Thursday, August 12, 2004

Kentucky Beckons

I will be spending a few days in scenic Bowling Green, Kentucky starting this weekend. Sadly, that means no blogging until I return next week. Try to soldier on without me.

Did Evolution Favor a Fondness for Alcohol?

From Wine Spectator:

Humans may be hardwired with an instinctual attraction to alcohol, theorizes Robert Dudley, a biomechanics professor at the University of California, Berkeley. He and a small group of other scientists are exploring the possible evolutionary origins of drinking, hoping to shed light on the relationships between humans, alcohol and health. This Darwinian approach to medical science has fermented debate in the research community.

Ethanol is found widely in ripe wild fruit, Dudley explained. When wild yeast lands on the fruit and feeds on the sugars, fermentation occurs. The riper the fruit, the more alcohol it produces.

Many birds and mammals, including our primate ancestors, depend heavily on fruit, Dudley said, and they may have learned to find this food source quickly by following the scent of ethanol. Basically, the smell may act as a chow bell, signaling animals from afar that dinner's ready. (In turn, the plants benefit, as their seeds get to hitch a ride, spreading to new areas through the animals' waste.)

Primates appear to have a highly developed sensitivity to the smell of ethanol, Dudley said, which may give them an edge over other fruit-eating animals. And this sensitivity may have been passed on to humans. Today, we continue to be attracted to foods that benefited our ancestors.

Personally, I despise alcohol. What does that say about my ancestors?

Wednesday, August 11, 2004

Kudos to Cartwright

My fellow evolution blogger Reed Cartwright, a graduate student at the University of Georgia, has reported that his first research paper has now been published. Congratulations! And mega-congratulations for managing to get published while still a graduate student!

There's just nothing like your first time...

The Evolution of Dembski's Mathematics

I have a lengthy post up at The Panda's Thumb on this topic. Enjoy!

Tuesday, August 10, 2004

Dembski's Math Paper

As part of his ongoing efforts to prove that he's something other than a hack, William Dembski posted this technical paper (in PDF format) at his website.

Dembski claims to have submitted this paper to the journal Complexity. Assuming this is true, we will have to wait for the journal's referrees to weigh in before learning the paper's fate.

However, the initial verditc is in. It is not favorable to Dembski. Cosma Shalizi is a post-doc in physics at the University of Michigan. He offers this devastating response to Dembski's paper. Parts of it get a bit technical, but the verdict is clear:

Dembski's paper seriously mis-represents the nature and use of information theory in a wide range of fields. What he puts forward as a new construction is in fact a particular case of a far more general idea, which was published forty-four years ago. That construction is extremely well-known and widely used in a number of fields in which Dembski purports to be an expert, namely information theory, hypothesis testing and the measurement of complexity. The manuscript contains exactly no new mathematics. Such is the work of a man described on one of his book jackets as “the Isaac Newton of information theory”. His home page says this is the first in a seven-part series on the “mathematical foundations of intelligent design” I can't wait. Or rather, I can.

The only thing I would add to Shalizi's comments is that the present paper has nothing whatever to do with evolution or ID. Presumably that connection is coming in future papers, but for now there is nothing. The only place where Dembski even mentions evolution is at the end of his paper, where he suggests possible applications of the apparatus he developed in the paper:

Distinguishing scientific theories in terms of informational continuity
and discontinuity. Classical physics consistently yields continuous information
spectra. By contrast, quantum physics yields discontinuous information
spectra. Likewise, classical evolutionary theories à la Darwin are gradualistic
and suggest continuous information spectra whereas saltational approaches to
evolution suggest discontinuous information spectra. To what extent can variational
information make this distinction rigorous and provide genuine insights
into the processes responsible for life’s evolutionary history?

Shorn of the technical jargon, it looks to me like Dembski is simply conflating “gradualism” in the biological sense with “continuous” in the mathematical sense. We'll have to wait and see if he has anything more clever than this in mind.

Monday, August 09, 2004

Hunter, Part 2

I now continue with my analysis of Cornelius Hunter's contribution to William Dembski's anthology, Uncommon Dissent.

In the first part of this series I analyzed Hunter's arguments about the fossil record. I pointed out that his entire argument collapses because he conflated two different questions: “Is the history of life as revealed in the fossil record consistent with evolution?” on the one hand, with “Can we determine specific lines of descent from the fossil record?” on the other.

Another place where Hunter gets things badly wrong is in his discussion of the universal genetic code. He writes:

The DNA code is routinely used as strong evidence for evolution, but why? Everyone knows that one cannot use a code without having a method for encoding and decoding the information that is being transmitted. And, of course, the sender and receiver must be using the same code for the system to work. Volumes have been written on the cellular machinery that is involved in nature's scheme for using the DNA code, and we still don't understand all the details. It is phenomenally complex and it is not easily explained as a product of Darwin's evolutionary process. (P. 208)

Let's take this one sentence at a time:

  • The DNA code is routinely used as strong evidence for evolution, but why? Actually, the universality of the DNA code, and the universality of the cellular machinery used to translate that code, are evidence for a universal common ancestor. If these universals were not present it would be essentially impossible to argue that any two modern species share a common ancestor somewhere in the past.

  • Everyone knows that one cannot use a code without having a method for encoding and decoding the information that is being transmitted. I have no idea what the point of this sentence is. What does this have to do with whether different species use different codes, or have different cellular tools for encoding and decoding?

  • And, of course, the sender and receiver must be using the same code for the system to work. The “sender”, and “receiver” in this analogy are the parents and offspring of a given species. So, yes, the offspring must be using the same genetic code and possess the same cellular machinery as the parents. Again, what does that have to do with whether these are different codes in use in different species?

  • Volumes have been written on the cellular machinery that is involved in nature's scheme for using the DNA code, and we still don't understand all the details. Well, at least we agree on something.

  • It is phenomenally complex and it is not easily explained as a product of Darwin's evolutionary process. And here we have the standard conflation of evolution with the origin of life. Evolutionary theory has nothing to say one way or the other about the origin of the code. The code is simply taken as a given. Evolution also does not explain the motions of the planets around the Sun, but no one thinks that's a legitimate objection to Darwin's theory.

But Hunter disputes the idea that evolution predicts a universal code. Picking up from where the last quote left off we find:

Furthermore, evolution does not predict there to be a universal DNA code. A number of explanations of the code's supposed evolution are currently under consideration. In one way or another, the code is supposed to have evolved from simpler codes; but if the code could have evolved over time, then it is easily conceivable that it could have evolved into several different codes. In other words, evolutionary theory could explain the existence of multiple codes in nature. As such, evolution does not require there to be a single DNA code. (P. 208)

Evolution does not require a single code, but universal common ancestry does. In principle life could have formed several times on Earth, with each origination event producing a different code. After these events life could have evolved by the standard mechanisms. As a hypothetical scenario this is fine.

But such a scenario would be hard to square with the patterns of descent suggested by all the various anatomical homologies that we find, and it is hard to square with the fossil record. In other words, we have copious evidence from fossils and homologies that there is a universal common ancestor for all life. If it then turned out that there were multiple genetic codes, each one leading to a different evolutionary experiment, we would have some serious dissonance in the data. So it is comforting that the code is, in fact universal.

Let's go a little bit further. Picking up where the last quote left off:

The universal genetic code doesn't seem like a good candidate to serve as strong evidence for evolution. Evolution has trouble explaining how the code and its attendant machinery came about, and evolution does not require there to be a single code. How then does the universal genetic code support evolution so strongly? The answer is that evolutionists believe that if the species had been created independently, they would not share the same code. (P. 208-209)

Here Hunter makes explicit the error of conflating evolution with the origin of life. And we have already discussed what evolution expects about a universal code. I would like to examine that last sentence, however.

Hunter includes a footnote to back up his assertion about special creation predicting that the code should not be universal. He refers us to Mark Ridley's textbook Evolution. Sadly, Hunter's footnote refers us to the first edition of the book, whereas I only have the second edition. So I will leave open the possibility that Ridley says something different in the first edition.

But in the second edition Ridley does not say anything remotely like what Hunter attributes to him. Ridley does discuss the relevance of the universal genetic code, but he does so in terms that are similar to what I have provided here. I'd be surprised if you could find a single scientist making the argument Hunter describes above.

The simple fact is that scientists to not defend evolution by speculating about what an intelligent designer would do and then showing that these expectations are not met. Scientists do sometimes argue this way when they are criticizing creationism, however. That is entirely reasonable. Creationists believe that God has certain attributes such as omnipotence and omnibenevolence, and it is natural to ask how those characteristics would be reflected in the creation.

Criticizing creationism is not the same as defending evolution, though most creationists fail to see the distinction.

The relevance of the fossil record to assessing the validity of evolution, and the significance of the univeral genetic code are not hard to grasp. Hunter, nonetheless, seems not to have grasped them.

Sunday, August 08, 2004

They're Coming for Your Children...

Here's the catalog copy for a new children's book entitled Help! Mom! There Are Liberals Under My Bed, by Katharine DeBrecht:

The story of two boys who dream about opening a lemonade stand when a strange thing happens...

Their dream gets stuck in Liberaland!

“Help! Mom! There Are Liberals Under My Bed! A Small Lesson in Conservatism” is a wonderful way to teach young children the valuable lessons of conservatism. In simple text, parents and children follow Tommy and Lou on their quest to earn money for a swing set their parents cannot afford. As their dream gets stuck in Liberaland, Tommy and Lou’s lemonade stand is hit with many obstacles.

Liberals keep appearing from behind their lemon tree, taking half of their money in taxes, forbidding them to hang a picture of Jesus atop their stand, and making them give broccoli with each glass sold.

Law after law instituted by the press-hungry liberals finally results in the liberals taking over Tommy and Lou’s stand and offering sour lemonade at astronomical prices to the customers.


Chess and Falsificationism

From Nature

Along with her colleague Ruth Byrne, she recruited 20 chess players, ranging from regular tournament players to a grand master. She presented each participant with six different chessboard positions from halfway through a game, where black and white had equal chances of winning and there was no immediately obvious next move.

Each player had to speak their thoughts aloud as they decided what move to make. Cowley scored the quality of the move sequences by comparing them with Fritz 8, one of the most powerful chess computer programs available.

She found that novices were more likely to convince themselves that bad moves would work out in their favour, because they focused more on the countermoves that would benefit their strategy while ignoring those that led to the downfall of their cherished hypotheses.

Conversely, masters tended to correctly predict when the eventual outcome of a move would weaken their position. “Grand masters think about what their opponents will do much more,” says Byrne. “They tend to falsify their own hypotheses.”

“We probably all intuitively know this is true,” says Orr. “But it's never a bad thing to prove it like this.”

The philosopher Karl Popper called this process of hypothesis testing 'falsification', and thought that it was the best way to describe how science constantly questions and refines itself. It is often held up as the principle that separates scientific and non-scientific thinking, and the best way to test a hypothesis.

My Neck of the Woods

Glenn Branch of the NCSE has called my attention to this disturbing article, from the Richmond Times Dispatch:

A Madison County School Board member has made a plea to his colleagues to include creationist teachings in the life-sciences classroom.

C. Douglas Farmer, a third-year board member and ordained Baptist pastor, said creation by divine order should be considered as much of a science as evolution, given equal classroom teaching time and offered to students in an insert in the life-sciences textbook.

“If we're going to approve textbooks that are biased toward evolution, there should be some sort of appendix glued in the front cover that emphasizes or points out that this text seems to be slanted toward the origin of species as strongly supporting evolution,” he said.

He would like a committee formed to study the legality of such a move, but the School Board unanimously approved a new science textbook without an insert and has not discussed forming a committee on the matter.

That quote in the third paragraph doesn't actually make any sense, but I think his intention is clear enough.

I've not been able to find any follow-up to this article, but I'll be keeping an eye on this.