely reasonable objective for a member of a species to strive for, to see that their species achieves a stable, long-term strategy for survival. However, the idea that it should be achieved by promoting fairness, justice, compassion, etc., is not a scientific requirement. As Harris notes, there could be many different peaks in the moral landscape — what are the objective reasons for picking those properties as the best elements of a strategy? He doesn’t say.

I’m fine with setting up a set of desirable social goals — fairness, justice, compassion, and equality are just a start — and declaring that these will be the hallmark of our ideal society, and then using reason and science to work towards those objectives. I just don’t see a scientific reason for the premises, wonderful as they are and as strongly as they speak to me. I also don’t feel a need to label a desire as “scientific”.

Like plums? Do something right away!

This is the first I’ve heard of this, but there is a devastating disease called Plum Pox Virus that kills trees bearing stone fruits, like plums and peaches, and the only way to deal with infected plants is to rip them out of the ground and destroy them. There has been a recent outbreak in Pennsylvania; don’t rush out to buy the last of the fruits in an apocalyptic terror, it’s just a hint of a potential problem for the future, but you can worry a little bit. And maybe you can promote some science that will help.

A new variety of plum called the Honey Sweet has been genetically engineered that is completely resistant to the virus. It is just now in the process of being deregulated by the EPA, and they’re looking for public comment (it’s a confusing site: look for “Public Participation for Coat Protein Gene of Plum Pox Virus”, and “Comment Due”; click on it and you can tell the government what they should do).

Work fast, this is the last day for input. For the plums!

Everything old is new again

If you’ve ever invited me out to give a science talk, you know that what I generally talk about is this concept of deep homology: the discovery that features that we often consider the hallmarks of complex metazoan life often have at their core a network of genetic circuitry that was first pioneered in bacteria. What life has done is taken useful functional elements that were worked out in the teeming, diverse gene pools of the dominant single-celled forms of life on earth and repurposed it in novel ways. The really interesting big bang of life occurred long before the Cambrian, as organisms evolved useful tools for signaling, adhesion, regulation, and so forth — all stuff that was incredibly useful for a single cell negotiating through space and time in a complex external environment, and which could be coopted for building multicellular organisms.

But if you don’t feel like flying me out to tell you all about it, Carl Zimmer has an excellent article on deep homology in the NYT, and he uses a new example I’ll have to steal: a genetic module that we use to regulate blood vessel growth that can also be found in yeast cells, where it is used to maintain cell walls.

Let’s hide that embarrassing conflict in American culture

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For many years, the NSF has been producing a biennial report on American attitudes (and many other statistics) about science called Science and Engineering Indicators. This year, as they have every year, they got the uncomfortable news that a majority of our compatriots reject human evolution and the Big Bang (that last one might have been partly because of the dumb way the question is phrased). What’s different, though, is that for the first time the NSF has decided to omit the fact.

This is very strange. It is a serious problem in our educational system that so much of the public is vocal in their opposition to a well-established set of ideas — these ought to be relevant data in a survey of national attitudes towards science. Why were they dropped? It isn’t because of an overt whitewash to hide our shame away, it seems — instead, it sounds like it’s an accommodationist’s discomfort with highlighting a conflict between religion and science. At least, that’s how I read the excuses given. John Bruer, a philosopher who led the review team on this section of the report, is open about his reasoning.

Bruer proposed the changes last summer, shortly after NSF sent a draft version of Indicators containing this text to OSTP and other government agencies. In addition to removing a section titled “Evolution and the Big Bang,” Bruer recommended that the board drop a sentence noting that “the only circumstance in which the U.S. scores below other countries on science knowledge comparisons is when many Americans experience a conflict between accepted scientific knowledge and their religious beliefs (e.g., beliefs about evolution).” At a May 2009 meeting of the board’s Indicators committee, Bruer said that he “hoped indicators could be developed that were not as value-charged as evolution.”

Bruer, who was appointed to the 24-member NSB in 2006 and chairs the board’s Education and Human Resources Committee, says he first became concerned about the two survey questions as the lead reviewer for the same chapter in the 2008 Indicators. At the time, the board settled for what Bruer calls “a halfway solution”: adding a disclaimer that many Americans didn’t do well on those questions because the underlying issues brought their value systems in conflict with knowledge. As evidence of that conflict, Bruer notes a 2004 study described in the 2008 Indicators that found 72% of Americans answered correctly when the statement about humans evolving from earlier species was prefaced with the phrase “according to the theory of evolution.” The 2008 volume explains that the different percentages of correct answers “reflect factors beyond unfamiliarity with basic elements of science.”

George Bishop, a political scientist at the University of Cincinnati in Ohio who has studied attitudes toward evolution, believes the board’s argument is defensible. “Because of biblical traditions in American culture, that question is really a measure of belief, not knowledge,” he says. In European and other societies, he adds, “it may be more of a measure of knowledge.”

I’ve emphasized the key phrases in that summary, and actually, I rather agree with them. These are issues in which ignorance isn’t the fundamental problem (although, of course, ignorance contributes), but in which American culture has a serious and active obstacle to advancing scientific awareness, the evangelical stupidity of religion. That is something different from what we find in Europe, and it’s also something more malevolent and pernicious than an inadequate educational system.

It seems to me, though, that that isn’t a reason to drop it from the survey and pretend it doesn’t exist and isn’t a problem. Instead, maybe they should promote it to a whole new section of the summary and emphasize it even more, since they admit that it is an unusual feature of our culture, and one that compels people to give wrong answers on a science survey.

Maybe they could title the section, “The Malign Influence of Religion on American Science Education”.

I also rather like the answer given by Jon Miller, the fellow who has actually conducted the work of doing the survey in the past.

Miller believes that removing the entire section was a clumsy attempt to hide a national embarrassment. “Nobody likes our infant death rate,” he says by way of comparison, “but it doesn’t go away if you quit talking about it.”

Exactly right. But if we do talk about it, we end up asking why it’s so bad, and then we make rich people squirm as we point fingers at our deplorable health care system. And in the case of the question about evolution, we make religious people, and especially the apologists for religion, extremely uncomfortable, because they have been defending this institution of nonsense that has direct effects on measurable aspects of science literacy.

Unfortunately, Bruer has also been caught saying something very stupid.

When Science asked Bruer if individuals who did not accept evolution or the big bang to be true could be described as scientifically literate, he said: “There are many biologists and philosophers of science who are highly scientifically literate who question certain aspects of the theory of evolution,” adding that such questioning has led to improved understanding of evolutionary theory. When asked if he expected those academics to answer “false” to the statement about humans having evolved from earlier species, Bruer said: “On that particular point, no.”

What was he thinking? The question on the NSF survey is not asking about details of the mechanisms of evolution, so his objection is weirdly irrelevant. I don’t know if he’s hiding away any creationist sympathies (that phrasing is exactly what I’ve heard from many creationists, after all), but it does reveal that he’s not thinking at all deeply about the issue. And for a philosopher, shouldn’t that be a high crime?

Bhattacharjee Y (2010) NSF Board Draws Flak for Dropping Evolution From Indicators. Science 328(5975):150-151.

The Large Hadron Collider will confirm the Bible

Good news: the Large Hadron Collider is operational, and has fired two particles together with a force of 7 trillion electron volts…and it’s only the beginning, since they’re going to ramp up the power gradually. It’s too bad Michio Kaku had to muck it up with a lot of nonsense.

“This is a huge step toward unraveling Genesis Chapter 1, Verse 1 – what happened in the beginning,” physicist Michio Kaku told The Associated Press.

“This is a Genesis machine. It’ll help to recreate the most glorious event in the history of the universe.”

Please, no. Genesis has zero correspondence to reality. We are not going to drill back through Biblical events to find the truth of Genesis 1:1, which reads, by the way, “In the beginning God created the heaven and the earth.” Is Kaku suggesting that the LHC will test that proposition? That is a genuinely tone-deaf thing for a scientist to say in fundie-infested America.

And of course, Answers in Genesis stands ready to appropriate the LHC for its purposes. It’s a rather bizarre support they offer to the LHC, though. You see, AiG does not accept the Big Bang, or any early event in the history of the universe that precedes 4004BC. So they have to tip-toe around it: nothing the LHC will discover can possibly confirm modern cosmology, but, they say, it can “give us some interesting insight into how God upholds His universe today”. Science works only because God makes it work.

The author, Jason Lisle, is quite possibly the most boring creationist I’ve ever read, so his essay here is scarcely worth reading unless you are really in need of a nap, but it does conclude with a useful revelation.

Whatever scientists discover about the universe from the LHC, it will show that the universe is upheld by God in a consistent way. This will therefore confirm that the Bible is true.

Get that? No matter what evidence is unearthed, no matter what science learns, no matter what history tells us, everything will be interpreted to confirm their freakish interpretation of the history of the universe. This is not science. There’s nothing you can say that is more contrary to the ideal of science than to claim that your ideas are completely impervious to the evidence.

For those who are hard of reading: I KNOW THAT KAKU’S WORDS WERE A METAPHOR. I DO NOT THINK HE IS A BELIEVER, LET ALONE A CREATIONIST NUTJOB.

Better?

I do think he said something stupid and thoughtless. And please learn something: saying something is a metaphor does not automatically make it good or even excusable. For some reason, the word ‘metaphor’ has become a kind of catch-all excuse whenever someone says something stupid and unjustifiable. It isn’t. This is almost as bad as rationalizing gobbledygook and nonsense by calling it art or poetry, which is so insulting to the muses of poetry that I expect Calliope and Erato and Polyhymnia to materialize and start thwacking everyone upside the head with a cithara or stuffing scrolls up their nostrils or strangling them with a veil.

Again, for those having trouble following along: METAPHOR IS NOT A MAGIC GET-OUT-OF-STUPID CARD.

Amok Time for crayfish

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This is quite possibly the most awesome biology photo ever taken. It is two blind-folded crayfish battling each other in clouds of fluorescent green urine. It’s a good thing it’s just a picture, because if it were a video, in 3D, with the Star Trek fight music playing in the background, every science nerd in the world would have to lie down and die in ecstasy. Don’t click on the little arrow below it! I won’t be responsible for the consequences! (Fortunately, I can’t put it into 3D motion, so I won’t be slaughtering my readership here.)

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The premise of this work is a small dilemma in sexual selection theory. The theory predicts that females are generally the choosy, limiting sex, so they should invest less in courtship — they can simply lie back, look alluring, and let the males fight it out over them before picking a winner. Males are expected to invest the most in courtship, because after all, winning gets them the big payoff with little expense, while females get the big expense of egg laying/pregnancy. That boys are traditionally expected to ask girls out on dates, not vice versa, makes a lot of sense in the context of this theory.

A possible contradiction to the theory, though, is the production of female pheromones to invite courtship. Many arthropods in particular — consider moths that produce olfactory signals that males have evolved enormous antennae to detect — use female-initiated signals to initiate courtship behavior in males, as if every day were Sadie Hawkins Day.

One way to resolve the contradiction, though, is to discover that the signal evolved for some other purpose than triggering courtship. Perhaps ancestral female moths were flying about smelling generically mothy, and male moths are simply homing in on something the females can’t help but produce.

Enter the crayfish, Pacifastacus leniusculus. Females in this species initiate courtship with a grand aromatic puff of urine, a kind of crustacean invitation to dance that I am quite glad our species does not emulate. In the photo above, it’s been visualized by injecting the crayfish with a dye, fluorescein, that can be seen against a black background with the proper illumination. The crayfish have been blindfolded so that their behaviors aren’t triggered by visual cues.

And the answer they discovered is that the copious urination is an aggression, not courting, signal. Males spew it out when they’re fighting with other males, females do it at the start of courtship, and males actually reduce the amount of urine produced during courtship. So they’re not saying, “I love you, come get me,” they’re saying “Grrr, fight, fight, fight” when they spray the tank with urine.

What’s the advantage to the ladies here? It’s the incitement. The crayfish live in high population densities, and stirring up a little trouble and getting the males to fight provides an opportunity to select a winner. It may also produce a local population of desirable contenders: a whiff of urine may encourage wimpy males to run away and avoid potential trouble, while the more aggressive males may home in on it.

Berry FC, Breithaupt T (2010) To signal or not to signal? Chemical communication by urine-borne signals mirrors sexual conflict in crayfish. BMC Biology 8:25.

Advice from believers is demonstrably worthless

Speaking of the ABC, I revisited their Global Atheist Convention blog, which I can say without hesitation was absolutely the worst effort any of the media put out. I think I prefer the blatant stupidity of a Gary Ablett to the mawkish blitherings of a gang of pious apologists — at least it’s honest. And that’s all they’ve got — the blog is still limping along with a series of tepid guest posts by people making weak excuses for their faith. It was supposedly a blog about the convention, but it never quite rose to the standard of even meeting their own aims — instead, it’s an exercise in breast-beating by sorry-assed theists.

It’s utterly negligible and irrelevant, unless you like the spectacle of Christians going boo-hoo-hoo. I did catch one gawdawful post by Chris Mulherin, though, which adds the additional fillip of seeing a Christian getting everything completely wrong. It’s embarrassing. I even addressed several of these points in my talk, and said the exact opposite of what Mulherin claims are truisms for atheists. Maybe I put him to sleep.

Anyway, here are 5 things that Mulherin claims are ‘unscientific beliefs’ that must be held to get science off the ground.

Five things that atheists (and others) believe that cannot be shown by the evidence of science:

  1. The universe is governed by the law of cause and effect.

  2. We can normally trust human rationality and the evidence of our senses.

  3. The axioms of mathematics and the laws of logic are true.

  4. Moral language makes sense and cannot be reduced to personal preferences. Racism, paedophilia, destroying the planet and chauvinism are wrong in a more binding sense than “I/we don’t like those things.”


  5. Humans have freewill and are not totally determined by the laws of science.     In order to live, converse, decide what I will put on my sandwich, or whether I will attend an atheist convention, I must have the freedom (within limits) to make decisions.

There is more to be said, and the debate can be complicated, but the gist of the idea is that science must take some things as given before it can start its work. Most atheists take the above truths as givens, despite the fact that none of them can be derived scientifically.

Ugh. See? This is what happens when you gather a band of happy theists to interpret the words of a convention of atheists — it goes plunging off the rails.

  1. Wrong. I think chance is a significant factor in the universe. Cause and effect are important but not necessarily assumed; causal relationships are what we test for in scientific experiments.

  2. Completely wrong. Quite the reverse, actually; science is a tool we use to correct for the unreliability of our minds and our senses. I know I don’t trust my perceptions at all, and consider independent confirmation a great reassurance.

  3. In an utterly trivial sense, “truth” is an outcome of logic and math, so yes, this is accurate, by definition. We do believe that there is a real universe, and we attempt to probe it empirically, and in that sense we suspect that there is an actual deeper material truth, but that’s about it.

    I do wonder, though, if logic is false, how Christians interpret the world. Wouldn’t that make everything arbitrary and chaotic? In that context, maybe the Bible is useful after all, since it is an awfully arbitrary book.

  4. Mulherin needs to read some Hauser. A lot of morality is driven by personal revulsion, nothing more. There is a greater binding sense, however: a rational decision that says that discriminating against fellow human beings, abusing the next generation, reducing the carrying capacity of our environment, and treating women as objects has long term consequences to our society that are deleterious to the preservation of culture. We do make an assumption our culture is worth preserving, of course, but then, so do people in all viable cultures.

    It’s very Darwinian reasoning, though. Maybe Mulherin hasn’t quite grokked that major insight.

  5. Free will is philosophical bullshit. You can have an entirely natural biology that is subject to investigation by science that is not some kind of clockwork, predestined sequence of events. I decide what to put on my sandwich, but “I” is an unpredictable product of very complex neurological activity, colored by history over a baseline of biological predispositions.

It’s extremely annoying to be told by a delusionist precisely what beliefs I must hold because I’m an atheist, when I don’t. It’s a bit like concern trolling: the helpful faith-head erects a squad of five straw men which he’ll then kindly offer to demolish from us to clear the illusions from our eyes. No, thank you: you believe in ritual sacrifice, god-men, magical supplications, and supernatural beings. Your advice on science is worthless except for comedy purposes.

Hannity and Carlson dislike science

As yet another examples of the derangement of conservative thought, Sean Hannity has been pushing a list of 102 examples of ‘wasteful’ stimulus spending. I don’t quite get it; this is money the government is disbursing to encourage jobs for the sake of jobs, and if they were hiring people to dig holes and fill them in again, it would accomplish their task. However, the money is being spent sensibly on projects that also improve the nation’s infrastructure in small ways and increase knowledge.

One of the targets of their scorn are science projects, including this one, improving the facilities at an insect collection in Michigan. You might not want to watch this if Hannity and Tucker Carlson make you gag, but the scientist in charge, Anthony Cognato, does a good job of making his case.

The bad guys are really reaching here. Carlson tries to imply that they didn’t need the money, that all they had to do was stick the ‘bugs’ in a refrigerator, but that doesn’t work — this is a working collection, you can’t just archive them away in a deep freeze, and storing a million-specimen collection in a bank of -80° freezers would be rather substantially more expensive than putting in more effective shelving. Cognato addressed this (that link is behind a paywall, sorry):

The interview began and Carlson transformed into an effective pundit for the Right; the questioning was quick, the topics a little disconnected, and at times he seemed to fish for a particular sound bite that would support the opinion that funding the collection was a waste of money. For example, he asked me a couple times if I could have controlled collection pests by just continually freezing the drawers that contain the specimens, thus making our purchase of new storage cabinets unnecessary. I answered repeatedly that freezing our thousands of drawers was not optimal for long-term preservation, that it drained time and resources, and kept researchers from using the collection for scientific studies.

Then they try to suggest that all the $200,000 did was to hire a few students at $8/hour, which is not true: those students weren’t in charge of building shelves. That was a professional job from a company called BioQuip. One of the workers at that company wrote in:

My job is one of the many that were affected by this grant. I work for BioQuip, the California company that manufactures the drawers that MSU bought. Our company employs 27 people whose jobs were all affected by this grant as well as the lumber company, glass company & trucking companies we use along the way. This grant has benefited the US economy, created & maintained US jobs on a level far greater than 4 jobs at a single university. Hannity & Carlson need to do their homework.

Of course, the Right doesn’t see this. Read the comments on Hannity’s site about this subject: it’s insane. Most of the people are ranting about Pelosi and Obama with no connection at all to the topic of the video…except for the weird Cyrillic comments (Russian spam of some sort?).

We’ve got to keep these nuts out of power.

How to make a snake

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First, you start with a lizard.

Really, I’m not joking. Snakes didn’t just appear out of nowhere, nor was there simply some massive cosmic zot of a mutation in some primordial legged ancestor that turned their progeny into slithery limbless serpents. One of the tougher lessons to get across to people is that evolution is not about abrupt transmutations of one form into another, but the gradual accumulation of many changes at the genetic level which are typically buffered and have minimal effects on the phenotype, only rarely expanding into a lineage with a marked difference in morphology.

What this means in a practical sense is that if you take a distinct form of a modern clade, such as the snakes, and you look at a distinctly different form in a related clade, such as the lizards, what you may find is that the differences are resting atop a common suite of genetic changes; that snakes, for instance, are extremes in a range of genetic possibilities that are defined by novel attributes shared by all squamates (squamates being the lizards and snakes together). Lizards are not snakes, but they will have inherited some of the shared genetic differences that enabled snakes to arise from the squamate last common ancestor.

So if you want to know where snakes came from, the right place to start is to look at their nearest cousins, the lizards, and ask what snakes and lizards have in common, that is at the same time different from more distant relatives, like mice, turtles, and people…and then you’ll have an idea of the shared genetic substrate that can make a snake out of a lizard-like early squamate.

Furthermore, one obvious place to look is at the pattern of the Hox genes. Hox genes are primary regulators of the body plan along the length of the animal; they are expressed in overlapping zones that specify morphological regions of the body, such as cervical, thoracic, lumbar, sacral/pelvic, and caudal mesodermal tissues, where, for instance, a thoracic vertebra would have one kind of shape with associated ribs, while lumbar vertebra would have a different shape and no ribs. These identities are set up by which Hox genes are active in the tissue forming the bone. And that’s what makes the Hox genes interesting in this case: where the lizard body plan has a little ribless interruption to form pelvis and hindlimbs, the snake has vertebra and ribs that just keep going and going. There must have been some change in the Hox genes (or their downstream targets) to turn a lizard into a snake.

There are four overlapping sets of Hox genes in tetrapods, named a, b, c, and d. Each set has up to 13 individual genes, where 1 is switched on at the front of the animal and 13 is active way back in the tail. This particular study looked at just the caudal members, 10-13, since those are the genes whose expression patterns straddle the pelvis and so are likely candidates for changes in the evolution of snakes.

Here’s a summary diagram of the morphology and patterns of Hox gene expression in the lizard (left) and snake (right). Let’s see what we can determine about the differences.

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Evolutionary modifications of the posterior Hox system in the whiptail lizard and corn snake. The positions of Hox expression domains along the paraxial mesoderm of whiptail lizard (32-40 somites, left) and corn snake (255-270 somites, right) are represented by black (Hox13), dark grey (Hox12), light grey (Hox11) and white (Hox10) bars, aligned with coloured schemes of the future vertebral column. Colours indicate the different vertebral regions: yellow, cervical; dark blue, thoracic; light blue, lumbar; green, sacral (in lizard) or cloacal (in snake); red, caudal. Hoxc11 and Hoxc12 were not analysed in the whiptail lizard. Note the absence of Hoxa13 and Hoxd13 from the corn snake mesoderm and the absence of Hoxd12 from the snake genome.

The morphology is revealing: snakes and lizards have the same regions, cervical (yellow), thoracic (blue), sacral (or cloacal in the snake, which lacks pelvic structures in most species) in green, and caudal or tail segments (red). The differences are in quantity — snakes make a lot of ribbed thoracic segments — and detail — snakes don’t make a pelvis, usually, but do have specializations in that corresponding area for excretion and reproduction.

Where it really gets interesting is in the expression patterns of the Hox genes, shown with the bars that illustrate the regions where each Hox gene listed is expressed. They are largely similar in snake and lizard, with boundaries of Hox expression that correspond to transitions in the morphology of vertebrae. But there are revealing exceptions.

Compare a10/c10 in the snake and lizard. In the snake, these two genes have broader expression patterns, reaching up into the thoracic region; in the lizard, they are cut off sharply at the sacral boundary. This is interesting because in other vertebrates, the Hox 10 group is known to have the function of suppressing rib formation. Yet there they are, turned on in the posterior portion of the thorax in the snake, where there are ribs all over the place.

In the snake, then, Hox a10 and c10 have lost a portion of their function — they no longer shut down ribs. What is the purpose of the extended domain of a10/c10 expression? It may not have one. A comparison of the sequences of these genes between various species reveals a detectable absence of signs of selection — the reason these genes happen to be active so far anteriorly is because selection has been relaxed, probably because they’ve lost that morphological effect of shutting down ribs. Those big bars are a consequence of simple sloppiness in a system that can afford a little slack.

The next group of Hox genes, the 11 group, are very similar in their expression patterns in the lizard and the snake, and that reflects their specific roles. The 10 group is largely involved in repression of rib formation, but the 11 group is involved in the development of sacrum-specific structures. In birds, for instance, the Hox 11 genes are known to be involved in the development of the cloaca, a structure shared between birds, snakes, and lizards, so perhaps it isn’t surprising that they aren’t subject to quite as much change.

The 13 group has some notable differences: Hox a13 and d13 are mostly shut off in the snake. This is suggestive. The 13 group of Hox genes are the last genes, at the very end of the animal, and one of their proposed functions is to act as a terminator of patterning — turning on the Hox 13 genes starts the process of shutting down the mesoderm, shrinking the pool of tissue available for making body parts, so removing a repressor of mesoderm may promote longer periods of growth, allowing the snake to extend its length further during embryonic development.

So we see a couple of clear correlates at the molecular level for differences in snake and lizard morphology: rib suppression has been lost in the snake Hox 10 group, and the activity of the snake Hox 13 group has been greatly curtailed, which may be part of the process of enabling greater elongation. What are the similarities between snakes and lizards that are also different from other animals?

This was an interesting surprise. There are some differences in Hox gene organization in the squamates as a whole, shared with both snakes and lizards.

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Genomic organization of the posterior HoxD cluster. Schematic representation of the posterior HoxD cluster (from Evx2 to Hoxd10) in various vertebrate species. A currently accepted phylogenetic tree is shown on the left. The correct relative sizes of predicted exons (black boxes), introns (white or coloured boxes) and intergenic regions (horizontal thick lines) permit direct comparisons (right). Gene names are shown above each box. Colours indicate either a 1.5-fold to 2.0-fold (blue) or a more than 2.0-fold (red) increase in the size of intronic (coloured boxes) or intergenic (coloured lines) regions, in comparison with the chicken reference. Major CNEs are represented by green vertical lines: light green, CNEs conserved in both mammals and sauropsids; dark green, CNEs lost in the corn snake. Gaps in the genomic sequences are indicated by dotted lines. Transposable elements are indicated with asterisks of different colours (blue for DNA transposons; red for retrotransposons).

That’s a diagram of the structure of the chromosome in the neighborhood of the Hox d10-13 genes in various vertebrates. For instance, look at the human and the turtle: the layout of our Hox d genes is vary similar, with 13-12-11-10 laid out with approximately the same distances between them, and furthermore, there are conserved non-coding elements, most likely important pieces of regulatory DNA, that are illustrated in light yellow-reen and dark green vertical bars, and they are the same, too.

In other words, the genes that stake out the locations of pelvic and tail structures in turtles and people are pretty much the same, using the same regulatory apparatus. It must be why they both have such pretty butts.

But now compare those same genes with the squamates, geckos, anoles, slow-worms, and corn snakes. The differences are huge: something happened in the ancestor of the squamates that released this region of the genome from some otherwise highly conserved constraints. We don’t know what, but in general regulation of the Hox genes is complex and tightly interknit, and this order of animals acquired some other as yet unidentified patterning mechanism that opened up this region of genome for wider experimentation.

When these regions are compared in animals like turtles and people and chickens, the genomes reveal signs of purifying selection — that is, mutations here tend to be unsuccessful, and lead to death, failure to propagate, etc., other horrible fates that mean tinkering here is largely unfavorable to fecundity (which makes sense: who wants a mutation expressed in their groinal bits?). In the squamates, the evidence in the genome does not witness to intense selection for their particular arrangement, but instead, of relaxed selection — they are generally more tolerant of variations in the Hox gene complex in this area. What was found in those enlarged intergenic regions is a greater invasion of degenerate DNA sequences: lots of additional retrotransposons, like LINES and SINES, which are all junk DNA.

So squamates have more junk in the genomic trunk, which is not necessarily expressed as an obvious phenotypic difference, but still means that they can more flexibly accommodate genetic variations in this particular area. Which means, in turn, that they have the potential to produce more radical experiments in morphology, like making a snake. The change in Hox gene regulation in the squamate ancestor did not immediately produce a limbless snake, instead it was an enabling mutation that opened the door to novel variations that did not compromise viability.

Di-Po N, Montoya-Burgos JI, Miller H, Pourquie O, Milinkovitch MC, Duboule D (2010) Changes in Hox genes’ structure and function during the evolution of the squamate body plan. Nature 464:99-103.