Jerry Coyne gets a bath, and other updates

February 16, 2014 • 3:48 pm

Gayle Ferguson, who is raising Jerry Coyne the Cat and his four female siblings, all abandoned at the tender age of three weeks, gives us photographs of Jerry and his littermates, as well as an update. The photos are in order at the bottom. Gayle’s notes:

1. Jerry after his bath last night.
2. Play-fighting with his sister Isis.
3. Being generally cute.
4. Asleep in a pile with three of his siblings (Jerry is the bottom cat. Cat on top of the pile is Hoover).

Not clear yet who the dominant cats are.  Hoover is the biggest and the most dominant feeder.  She jumps to attention when she detects the milk and when she was really hungry she would attack the syringe and swat it furiously then screech like a tortured kitten when the milk didn’t go inside her mouth straight away.  She’s the most aggressive, and also seems to frighten easily.

Jerry has the loudest miaow.  He’s toned it down recently, but he’s definitely not shy about telling me when he wants more noms!

Isis is the most affectionate and the loudest purrer.  Ginger girl likes to sit and look at me until she catches my eye, then she miaows!

Bath

By the way, several readers suggested, based on an earlier photo, that Jerry Coyne might be polydactylous. I asked Gayle to count his toes, and here’s her reply:

He’s got the normal number of toes.  It’s just that his toes are very fluffy.

Play fighting

Cyte

Pile

Deer rescued from ice by a Hovercraft

February 16, 2014 • 2:28 pm

This is a winter heartwarmer: two female deer rescued by kindly souls using ropes and a Hovercraft. They had fallen on an icy lake and couldn’t get up.

Shot 100% on the HD HERO3® camera from http://GoPro.com.

James saw a Facebook post about some deer stuck out on the ice in the middle of Albert Lea Lake, so he called up his dad and they broke out the hovercraft. It’s a father son rescue mission unlike anything you’ve ever seen.

A big stink at The Big Think: the supposed shortcomings of “Darwinism” touted by a quasi-creationist “thinker”

February 16, 2014 • 12:00 pm

I thought The Big Think site was devoted to innovative, cutting-edge ideas. But when I went over there, I was surprised by today’s Big Thought:

Screen shot 2014-02-16 at 11.55.36 AM

What? It’s good at explaining losses (degeneration of useless structures via random mutation or selective elimination, etc.), but not gains of function? That’s an old creationist trope. What gives?

So I read the article, “The trouble with Darwin,” by Kas Thomas. It was dreadful—truly dreadful, carrying the implication that there’s something pretty wrong with modern evolutionary theory.

But modern evolutionary theory is not by any means “Darwin,” although he conflates that theory with what Darwin said in 1859. That’s not kosher because Darwin, while being right in the main, was wrong on several counts (genetics for one). And while there were problems with the theory Darwin adumbrated in 1859, advances in the last 155 years have resolved many of them. Yes, of course there are still things that evolutionary biologists don’t understand, but that doesn’t mean that there’s something wrong with its basic framework.

But first, who is Kas Thomas? I hadn’t heard of him, so I looked at his bio at Big Think. This is it:

Kas Thomas is a longtime cognitive dissident and menace to sacred-cow-kind. A graduate of the University of California at Irvine and Davis (with degrees in biology and microbiology) and a former University of California Regents Fellow, Thomas has taught biology, bacteriology, and laboratory physics at the college level. He was on the Inventions Committee at Novell, Inc. and is the holder of seven U.S. software patents. He has a long and varied background in technical writing (most recently serving as a Technology Evangelist for Adobe Systems) and is in love with the word heterodoxy.

Thomas almost certainly wrote that himself, and seems proud to be a contrarian. The problem is that when he applies his heterodoxy to evolution, he produces not a Big Think but a Big Fail. 

What, exactly, are those shortcomings of evolution? It turns out that none of them are shortcomings. Some are areas where we already understand stuff (and where Thomas doesn’t seem to know the literature), and others are areas of active research. Further, the implication that evolution is impotent to explain gain of function, as noted in the “Big Idea of the Day,” is not even wrong.  

Here’s what, according to Thomas, is supposed to elude evolutionary biology (Thomas’s words are indented.)

1. An understanding of speciation (and the origin of life):

Darwin’s landmark work was called The Origin of Species, yet it doesn’t actually explain in detail how speciation happens (and in fact, no one has seen it happen in the laboratory, unless you want to count plant hybridization or certain breeding anomalies in fruit flies).

Wrong. We we’ve actually seen speciation happen in nature over human lifetimes, via that same mechanism used in the lab (polyploid speciation). And we’ve seen incipient speciation among populations within a species (try the three-spined stickleback fish.)

Yes, Darwin failed to explain the origin of species because he didn’t conceive of species properly—as reproductively isolated entities—and so couldn’t address the problem. Nor did he know about genetics, which is essential to understanding speciation.  But we now have a good handle on how speciation works: we know the reproductive barriers that arise in lineages to divide populations into new species, and we know something about the evolutionary forces and the genetic changes that go into making those species. I should know, for I wrote an entire book on the process (Speciation, co-authored with Allen Orr). Thomas is way, way out of his depth here. He also says this:

[Evolutionary theory] is also terrible at explaining the speed at which speciation occurs. (Of course, The Origin of Species is entirely silent on the subject of how life arose from abiotic conditions in the first place.)

Well, since speciation is often promoted by the origin of geographic barriers or climatic changes, or rare migration events, it’s not easy to predict the rate. But in many cases were are perfectly cognizant of why speciation is faster or slower. Invasion of islands, for instance, speeds it up, as does the origin of geographic barriers like the rise of mountains. The rise of the Isthmus of Panama promoted speciation in several marine species in the last 3 million years. Sexual dimorphism seems to speed up speciation in birds because it allows for stronger sexual selection, which can create mating isolation. Chapter 12 of my book is, in fact, devoted largely to investigating which factors speed up or slow down speciation.

As for the origin of life, that is of course a tough problem, for it’s hard to investigate what happened in a primordial broth even where not even cells were present. Nothing is preserved for us to see except extant descendants of the Ur-organism. But that’s hardly a criticism of evolutionary theory. We do in fact have theories to explain how life began; we just don’t yet know how to distinguish among them. But we do know some things, and one of them is this: life on earth today descended from a single primordial species. (You can Google the evidence, which involves the use of similar genetic codes in all organisms to make amino acids, the ubiquitous use of L-amino acids, phylogenetic trees, and so on.)

2. How natural selection creates new features.

Almost everything in evolutionary theory is based on “survival of the fittest,” a tautology that explains nothing. (“Fittest” means most able to survive. Survival of the fittest means survival of those who survive.) The means by which new survival skills emerge is, at best, murky. Of course, we can’t expect Darwin himself to have proposed detailed genetic or epigenetic causes for speciation, given that he was unaware of the work of Mendel, but the fact is, even today we have a hard time figuring out how things like a bacterial flagellum first appeared.

When I saw this, and the reference to both the “tautology” argument (a creationist notion long since discredited) and the bacterial flagellum (a trope of the Intelligent Design [ID] movement), I realized that Thomas is simply regurgitating ID and creationist “problems” with evolution. That’s a pretty dire thing to publish on the Big Think.

In fact, we do have a good idea how the bacterial flagellum first appeared: it is related to a secretory system that was already present in bacteria. If you want to see a likely explanation, read Pallen and Matzke’s paper in Nature Reviews Microbiology (vol 4:784-790; 2006).

I’m not sure what Thomas means by the murkiness of how new survival skill arise, but we now have several hundred examples of natural selection in action, which is of course is how those skill arise.  We have seen the origin of antibiotic resistance in bacteria, insecticide resistance in insects, changes in the size of finch beaks, the darkening of moth colors due to selection in a new, polluted environment, and many other cases (Wikipedia gives some as well, and for many other examples you can read John Endler’s book Natural Selection in the Wild.) These are all, of course, “survival skills”, or rather “reproduction skills”, since the currency of natural selection is offspring number.

3. “Gain of function.” 

When I was in school, we were taught that mutations in DNA are the driving force behind evolution, an idea that is now thoroughly discredited. The overwhelming majority of non-neutral mutations are deleterious (reducing, not increasing, survival). This is easily demonstrated in the lab. Most mutations lead to loss of function, not gain of function. Evolutionary theory, it turns out, is great at explaining things like the loss of eyesight, over time, by cave-dwelling creatures. It’s terrible at explaining gain of function.

This again is a creationist trope, which makes me even more certain that Thomas has simply absorbed and regurgitated things from the ID literature (see below as well). Yes, of course most mutations are deleterious, but new ones arise that are advantageous, and those can lead not to loss of function (which we understand about as well as we understand gain of function) but to new functions.

Gene duplication, whereby a single gene simply duplicates, resulting in two or more copies on a chromosome, is a great way to gain functions, as it has in human hemoglobin (the various forms of human hemoglobins, which have different functions, arose from duplication of one ancestral locus). My colleague Manyuan Long in Chicago has shown the origin of new genes in fruit flies—genes with novel functions—by splicing together drastically different genes.

Further, Rich Lenski and other microbiologists have shown the origin of new functions in bacteria in both the lab (ability to digest citrate) or the wild (bacteria that evolved the ability to digest nylon).

We can see new functions originating in the fossil record, too. They come from coopting of old functions, which is how natural selection almost always works. The legs of land animals evolved from the bony fins of ancestral fishes. Feathers started out as small filaments on dinosaurs, useless for flying but perhaps good for thermoregulation. The swim bladders of fish evolved from lungs (people usually get this backwards), and swim bladders surely represent new functions. I could go on and on, but this is enough to show that Thomas is again out of his depth, spewing ID claims without knowing that they’ve already been refuted.

4. The Cambrian Explosion, human intelligence, and other stuff.

[Evolutionary theory] doesn’t explain the Cambrian Explosion, for example, or the sudden appearance of intelligence in hominids, or the rapid recovery (and net expansion) of the biosphere in the wake of at least five super-massive extinction events in the most recent 15% of Earth’s existence.

The mention of the Cambrian explosion, of course, comes straight from Stephen Meyer’s new Intelligent Design book saying that because we don’t understand how many major body plans originated so rapidly (by “rapidly,” we’re talking 20 million years), Jesus must have done it.  But our lack of understanding is due not to a paucity of theories, but to a surfeit of theories (oxygen, predators, gene regulation, and so on), and our present inability to distinguish among them.

And yes, we don’t understand how human intelligence arose: again, we have a surfeit of theories but a paucity of evidence. Some scientists, like Dick Wrangham, think that our big brains were the result of the taming of fire, others by sexual selection, tool use, bipedality, or other features. Perhaps some day, when we can unravel the genetic basis of differences in intelligence between humans and other primates, we’ll understand more.

But these are simply the problems inherent in any historical discipline, like science and cosmology. A science that has solved all its problems is a dead science. Here are a few more unsolved problems of evolutionary biology: how did sexual reproduction originate? What is the evolutionary significance in the difference of human morphology among ethnic groups? How does sexual selection operate to create differences between males and females? How important is “neutral” genetic variation in the evolution of trait differences (not DNA sequences) between species and populations?

At the end, Thomas offers a lame disclaimer:

Of course, the fact that classical evolutionary theory doesn’t explain these sorts of things doesn’t mean we should abandon the entire theory. There’s a difference between a theory being wrong and being incomplete. In science, we cling to incomplete theories all the time. Especially when the alternative is complete ignorance.

Note that “Darwin” has now been replaced by “classical evolutionary theory,” which I take to mean “modern evolutionary theory,” or neo-Darwinism. That, after all, is the current state of the art. So why did Thomas drag Darwin into his title? Because he wanted attention.

And yes, Thomas says that, just maybe, evolution theory might not have to be abandoned. But the damage has already been done. In his piece, Thomas raised a number of non-problems with evolutionary theory that will mislead the general reader, and most of those problems are lifted from the Intelligent Design/creationist playbook.  That kind of article does not belong on The Big Think. It’s a lame, error-ridden piece designed to bolster Thomas’s self-described penchant for heterodoxy and sacred-cow goring.

“The trouble with Darwin” is a mischaracterization of evolutionary theory, laden with distortions. It’s damaging to the public understanding of science, for the average reader won’t know the relevant science, and it’s contemptible. Shame on The Big Think. And, especially, shame on Thomas.

________

UPDATE:  Reader “profon” posted Thomas’s Twitter response to the comments, and many of those responses cited scientific arguments against Thomas’s position. I want to put profon’s capture above the fold, for it shows how clueless Thomas really is about his opposition:

Picture 1When someone calls their intellectual and scientific opponents “haters,” then you know they’ve lost all credibility. Thomas won’t respond except to ad-hom his “haters”. That’s truly lame.

h/t: Ant

In defense of creationists?

February 16, 2014 • 6:55 am

The Week appears to be a garden-variety news magazine without an obvious agenda, but it’s recently published a number of very silly articles on religion and creationism. One of the silliest appeared about a week ago, and is called “In defense of creationists,” by Michael Brendan Dougherty. Of course after reading this kind of incoherent mind-dump one wants to know who the author is; and Dougherty is described this way:

Michael Brendan Dougherty is senior correspondent at TheWeek.com. He is the founder and editor of The Slurve, a newsletter about baseball. His work has appeared in The New York Times Magazine, ESPN Magazine, Slate and The American Conservative.

By “creationists,” Dougherty refers to young-earth Biblical creationists, and he’s not one of them: he appears to have a somewhat hedged acceptance of evolution. So why does he defend Biblical literalists?

It’s not completely clear, but it appears to be that he has an aversion, as do many of us, against Sophisticated Believers (S.B.s) who pick and choose (without clear reasons) which parts of the Bible are literally true and which are metaphorical. Give us a diehard buy-it-all-literalist, some of us say (me included!), rather than a weaselly metaphorizer who sees himself as superior to both atheists and fundamentalists. At least the straight creationists (and atheists!) have a guiding principle for interpretation: it’s all correct (or, in the case of atheists, made up by humans)! Dougherty’s views, and this piece, were inspired by the reaction of Sophisticated Believers to the Ham/Nye debate, who held their noses when listening to Ham’s Genesis literalism.

The problem with the piece, beside its incoherence—Dougherty doesn’t seem to have thought through his own feelings on the issue, and that shows—is that in the end he buys into the same pick-and-choose mentality as do the Sophisticated Believers he rejects, undercutting his whole thesis.

Dougherty starts poorly, saying that Biblical literalism is a recent innovation:

It took until about the late 19th century and hundreds of years of liturgical self-demolition within the Protestant tradition for this rich understanding of Genesis and Revelation to be reduced to a replacement science textbook and a ripped-from-the-headlines Michael Bay–style blockbuster. Six-day-ism, the theory of the Rapture, and even the juvenile “How many bricks?” re-reading of Revelation by Jehovah’s Witnesses are all modern phenomena.

This is weaselly, for although many Christians might not have seen Revelation or a real six-day creationism as true, for millennia Church fathers and believers alike saw essential components of the Genesis story, including creation ex nihilo, Adam and Eve, and the Fall, as literal truths. Augustine and Aquinas, for instance, believed in both a symbolic and literal interpretation of scripture, so they bought the Adam and Eve story as genuine truth (i.e., a real “replacement science textbook”), but also one that bore a metaphorical interpretation. Here Dougherty deliberately misleads the reader into thinking that literalism is a recent phenomenon. This is a common trope among apologists and faitheists, but it’s a lie, and I don’t understand why it’s gotten such traction.

Before he tells us why he is defending creationism, Dougherty has to get in a few licks against science (even though he accepts it):

[The views of Sophisticated Belief are] a pose, barely more literate in science than the creationism it opposes as illiteracy. The Big Bang and evolution are subject to further refinement and perhaps dramatic refutation on evidentiary terms. To submit to the authority of science does not mean to place one’s personal and irrevocable imprimatur on today’s most supported theories. It simply means accepting the rational process of investigating claims about nature through rigorous observation and experimentation. What does it mean when laymen say they “believe in” a scientific theory? Must they decide between Stephen Jay Gould and Richard Dawkins on “punctuated equilibrium?” Who is supposed to be impressed by these declarations?

“Subject to further refinement and perhaps dramatic refutation on evidentiary terms?” Well, yes, in principle evolution and the Big Bang could be shown to be wrong, but it’s not likely, and to imply that “further refinement” may do this is simply being disingenuous. I’m not sure why the more arcane Gould vs. Dawkins debate on punctuated equilibrium is dragged in here, as most of it is resolved (yes, the fossil record often shows jerkiness rather than smooth change, but Gould was dead wrong in claiming this pattern absolutely requires a new, non-neo-Darwinian process). I suppose Dougherty, who probably knows little about that debate, wants to convince readers that the presence of any active controversies in science (and he should have used a better example, like the meaning of dark matter), undercuts the whole scientific enterprise.

Finally, Dougherty tells us why he doesn’t like the more Sophisticated Believers who badmouth Ken Ham:

As the debate between Ham and Nye unfolded, I found myself more and more disgusted with some of the self-styled “sophisticated” Christians performing their giggles at Ham for all the world to see.

There was something just a little ugly about all these Christians rushing up to their platforms, drawing attention to the sweat on their brow, putting a concerned look upon their faces, and proclaiming that fundamentalism is a “modern” error. And then when they were sure everyone was listening, lifted up their eyes heavenward to pray, “God, I thank you that I am not like this mouth-breather Ken Ham.” With a great urgency, but very little understanding of cosmology or the various theories of evolution, they recited their absolute fidelity to these theories. These anxious-to-please Christians were telling important truths, but in the spirit of a lie.

I’m not sure what he’s trying to say here.  What does he mean by accusing S.B.s of “telling important truths” (we’ll get to those “truths” later), but “in the spirit of a lie”? What is “the spirit of a lie”? I suppose he just doesn’t like some Christians denigrating the views of other Christians, even though Dougherty actually agrees with the sophisticated Christians! Here’s where it’s evident that the man doesn’t know what he’s trying to say. He simply likes the tenacity of fundamentalists, even if they’re wrong:

On the other hand, I’ve always found those Christians who hold to six-day accounts of man’s origin difficult to refute and even more difficult to despise. There is a certain strength and flexibility to their tautology. Further, even though they’re wrong on the science, they are right about the things that really matter to the human heart and to human civilization.

Flexibility? Really? Since when are fundamentalists flexible? And what is the tautology in their belief? Further, if they are right about the things that really matter to the heart and to our civilization, then so are the Sophisticated Believers! This becomes clear when Dougherty tells us why the fundamentalists are superior:

So I do not think that Ken Ham–style creationists should get to rewrite biology textbooks according to their very peculiar reading of Scripture. But I admire their bullheadedness. They have gotten lost in the woods while trying to protect the big truths of Christianity: that God created the world, that we are dependent on him, that we owe him everything, and that he loves us even though we are sinful. In the world most of us inhabit, day to day, the world of lovers, wriggling kids, disease, war, and death, the sureness of God’s love is relevant in a way that the details of early hominid fossils never will be, glorious as they are. Have some perspective, people.

. . . But the bulk of creation’s fundamentalists are deeply sincere. And, better than that, they are willing to be, in St. Paul’s words “fools for Christ’s sake.” They do not live for the world’s esteem. And so when the world next discovers a sophisticated ideology to get around “Thou shall not murder,” I’d rather have one cussed fundie next to me than the whole army of eye-rolling Christians lining up to denounce him.

But that is precisely what the Sophisticated Believers think as well. Why are fundamentalists protecting these “truths” as opposed to the S.B.s? And really, do Sophisticated Believers try to justify murder? Which ones? Dougherty doesn’t answer these pressing questions.

I guess what he really doesn’t like is that the S.B.s roll their eyes when they listen to Ken Ham. Further, it’s apparently the fundamentalists, not the S.B.s, who enforce morality and the Golden Rule, while the Evilutionists tell us it’s okay to murder and sterilize people:

In protecting that big truth of creation — that we are all made in God’s image and all endowed with supreme dignity — fundamentalists zealously guard things that follow logically from that. Things like the commandment “Thou shall not murder.” Anti-evolutionists often set themselves against “Darwinian theory” because they deplored social Darwinism, eugenics, and other evils that seemed to spring forth from minds overexcited by the latest theories of man’s origin.

Isn’t Dougherty aware that eugenics and Social Darwinism went by the board decades ago, and that almost no evolutionists embrace that stuff? Here he sounds like the fundamentalists with whom he disagrees—but sympathizes.

So here’s Dougherty’s big problem: he himself winds up behaving precisely like a Sophisticated Believer. While rejecting the fundamentalist assertion of Biblical literalness (yet admiring the bullheadedness of its adherents), Dougherty ends up picking and choosing what he sees as the Real Big Truths of Christianity:

. . . that God created the world, that we are dependent on him, that we owe him everything, and that he loves us even though we are sinful.

Could you please tell us, Mr. Dougherty, how you know that God created the world, that he loves us, and that we are sinful? Did you take those bits out of the Bible, or do you have independent evidence for those claims?

If this list of what Dougherty calls Christianity’s “big truths” doesn’t come from selective reading of the Bible, then I don’t know its origin. (Presumably he’s ignoring the Old Testament, where God doesn’t particularly love everyone.) Dougherty has no more reason to believe these “big truths” than do the fundamentalists for believing in original sin or the End Times.

The people who should be rolling their eyes are not the Sophisticated Believers, but the readers of Dougherty’s piece. He should not be allowed near a keyboard until he figures out a). what he wants to say, and b). is able to make a coherent argument while not espousing the very mindset he decries.

At any rate, I still find myself disliking the Sophisticated Believers more than the fundamentalists.  I’m not quite sure why, for the fundies do just as much damage, if not more, to science education. I suppose it’s the feeling that the S.B.s really are being intellectually dishonest, ignoring the nasty bits of scripture while deciding, without obvious guidelines, which ones are real and important.  And I can’t help but feel that S.B.s, who I presume are more educated, should be more aware of their disingenuousness. But as Michael Shermer tells us, the smarter folks are better at rationalizing their beliefs.

Two squabbling birds. . .

February 16, 2014 • 5:30 am

Maybe I should add a new tag called “Avian altercations,” as we’re getting a lot of such photos. This picture comes from Rob Bate, president of the Brooklyn Bird Club, who also sent a message:

Thanks for promoting birds on your site.  We in the birding community welcome any publicity for bird diversity especially beyond the more charismatic birds like hawks, eagles and swans which attract everyone’s attention.

I’m sure your are inundated with bird photos these days but thought I’d send along this one of a Ring-billed Gull (our most common gull in New York) and a Common Crow.  The crow was pilfering the food brought out by the gull onto the ice here in Brooklyn’s Prospect Park.  It’s hard to say who was winning the battle but it looked more like a dance.  The gull is a juvenile and the crow shows a lot of wear on his tail feathers as he has not yet molted into fresh breeding plumage.

Crow and Gull 1

The good news: Jerry Coyne is healthy!

February 15, 2014 • 3:25 pm

Let’s end this day on an positive note. According to reader Gayle Ferguson, who is fostering five tiny kittens abandoned by a cruel miscreant, the only male in the lot—named Jerry Coyne—is recovering from illness. Jerry Coyne had a respiratory infection, but now it’s almost gone; and the little guy is, like his namesake, vociferously demanding noms and fusses. Here’s Jerry Coyne’s latest portrait:

Jerry CoyneIsn’t he lovely? If you’re a kiwi, do consider adopting Jerry Coyne (you have to keep both of his names) or one of the four lovely female tabbies.