Intelligent Design Fan DaveScot Demonizes Chance

June 25, 2008

Over at Uncommon Descent, helper-honcho DaveScot has a post up claiming that Richard Lenski’s now famous E Coli. evolution paper commits a fatal error right in the first paragraph.

I started reading Lenski’s full paper myself to see what raw data was provided and I got no farther than the first paragraph beyond the abstract when I encountered a bias error that a chance worshipper (sic) would never notice. My emphasis:

At its core, evolution involves a profound tension between
random and deterministic processes. Natural selection
works systematically to adapt populations to their prevailing
environments. However, selection requires heritable variation
generated by random mutation
, and even beneficial mutations
may be lost by random drift. Moreover, random and deterministic
processes become intertwined over time such that future
alternatives may be contingent on the prior history of an evolving
population.

The bold portion is patently wrong. Selection operates on any heritable variation whether random or not. That the authors would use the language they did (random variation) and the peer reviewers didn’t notice it is testimony to the chance worshipper (sic) bias that pervades evolution
research.

In case you missed him repeating it for emphasis, DaveScot has recently begun to refer to scientists as “chance worshipers,” proving that if you can’t argue on par with someone, your best fallback is to ridicule them with cutesy names that belittle their arguments by implying that they are mere dogma.

But why is it that scientists like Lenski so often speak of “random” mutation? Because that’s exactly what they observe when they look at how variation emerges in genomes over time. While it’s true that selection could, in theory, work on non-randomly selected traits, that’s just not what we see happening in practice, and not particularly relevant to what Lenski is describing in any case. In fact, the whole point of Lenski’s paper is about the power of contingency: the way even random events open or close doors of possibility.

Part of the problem, perhaps, is that DaveScot doesn’t quite understand what scientists mean by “random” in this context. No biologist literally means that events like mutations occur with no causal explanation: that literally anything can happen to anything. What they mean is that the mutations that do occur, caused by all sorts of different processes, copying errors, and so on, are not correlated in any observable way with the outcomes they generate.

This misunderstanding quickly gets DaveScot into trouble when he tries to provide evidence that mutation isn’t random:

The Scripps researchers, in a nutshell, discovered that E. coli, when stressed (such as running out of food as in Lenski’s experiment or in the presence of antibiotics in the Scripps experiment) selectively increases the mutation rate on certain genes. Thus the mutations in this case are not random but rather directed at a certain area in an attempt to solve a certain problem.

But the paper in question does not, in fact, suggest that the mutations in question aren’t random. What it describes is a particular mechanism E. Coli have for essentially inducing more copying error (reducing the fidelity of inherited traits) in response to environmental pressures. There’s no evidence that the E Coli. are actually specifically choosing certain mutations over others based on any foreknowledge of whether those mutations will be beneficial or not. All they’re doing is tossing the dice more often on a particular set of genes.

And while the fact that a particular set of genes is singled out for modification is certainly interesting an interesting feature (though not unlike many other genetic known features that conserve certain parts of the genome), it’s still just a mechanism within the E Coli. itself, not a mark of intelligent intervention, intelligence, or foreknowledge.

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More Early Tetrapod Fossils Help Uncover the Origin of Life on Land

June 25, 2008

Another interesting specimen uncovered in the sprawling family tree of the early tetrapods (the four-limbed fishy conquers of land): Ventastega curonica.

It’s worth noting, yet again, how fossil evidence generally works when it comes to evolution. Discerning the exact ancestry of most specimens is generally implausible… but that’s not really what scientists require in the first place. What they want and need is to flesh out the overall family tree:

Scientists don’t think four-legged creatures are directly evolved from Ventastega. It’s more likely that in the family tree of tetrapods, Ventastega is an offshoot branch that died off, not leading to the animals we now know, Ahlberg said.

“At the time, there were a lot of creatures around of varying degrees of advancement,” Ahlberg said. They all seem to have similar characteristics, so Ventastega’s find is helpful for evolutionary biologists.

Of course, some people, such as the science journalists that penned the piece, seem a little rusty on the concept:

Ventastega is the most primitive of these transition animals, but there are older ones that are oddly more advanced, said Neil Shubin, professor of biology and anatomy at the University of Chicago. He was not part of the discovery team but helped find Tiktaalik, the fish that was one step earlier in evolution.

“It’s sort of out of sequence in timing,” Shubin said of Ventastega.

Shubin’s likely point here, rather poorly represented in the article, is not that we’d necessarily expect to see Ventastega specifically “in sequence,” but simply that it isn’t on the direct line from which all land animals are descended.

To many lay readers, however, the “primitive” and “out of sequence timing” might seem like elements of a mystery: why would something still have “old” features?

But in fact, if Ventastega is an cousin/offshoot of the branch from which all later land animals are descended, then these terms are really only relative. Ventastega, after branching off from other tetrapods, went its own way: retaining some traits that became modified in the main tetrapod line, and gaining some traits unique to its own branch.

The former retained traits are “primitive” only in the sense that they are more like what earlier tetrapods had than what the particular line of tetrapods that we care most about went on to change. Had those tetrapods gone extinct and Ventastega’s descendants gone on to father all life on land, we’d be talking about the “primitive” traits of the formerly mainline tetrapods, compared to Ventastega.


Anti-Evolutionary Expelled Falls Off the Radar?

May 13, 2008

4 weeks in, and Ben Stein’s anti-evolutionary expose Expelled appears to be petering out on its run. Last weekend it only took in 0.3 million from its remaining 402 theaters, bringing its total haul to a respectable $7.2M It’s still not clear how much the film actually cost to make (probably not too much), or how much it cost to promote (probably quite a lot, considering the pricey markets they bought ads in), and thus whether Premise Media will ultimately break even.

More notably, there doesn’t seem to be any signs as of yet that the film has become the sort of cultural sensation its producers had hoped: no students raising their fists in biology classes, and aside from the pre-orchestrated “academic freedom” bills (many of which seem to have lost some steam themselves), little political impact. The movie’s blog hasn’t been updated in 3 weeks.

So what more is there to say at this point? Intelligent Design has a new corporate ally on the block, and for its opening salvo, it butted heads with the mainstream media and scientists, and mostly just ended up replaying the same old battles one more time. All without anyone having much new to say or any side accomplishing much.

Other than that, I really can’t think of anything. The larger debate goes on, unabated, with yet more bad blood between the participants. C’est la vie, I suppose.


Human Dignity: An Ethically Useless Concept

May 12, 2008

Last year Steven Pinker wrote a fantastic article on bioethics that somehow had escaped my notice until a commenter recently brought it to my attention: The Stupidity of Dignity.

The point of his essay is not, as one might fear, that human beings lack an inherent dignity or moral importance. It’s that the term “dignity” has been so constantly abused that it has become almost worthless in moral debates. It’s incoherently defined, capable of having nearly any property, even contradictory ones. And it’s all too often used simply as a proxy for the philosopher’s or theologian’s subjective dislike of some behavior or idea.

Here’s the key point of the article:

The problem is that “dignity” is a squishy, subjective notion, hardly up to the heavyweight moral demands assigned to it. The bioethicist Ruth Macklin, who had been fed up with loose talk about dignity intended to squelch research and therapy, threw down the gauntlet in a 2003 editorial, “Dignity Is a Useless Concept.” Macklin argued that bioethics has done just fine with the principle of personal autonomy–the idea that, because all humans have the same minimum capacity to suffer, prosper, reason, and choose, no human has the right to impinge on the life, body, or freedom of another. This is why informed consent serves as the bedrock of ethical research and practice, and it clearly rules out the kinds of abuses that led to the birth of bioethics in the first place, such as Mengele’s sadistic pseudoexperiments in Nazi Germany and the withholding of treatment to indigent black patients in the infamous Tuskegee syphilis study. Once you recognize the principle of autonomy, Macklin argued, “dignity” adds nothing.

The rest of Pinker’s article basically argues that despite an entire volume full of responses to Macklin’s challenge, the mostly conservative and religious Presidential Council on Bioethics have failed to answer it. In some cases, as with the notorious Leon Kass, they did worse than fail, exposing bizarre theocratic preoccupations that celebrate death and bemoan liberty in life.

A tour de force. Anyone know of any good responses to, or critiques of, this piece from conservative critics?


Best of Pharyngula: Praise for the Platypus

May 10, 2008

Whatever you think of PZ Myers, his writing on biological topics is indispensable when it comes to correcting common misunderstandings and misrepresentations about evolution. His latest article, dissecting the newest draft of the platypus genome and its implications for evolutionary taxonomy, is a must read.

The platypus used to be a favorite of creationists: it was a supposed chimera of different animal kingdoms and supposedly a startling mystery for evolution’s picture of common descent. These days, however, creationists have mainly given it up as a lost cause: getting exposed as so wrong, so many times, gets humiliating. Instead, it’s the modern news media, always awash in its rarely updated panoply of stereotypes and clichés, that still gives us breathlessly confused descriptions of the platypus as a “part bird, part reptile and part lactating mammal.”

Understanding what the various “strange” features of the platypus really are and how they fit into the larger history of mammals is essential for anyone who wants to understand how evolutionary biology really works.


Office of Special Counsel Raided by FBI: The Expelled Connection

May 9, 2008

It might otherwise go without notice that the FBI recently raided the Office of Special Counsel, an agency created in the 1970s to protect federal employees from political retaliation for doing their jobs (which includes acting as whistleblowers on government misconduct).

What’s the core issue under dispute? That director Scott Bloch ran the Office of Special Counsel itself as a highly partisan machine: quietly soft-pedaling investigations of political allies, selectively ignoring or betraying the very whistle blowers the agency supposedly exists to protect (most prominently any and all claims of discrimination based on sexual orientation), and issuing fact-free accusations of misconduct against political enemies.

One of the latter cases involved none other than Richard Sternberg, Expelled’s cause célèbre. In that case, the OSC, despite having no jurisdiction (since Sternberg was not a federal employee in the first place), issued a letter claiming that they could substantiate Sternberg’s claims of persecution. Ed Darrell (who alerted me to this story) notes how that one played out:

The mackarel by moonlight in that story (both shining and stinking at the same time) was a letter from the Office of Special Counsel which, while claiming to have found unspecified evidence of wrongdoing [in the Sternberg case], said that OSC was the wrong agency to prosecute wrong-doers (OSC had an obligation to turn over any evidence of wrongdoing to the right agency, but Stein doesn’t mention that; there never was any evidence turned over to anyone). (emphasis added)

Bloch is currently in hot water because he was part of the apparent Bush administration “coincidence” involving the illegally deletion of millions of e-mails and other computer records, which critics suspect might have contained embarrassing or incriminating evidence. The FBI has focused on Bloch in particular for basically doing to his own employees what his own agency supposedly exists to prevent.


Kenneth Miller’s Editorial on Ben Stein’s Anti-Evolutionary Expelled

May 8, 2008

Kenneth Miller, author of “Finding Darwin’s God,” and the very sort of religious scientist that Expelled’s producers avoided like the plague, has an editorial out today, lambasting the film and Ben Stein’s recent comments that “science leads to killing people.”

Good read from an important voice in this debate. And his new book, “Only a Theory,” which I’m quite excited to read, comes out next month!

HT: Gospel of Karen