Pleiotropy

Oh my dog, this is too precious not to share: Jerry Coyne blogged about his visit to Puebla, and posted a ton of pictures of the invited luminaries. One of them is Coyne himself with detestable Dinesh D'Souza. D'Souza used to date Ann Coulter.

Fig. 11. The picture that will ruin me. With Dinesh d’Souza. I figured that since I chided P.Z. for posing with Michael Ruse, I should give him a chance to reciprocate. Unlike Ruse, however, Dinesh seemed like a nice guy. I shook the hand that fondled Ann Coulter!

Eeeeeeew. Smitten for eternity! I wouldn't have done that. Reputation, career, sexlife... all are now in serious danger.

Just in case you haven't already seen it on Pharyngula, I present the Intelligence Squared Debate - Christopher Hitchens and Stephen Fry vs. The Catholics. While it's a whole 45 minutes of your precious time (I hope your time is precious), it is well spent whether you're interested in debates on religion or not, just because both Christopher Hitchens and Stephen Fry are such eloquent and forceful speakers.



My own take on the question of whether the Catholic Church is a force for good in the World or not is that I don't know. I am not really religious (in fact, I make Dawkins look like a choirboy), but I have to say that in answering the question fairly, one must weigh the good things that the Catholic Church does against the bad things that it is responsible for. The bad things include both sponsoring and failing to properly punish clergy who rape children - when it is known that the raping happens again and again, the Church should know to do something radical to prevent it, which it has not done (e.g. shutting down those positions of authority altogether). But those unquestionably bad things must be weighed against the good things the Church works, and I don't know what those are, or what the magnitude of them would be. It could be that many a child's life and virginity is saved in the sanctity of churches and by clergymen around the globe. I don't know. It could also be that whole societies would fall into disarray should the Catholic Church suddenly cease to exist. I find that unlikely, but I admit I don't have the data to deny it.

If I had to venture an educated guess, I'd say that yes, the Catholic Church is a force for good in the World, but not nearly as much as it is a force of poverty, superstition, rape, murder, death, misery, and the propagation of falsehoods.

Raymond T. Pierrehumbert, University of Chicago professor in geophysics, thoroughly dismantles Steven Levitt's claim* as presented in Superfreakonomics that "it [is] pointless to try to solve global warming by building solar cells, because they are black and absorb all the solar energy that hits them, but convert only some 12% to electricity while radiating the rest as heat, warming the planet."

In an open letter to Levitt, Pierrehumbert uses very simple math to make it clear how bogus that claim is. Along the way we learn how pathetically small an area of the globe would have to be covered with solar cell to meet the whole world's electricity demands. Placed in the middle of the Arabian Peninsula, I contend that the negative effects it would have on humans and wildlife there would be worth the benefit.

The question of Levitt's negligence is important for two reasons. 1) Global warming is a serious issue, and it would hurt us all if such bogus claims get a foothold, turning public opinion against ideas that can alleviate the problem. 2) After reading Freakonomics, I felt elated by Levitt's approach, and baffled by many of the facts that he unearths. I wish to be able to continue to trust his word, but with such negligence it gets harder.

Now I'll be eagerly waiting for a reply from Levitt. I'll applaud him if he apologizes...

* Actually, the claim was made by Nathan Myhrvold, but the whole point of Pierrehumbert's letter is that Levitt should have been more critical of this claim before reiterating it in his book.

When artificially inseminating sows Danish pig farmers simulate the copulatory action of the boar, and this is beautifully (dare I say romantically) demonstrated in a video shown during this talk by Mary Roach on TED: 10 things you didn't know about orgasm:



Do watch this video - it is throughly entertaining. For a quick overview, here are the ten facts about orgasm:

1. Unborn babies can have them.
2. You don't need genitals.
3. You can have them when you're dead.
4. Orgasm can cause bad breath.
5. And cure the hiccups.
6. Doctors once prescribed orgasm for fertility.
7. Pig farmers still do.
8. Female animals are having more fun than you think.
9. Studying human orgasm in a lab is not easy.
10. But it sure is entertaining.

Also tossed in: Week old human semen is of lower quality, so now men have an evolutionary excuse for masturbating.

There is a story going around that I have been unable to confirm, saying that more people named Ken move to Kentucky than expected on average. In the light of that it is no wonder that a pair of scientists by the names Masters and Johnson would be particularly interested in the science of orgasm, wouldn't you agree?

Dinesh D'Souza has a book out on the evidence for life after death, Life After Death: The Evidence. Should you be in doubt, this would be the place to go for any evidence there is for life after death. Right?

Well, D'Souza's kind of evidence is not the regular kind that you and I like to see. An example from a short article in SFGate (actually, it's the only one he presents here):

Material things like bodies are perishable but immaterial things like ideas aren't. So we, like nature, might have a built-in progression from perishable matter to imperishable mind. The time will come when our bodies will irretrievably break down, but it is possible, indeed suggested within the script of nature, that a part of us might outlast these mortal coils.

"Bodies are made of matter, so they can die. Ideas are not made of matter, so they cannot die. Therefore it might be that out bodies can progress from matter to pure mind, and thus avoid death. The evidence from nature is that our minds will not die." Isn't that what he is saying?

What a load of shoddy, fifth-rate, dimwitted nonsense. Completely void of substance, and... nothing to do with evidence.

That evidence from nature is, ironically (given that D'Souza is a creationist), evolution. He argues that because evolution progresses from chemistry though cells onto mind, so must our minds survive our dying bodies.

That of course just does not follow. On top of that, he builds his argument on the claim that ideas aren't material, but they are too. Ideas are located in the brain and exist only as long as the brain works. Ideas emerge from the chemical and physical properties of the brain, and cease to exist along with the brain. Emergence does not imply anything immaterial.

Along the way he manages to show how fundamentally he does not understand evolution:

Most biologists emphatically deny that there is a plan. Evolution, they say, is based on chance and random accident.

They so do not - evolution is much more than chance.

De Duve's "The Tree of Life" has eubacteria and archaebacteria at the root, then simple eukaryotes, then more complex multicellular organisms, then fungi and plants, then fishes, then reptiles, then mammals, and finally humans.

Whatever de Duve meant, this quote satisfies D'Souza's fantasy that humans are the pinnacle of life (again, despite he is a conservative Christian who does not believe in evolution after all). However, it does not follow from evolutionary theory, or nature, or science, or PNAS* that humans are the apex of evolution.

But, I do agree with him about there being life after death: My life after your death. My children's life after mine.

* Got the pun?

Eugenie Scott gets the last word in an entertaining exchange with Ray Comfort (aka the bananaman) about his publication of Darwin's Origin with a long foreword by Comfort. Comfort is clueless or devious. Or both. Both.

Scott ends her rebuttal with a note about a young-earth creationist:

I close with another quote. Todd C. Wood is a young-earth creationist—indeed, the director of the Center for Origins Research at Bryan University, founded in honor of the creationist hero William Jennings Bryan—who rejects evolution for biblical reasons, just like Comfort. Wood insists, "The Bible reveals true information about the history of the earth that is fundamentally incompatible with evolution."

But unlike Comfort, Wood is a trained scientist. And as such, he recognizes that the scientific basis of evolution is strong:

Evolution is not a theory in crisis. It is not teetering on the verge of collapse. It has not failed as a scientific explanation. There is evidence for evolution, gobs and gobs of it. It is not just speculation or a faith choice or an assumption or a religion. It is a productive framework for lots of biological research, and it has amazing explanatory power. There is no conspiracy to hide the truth about the failure of evolution. There has really been no failure of evolution as a scientific theory. It works, and it works well.

Anyone who honestly examines the data supporting evolution—even a young-earth creationist—concludes that the science is strong. If you reject evolution, you are doing it for religious reasons. You're entitled to your religious opinions—but not to your own scientific facts.

This is baffling. Wood puts so well what evolutionary biologists want to scream at the top of their lungs. But then how on Earth can Wood be a creationist? It is a deep, deep mystery to me that he can reject evolution. How does he reconcile the evidence that he sees for evolution with his rejection of it? Just for once, I seriously do not understand the underlying reasoning. Please help!

Governor Schwarzenegger vetoed some bill by sending this stern letter to the members of the California State Assembly:

I am returning Assembly Bill 1176 without my signature.

For some time now I have lamented the fact that major issues are overlooked while many unnecessary bills come to me for consideration. Water reform, prison reform, and health care are major issues my Administration has brought to the table, but the Legislature just kicks the can down the alley.

Yet another legislative year has come and gone without the major reforms Californians overwhelmingly deserve. In light of this, and after careful consideration, I believe it is unnecessary to sign this measure at this time.

Sincerely,
Arnold Schwarzenegger

Okay, so he didn't like it. What of it? Well, take a look at how it was printed:



a⋅cros⋅tic  [uh-kraw-stik, uh-kros-tik]
–noun
1. a series of lines or verses in which the first, last, or other particular letters when taken in order spell out a word, phrase, etc.

Try first.

Enough hints. Mathematicians have apparently been all over it calculating the probability that this is pure chance. Not too high, however you go about it. Not unless the message went through many iterations with random mutations and selection for that particular acrostic message. I don't think that's how they write letters in Sacramento, but I could be wrong.

So good for him. Acrostics are fun, and if that's how he feels about the bill, then go for it, I say (without commenting on the politics).

Evolutionary theory is not the easiest of scientific theories to apply to "daily" phenomena, just because it (usually) takes place over long periods of time (but not always: lizards, viruses, bacteria). It is therefore always exciting when a new area of application is proposed.

A NASA scientist suggests that evolutionary theory will help find alien life.

Dr John Baross, a researcher at the Nasa Astrobiology Institute, said: "I really feel that Darwinian evolution is a defining feature of all life.

"And so the limits of Darwinian evolution will define the range of planets that can support life – at least Earth-like life."

While I don't think evolution need be a defining trait of life, I do agree that it makes sense to expect it to happen to all life - at least it's a fair way to go about looking for it.

However, in what seems to be an attempt to rub shoulders with Ray Kurzweil, he goes not just too far in his predictions, but lightyears past what seems reasonable:

He said: "I predict in the next five to ten years, we will make discoveries that will lead to theories and ideas at least as profound as Darwin's."

Within ten years we will have new theories that match common descent and natural selection in scientific importance?!!1! I can understand when people are very, very, excited about their research, but this is waaaay over the top.

But I wish NASA good luck with their endeavors, and hope to see extra-terrestrial life discovered any time now...

On August 28th, 2009, PNAS published a paper communicated by Lynn Margulis (i.e. it did not go through proper peer-review), by Donald I. Williamson, which began like this.

I reject the Darwinian assumption that larvae and their adults evolved from a single common ancestor. Rather I posit that, in animals that metamorphose, the basic types of larvae originated as adults of different lineages, i.e., larvae were transferred when, through hybridization, their genomes were acquired by distantly related animals.

It was described as the worst paper of the year by Jerry Coyne.

Then Michael W. Hart and Richard K. Grosberg write a paper in PNAS approved on October 13, 2009 that this is folly (also blogged by Coyne):

Williamson [(2009) Proc Natl Acad Sci USA 106:15786–15790] has made the astonishing and unfounded claim that the ancestors of the velvet worms directly gave rise to insect caterpillars via hybridization and that evidence of this ancient “larval transfer” could be found in comparisons among the genomes of extant onychophorans, insects with larvae, and insects without larvae. Williamson has made a series of predictions arising from his hypothesis and urged genomicists to test them. Here, we use data already in the literature to show these predictions to be false. Hybridogenesis between distantly related animals does not explain patterns of morphological and life-history evolution in general, and the genes and genomes of animals provide strong evidence against hybridization or larval transfer between a velvet worm and an insect in particular. [Emphasis added.]

This has led to a comment by Gonzalo Giribet in PNAS on October 30th, 2009:

What remains to test from Williamson’s phylogenetic speculation? Why did the author ignore the weight of phylogenetic evidence that utterly falsifies his claim?
      Perhaps the most amazing thing from this article is not the bold proposal, but the fact that the author believes that there is a research program behind his claims: ‘‘As an initial trial, it should be possible to attach an onychophoran spermatophore to the genital pore of a female cockroach and see if fertilized eggs are laid’’ (1). I am not sure this can be taken seriously. [Emphasis added.]

And this in turn prompted a reply from Williamson in the same edition (this is not the full reply):

This example is part of my much larger thesis that the basic forms of all larvae were transferred from other taxa, and they all originated as adults (4). Across the animal kingdom, I claim that larvae were acquired from animals at all levels of relationship: bilateral larvae of radial echinoderms originated in an animal in a different superphylum from echinoderms, but most crustacean larvae were acquired from other crustaceans. As yet, no geneticist has carried out tests for larval transfer along the lines that Giribet suggests, but I hope my PNAS article (3) will prompt some of them to do so.
     Since 2000, several workers have suggested that many planktonic larvae were ‘‘secondarily acquired’’ and have been ‘‘intercalated’’ into the life histories of echinoderms, molluscs, and other phyla (ref. 5 and references therein). These authors do not discuss the sources of these intercalated larvae or mention my work, which does, but they seem to be following in my footsteps, unwittingly, and some distance behind.

(...)

I thank Giribet for drawing attention to my paper (6) that outlines the importance of hybridization in the Cambrian explosion, and in which I claim that there is no cladistic explanation of the origins of phyla. We are indebted to Darwin for his description of a gradual and continual type of evolution, but biologists should also recognize the importance of saltational and sporadic evolutionary processes like symbiogenesis and hybridogenesis. [Emphasis added.]

Wonderful reply, really. He expects researchers to take his idea seriously and actually perform experiments to test it (I am aware that creationist would have a field day with such a remark, thinking all ludicrous claims should of course be tested or else stand as a gaping hole in evolutionary theory), while many better hypotheses could be tested instead. It's not like coming up with hypotheses to test is much a a problem, you know.

Also, you gotta love his delusions of grandeur: "they seem to be following in my footsteps, unwittingly, and some distance behind." Guffaw! It's not the first time I have seen ageing scientists worried sick over their legacy.

The last highlighted sentence about symbiogenesis and hybridogenesis makes it clear why Margulis would let this paper slip through (or pushed it through, rather). An honest comment from her on this whole episode seems warranted at this time.

Slap me thrice and hand me to me mamma. There are plans to produce a movie about the prophet Muhammad.

American Barrie Osborne, who also produced The Matrix, told Reuters the film would be an "international epic" aimed at "bridging cultures".

Isn't that just incredibly ironic? It is considered blasphemy to depict the prophet, so they're are planning to come up with clever way to avoid him actually being onscreen. No, really!

Osborne says the film, which is being financed by a Qatar-based company, would feature English-speaking Muslim actors, although in keeping with Islamic law, it wouldn't actually depict the prophet on screen (which has got to be bad news for Tony Shalhoub, who'd normally be a shoo-in for the part). Osborne hopes the story of Muhammad would "educate people about the true meaning of Islam."

If they get away with making a film where the main character is never actually seen, they'll really have made an epic movie.

I can't wait to see it. The true meaning of Islam... When Muhammad was in Mecca, he was very friendly and accommodating, because he was not yet powerful. At Medina he had gained power, and was then unforgiving in his persecution of the infidels. Charming. Consummating a marriage with a nine-year old. Can't wait to see how they'll handle that.

Philip Clayton is a professor of religion at Claremont Graduate University (where I am enrolled in a joint Ph.D. program with Keck Graduate Institute). He writes today in 'religion dispatches - exhilarating breakfast since 2008' (?) about the religion wars under the title Evolution and Creation Fight to the Death: What Emerges from the Ashes. Funny title. It supposes some synthesis that will emerge after the fall of evolution (and religion. Whatever), but anyone who knows what science is about knows that this can never happen. 'Can never' as in 'is logically impossible.'

He writes, and I reply in red:

A moment’s reflection reveals multiple ways in which these two great products of the human spirit can be distinguished: religion asks about the why, science explains the how [Why what? It's not religion that asks, it's people. And religion has no answers that the non-believers can use for anything]; science researches matters of empirical fact, while religion is concerned with matters of ultimate values [don't need religion for that]; scientists use empirical techniques and theories to account for the physical and natural world, whereas religionists are concerned with the metaphysical and the supernatural [which they believe exists, but that's where it ends - such belief can be used for naught]; science studies how the heavens go, religion how to go to heaven.

One does not need to find all these formulations adequate (I, for one, do not) in order to doubt that science demands the death of religion or religion the death of science. Here’s the point: only when one affirms some sort of “live and let live” policy is it possible even to begin a serious discussion about evolutionary biology and (say) belief in God. [Or (say) belief in Xenu, or (say) in astrology, or (say) crystal healing, or (say) Allah, etc. etc. etc.]

When evolutionary and religious explanations are construed as fighting for the same territory, they will unleash their weapons upon each other—as today’s religion wars show. When we recognize and acknowledge their different strengths, a far more interesting discussion emerges. [All we are asking is that religionists get off our freakin' turf. You can go ahead and discuss what the two can do in symbiosis, and we'll be watching from the sidelines, during our lunch break, to see what progress you make. I trust it will be nothing tangible, as is always the case when religion is involved.]

This new debate is challenging because it requires both sides to give up certain hegemonic claims: scientists, the claim that science provides the answer to all metaphysical questions [No, that there is no metaphysics, or, equally good, that we cannot know anything about it]; and religionists, the claim that they know better than science how nature works. Yet a whole series of fascinating questions arises when hegemony is off the table: is there a directionality to evolution or is it, as Stephen Jay Gould thought, a “drunkard's walk”? [That's a question ssquarely within science, and one religionists can add nothing to.] Do the emergent worlds of culture, ideas, philosophy, art, and even religion make any irreducible contributions to explaining what it is to be human? [Is 'What it is to be human' a scientific question? If yes, then the answer is no. If no, then whatever.] How (if at all) could a divine influence on cosmic history be compatible with the scientific study of the cosmos? [Science can say nothing here. Religionists can say whatever they want, for it can never be refuted, nor will it make any difference whatsoever, unless people start banging each other on the head with it.] What kind of influence would it have it be? [sic] Will humans respond more appropriately to the global climate crisis when scientific data are combined with religious values and motivations for action? [Possibly, but only because they are already thoroughly entrenched in religion, and for no other reason.]

I implore you, Clayton or anyone else, please tell me what it is that religionists can bring to the table that people who aren't religious can benefit from in any way. In this article he says nothing in answer to this. It really is only huff and puff on his side.

If you think that I don't think that "Christian theology" deserves a department devoted to it, and if you suspect that I think philosophizing about imaginary entities does not belong among academic endeavors at all, then you would have hit the nail on the head.

A little while back I reported about two papers by authors that stated that Darwin was wrong about the vermiform appendix, but that it does have a function. One of the authors, Bill Parker, recently emailed me a reply to my post and that of the commenters, and I deliver it here in full with permission:

We are careful to state that we have not actually
"directly demonstrated" the function of the appendix. However,
we have deduced what appears to be the function, and that
deduction is supported by a wide range of observations in
the fields of immunology, anatomy, medicine, and microbiology.

In fact, it is very difficult to imagine that the cecal
appendix is not a safe-house for bacteria. We know the
biofilms are the thickest there and the most secluded, and we
know the biofilms are protective, so we would need an
extraordinary explanation if we were to come to a different
conclusion. Sometimes a deduction is very strong. One of
your bloggers does not seem to appreciate that
"demonstration by deduction" is possible.

Nevertheless, we refer to "the apparent function" rather
than "the function" of the appendix when we are writing.

That being said, one of the main reasons we spent two years
working with evolutionary biologists at Arizona and
digging through the literature for that paper in the Journal
of Evolutionary Biology was to test the only "alternative"
to our deduction of the function of the appendix. As you
pointed out, that alternative was proposed by Darwin and
was still widely accepted, even in the scientific literature.

I noticed that one of your bloggers was hoping for a quick
and easy experiment to nail things down....
Unfortunately, we can't simply measure recovery from diarrhea
in people with and without an appendix for the answer. The
immune systems in people without an appendix are apparently
different than those in people without an appendix...as
indicated by the fact that one group got appendicitis and one
group did not. Perhaps more importantly, we don't know how
severe the diarrhea would have to be to necessitate the
apparent function of the appendix, and we have no idea if lab
animals would be suitable for a test, since we know they have
immune systems that are substantially modified by hygiene.

Parker also let me know that they have recently sent another paper on the cecal appendix and its function for review. Stay tuned.