Sunday, February 18, 2007


Dawkins on CNN

On January 31, 2007, CNN's Paula Zahn aired a segment about the intolerance faced by an atheist family. A transcript and links to the video are here . The story was discussed by the evening's panel: a journalism professor, a conservative columnist, and a sports writer. The panel had previously discussed Joe Biden's comments about Barak Obama, the politics of obesity, and racism in the NFL.

All the panelists agreed that "this is a Christian country", that freedom of religion doesn't mean freedom from religion, and that "they should just shut up" and not try to impose their religious beliefs on others. Of course since this is a Christian country it's all right for them to impose their beliefs. Like putting "In God We Trust" on currency. It's a bit ironic that the sportswriter was the most insistent defender of religious freedom. We ought to expect better from a journalism professor.

The furor persuaded Zahn to tape a short interview with Richard Dawkins. It got delayed by the fuss over the death of Anna Nicole Smith, but finally got on the air. Transcript is here.

Dawkins's last answer, that this is the only life there is, so we should cherish it, is brilliant, but some of the other responses could, IMHO, be better. Herewith Zahn's questions and my fantasy answers:

ZAHN: But why do you think they are so remarkably intolerant of atheists?

WENDT: Psychologists and anthropologists have good evidence that one of the functions of religious belief, and especially ritual, is the strengthening of group solidarity. If you profess the same beliefs as everybody else, and especially if you make the same sacrifices of time and material goods, people take it as a sign that you are one of the group, that they can trust you. One of the features of American religion is that "people of faith" have weakened the criteria in such a way that almost any kind of Supreme Being can qualify someone as trustworthy. Of course atheists deny that any such being exists, so we are automatically untrustworthy, and thus are outsiders.

ZAHN: Certainly, you have encountered people, though, who are intimidated by your message, that, in some way, it puts perhaps their own faith in doubt?

WENDT: I should think you would want to doubt your faith. Do you actually want to risk believing things that aren't true?

This time, the panel after the interview included an atheist. Again, I wish she had given sharper answers. My suggestions:

ROBERTS: Do atheists bring this on themselves by going to Supreme Court with campaigns like trying to take the words "under God" out of the pledge, trying to take the words "In God we trust" off of the currency?

WENDT: I've never sued anybody. Are you willing to be lumped with Christians who kill doctors who perform abortions? I grant that that's extreme; but Christians get away with so much that it's hard to find an example that mainstream Christians would disavow.

Anyway, why do you want "In God we trust" on currency in the first place? Do you have to remind yourselves all the time that you are supposed to trust in God? You don't actually do it, you know. The book of Proverbs says "Trust in the Lord with all your heart, and lean not on your own understanding". But most Christians lean on their own understanding as hard as they possibly can, and trust in the Lord only for things they don't yet understand. If you really trusted in God you wouldn't need an army (remember the story of Gideon?), and you wouldn't need polio vaccine. When I was growing up, in the 1940s and '50s, there was a polio epidemic about every other summer. Pious parents would pray to God that he spare their child from this dread disease; if the child got the disease anyway, the parents were expected to consider it a test of their faith. Then Jonas Salk developed his vaccine; virtually everybody was vaccinated, and in a couple of years polio was no longer a problem in developed countries. Presumably God had to find a different way to test people's faith. Maybe that's why he keeps cancer around.

And people who withhold medical care from their children because "God will provide" are prosecuted for child abuse.

PETERSON: Then, where do you get your morals from? Christians get their morals from God, from the -- from the Bible, from God. Where do you get yours from?

WENDT: Morals are evolved into the human brain. The brain that survives best in a social setting is one that automatically knows that it gets along best by being nice to people. Brains don't naturally understand evolution well, but we have a need to identify an agent. We invent supernatural beings to fill our gaps. Humans don't get morals from God, we get gods from morals.


Of course all this is a bit too long for the brief window on TV. Thank god (so to speak) for blogs!

But maybe this is like trying to teach a pig to sing: It doesn't work, and it annoys the pig. It might not be a good idea to tell your boss that she is being irrational. Scott Atran advises

Do Not Shut Up In The Face Of Irrationality, But Know Who You Are Dealing With And Act Accordingly. Some religious people are irrational, as most us are in many situations in our lives, as when we fall in love, or hope beyond reason. Of course, you could be uncompromisingly rational and try whispering in your honey's ear: "Darling, you're the best combination of secondary sexual characteristics and mental processing that my fitness calculator has come up with so far." After you perform this pilot experiment and see how far you get, you may reconsider your approach. If you think that approach absurd to begin with, it is probably because you sincerely feel, and believe in, love.

Some religious people are very irrational and dangerous, but these are the people that I study and deal with on a personal level, trekking with mujahedin, interviewing jihadi leaders, and engaging suicide bombers directly. What I do believe is that the terms of engagement that Harris proposes for confronting irrationality generally would be deadly if applied to such cases.

The excerpt is from this discussion, which is well worth reading.

Saturday, September 09, 2006


Going Straight

After several decades of being something of an autodidact in biology, I'm actually getting some formal education. I've enrolled at Indiana University/Purdue University at Indianapolis (IUPUI), which is a joint venture between IU Bloomington and Purdue at West Lafayette. It includes the IU Schools of Medicine and Dentistry, so there's a lot of strength in biology. Eli Lilly, the pharamceutical company, is a nearby resource.

My course is Biology K101. The course uses the Just-in-Time approach, in which students are asked to complete a Web-based warm-up exercise aafter the reading on a topic, but before the lecture. This gives the teacher a heads-up on topics that students may not understand.

My knowledge of biology is kind of a mile wide and a yard deep. I hope to get from this course more detail and depth, some lab experience, and the chance to meet some real biologists.

It should also give me some blog topics.

So my adventure begins.

Saturday, August 26, 2006


More Sources of Information

This is a sequel to my previous post on biological information.

Two things come to my mind when I think about information theory: communication theory (a la Shannon) and decision theory. Communication theory treats information as something to be transmitted as accurately as necessary; decision theory treats information as something that may make a difference.

Note that the decision-theory definition covers both human information and the sort of biological information that I talked about last time.

William Dembski, the apostle of "intelligent design", says "The fundamental intuition underlying information is not, as is sometimes thought, the transmission of signals across a communication channel, but rather, the actualization of one possibility to the exclusion of others." This is similar to my definition of information as "something that makes something happen". Notice, though, that information always seems to act with at least one remove: information molds the actor, rather than acting itself. With humans, the information changes the actors mental picture of the world, so the actor may act differently. In chemistry, hence (for our purposes) in biology, the information shapes the electric fields, so electrons act differently.

There has been lots of analysis of Dembski's concept of "complex specified information", so I won't belabor that. My quarrel is with his assumptions about information itself.

Dembski treats information as a free-floating concept: "For an example in the same spirit consider that there is no more information in two copies of Shakespeare's Hamlet than in a single copy. This is of course patently obvious, and any formal account of information had better agree." But in the real world this statement isn't always useful. If you have two copies of Hamlet, two people can read it at the same time, so decisions about staging and such can be made sooner. And it's by no means clear that an organism is indifferent to a second copy of a gene. The effects of Down syndrome are the result of a second copy of an entire chromosome.

Another result is the leaf-eating monkeys. Here a gene is duplicated; one copy still serves the original function, leaving the other gene free to mutate into a slightly different form, enabling the monkeys to get more nutrition from leaves.

In the first case the formal quantity of information is the same, but the effective quantity is different. The second case is information "created" by a non-intelligent mutation. Just because human information is always intelligently caused doesn't mean that biological information has to come from intelligence.

Using Dembski's Hamlet analogy leads you to miss the fact that information is more than just a mathematical description.

Sunday, July 09, 2006


Biological Information I: The Medium Is Too the Message

Creationists are extremely fond of saying that information can be created only by intelligence, therefore evolution is false. (I include advocates of "intelligent design" here; more on that some other time.) George Gilder, the futurist, has an article in this vein on National Review Online. The article is subscriber-only, but the Discovery Institute has a copy. Gilder's contention is that DNA is information, and that "[w]herever there is information, there is a preceding intelligence." His italics, because this is the center of his argument.

The misunderstandings of all sorts of things come thick and fast, so I gave up trying to fisk the entire article; there's just too much nonsense. I'll limit myself to the place where he most goes off the rails.

Gilder talks about Claude Shannon's theory of communication. Gilder follows most creationists in calling it a theory of information, which is the foundation of much of his confusion. Shannon was concerned about communicating information over potentially noisy telephone lines; he wanted to know how fast information could be transmitted while still allowing the user to select the correct message from all the possibilities. He specifically said that the meaning is irrelevant; what counts is sufficiently accurate communication.

Gilder correctly says that Shannon separated the information from the channel across which it's transmitted.
Crucial in information theory was the separation of content from conduit — information from the vehicle that transports it. ... In my book Telecosm (2000), I showed that the most predictable available information carriers were the regular waves of the electromagnetic spectrum ... . Whether across time (evolution) or across space (communication), information could not be borne by chemical processes alone, because these processes merged or blended the medium and the message, leaving the data illegible at the other end.
What Gilder misses here is that DNA is not a transmission channel, rather it's a storage medium. The information in DNA is copied from one generation to the next, with occasional mutation.

Gilder has a section titled "The Medium [Is] Not the Message". This is a reference to an aphorism of Marshall McLuhan, who is most famous for saying "The medium is the message". It's easy to misunderstand this: McLuhan meant (approximately) that the social effects of the availability of a new medium -- printing press, television, Web -- are more important than any specific content.

Gilder continues to miss the biological point:
Information is defined by its independence from physical determination: If it is determined, it is predictable and thus by definition not information. ...
Then maybe DNA isn't information. Or maybe the news is the same in each generation.
Biologists commonly blur the information into the slippery synecdoche of DNA, a material molecule, and imply that life is biochemistry rather than information processing.

Gilder seems to treat information as a sort of Platonic non-substance, floating above the material world. But information always has a material representation. On paper it's ink, in a wire it's fluctuating current, in an optical fiber it's a flux of photons. The fundamental problem with Gilder's analysis is that in chemistry, and by extension biology, the medium is the message -- there's no way to separate them. If you define information as something that makes something happen, in chemistry that something is the shapes of the molecules. If you want to say that life is information processing, then you have to say that the shape of the molecule is the information, and the chemical reaction is the processing. An alternative is to abandon the idea that DNA is information, or that life is information processing. Gilder never really establishes that point, he only asserts it.

If you want to say that DNA is a computer, or that life processes are computer-like, then you have to admit that each enzyme is its own processor, and that also its own code. There is no possible way to separate the code from the processor. But as Gilder says, this is one of the key features of a computer. So where does that leave the computer metaphors?

Gilder has a lot of high-flying rhetoric, but horrible science. Biologists feel that Dawinism, in its modern incarnation, is increasingly illuminating life. In a manner that is completely characteristic of "intelligent design" rhetoric, Gilder gives not the slightest hint of how science might use this "new aim" to "solve the grand challenge problems". The new aim is not ultimately redemptive; on the contrary, it remains ultimately blinding.

Creationists are fond of pointing to the many times that the scientific establishment refused to accept ideas that ultimately triumphed. The implication is that "intelligent design" will join that group. (They forget that scientific ideas are accepted on the basis of evidence, and that new ideas need new evidence, not just rhetoric.) Gilder, for his part, takes a gratuitous swipe at the idea of parallel universes as a response to some of the explanatory problems that science faces. He says that "[t]he effort to explain the miracles of our incumbent universe by postulating an infinite array of other universes is perhaps the silliest stratagem in the history of science. " Funny, that's just what Martin Luther said about Copernicus's idea that the earth moves.

ADDED LATER: Tom Schneider's Web site applies Shannon's theory to molecular machines. More on this when I've digested Schneider's stuff.

Wednesday, June 28, 2006


The Second Genetic Code

An article in a creationist magazine claims that the DNA code is yet another death-knell of evolution (Mark Twain's remark that "rumors of my death have been greatly exaggerated" comes to mind). The author says
It was in 1953 that James Watson and Francis Crick achieved what appeared impossible--discovering the genetic structure deep inside the nucleus of our cells.
Reading Jim Watson's book The Double Helix gives you an idea of just how impossible it seemed. That is, not at all. A few years earlier, various experiments had shown that deoxyribonucleic acid, DNA, carries the genetic information that produces proteins. Watson and Crick were confident that it would be possible to determine the physical structure of the DNA molecule, because the structure of other molecules had been figured out. Watson's book is a revealing account of the effort, including the rivalry with Linus Pauling, who also was confident that he could discover the structure. (A little too confident, maybe. Read the book.)

In the years after 1953, biologists concentrated on figuring out just how DNA translated into protein. Horace Freeland Judson's massive book The Eighth Day of Creation is the best account I've found. (The title seems to echo a quote from Thornton Wilder: "Man is not an end but a beginning. We are at the beginning of the second week. We are children of the eighth day.")

After some statistics about the amount of information crammed into such a small space, the article says

Let's first consider some of the characteristics of this genetic 'language.' For it to be rightly called a language, it must contain the following elements: an alphabet or coding system, correct spelling, grammar (a proper arrangement of the words), meaning (semantics) and an intended purpose.

Scientists have found the genetic code has all of these key elements. "The coding regions of DNA," explains Dr. Stephen Meyer, "have exactly the same relevant properties as a computer code or language".
The first problem with this is the talk about "grammar" and "intended purpose". Nothing in the genetic code corresponds to anything that we would normally call "grammar". DNA is a chemical template for the formation of RNA. Most RNA goes on to serve as a template for the formation of protein. Also, there is no semantics at the DNA level, as I show later.

I'm going to assume some knowledge of how proteins get made. For review, here are articles about amino acids, DNA. and RNA.

The creationist article continues:
Besides all the evidence we have covered for the intelligent design of DNA information, there is still one amazing fact remaining--the ideal number of genetic letters in the DNA code for storage and translation.
Moreover, the copying mechanism of DNA, to meet maximum effectiveness, requires the number of letters in each word to be an even number. Of all possible mathematical combinations, the ideal number for storage and transcription has been calculated to be four letters.

This is exactly what has been found in the genes of every living thing on earth--a four-letter digital code. As Werner Gitt states: 'The coding system used for living beings is optimal from an engineering standpoint. This fact strengthens the argument that it was a case of purposeful design rather that (sic) a [lucky] chance."
What got me onto this subject is the claim that "The coding system used for living beings is optimal from an engineering standpoint". The article says "the copying mechanism of DNA, to meet maximum effectiveness, requires the number of letters in each word to be an even number". This makes no sense. There are actually three "letters" in each "word". (I'll omit the quotes from here on. Anthropomorhpic-sounding terms are handy metaphors, nothing more.)

A four-letter alphabet is needed only if each word is to be the same length. That's not optimum, though. It would be more efficient if the DNA code used something like Huffman coding, which uses shorter words for more frequent things. Such a code is prefix-free, which means that no word is ever the prefix for any other. Thus if "A" is used for the most frequent amino acid, every other word will begin with some other letter. So when you are reading the text, you don't need any indication of where a word stops and the next one begins. (Francis Crick tried a similar scheme early on in the figuring-out of the genetic code, but it didn't work.) A biologist has calculated that "[t]he restriction to a fixed codon length of three bases means that it takes 42% more DNA than the minimum necessary, and the genetic code is 70% efficient."

So why didn't evolution produce a more efficient code? The biologist has some suggestions, but it seems to me that the major reason is that DNA doesn't code for protein. DNA codes for RNA. Since the function of this RNA is to tell other machinery how to code for protein, it's known as messenger RNA (mRNA).

A string of mRNA hooks up with a ribosome, which is part RNA and part protein, although the RNA seems to be the more important part. Another piece of RNA called a transfer RNA (tRNA) hooks onto the combination of ribosome and mRNA, carrying an amino acid. The tRNA has chemical hooks that recognize three specific letters in the mRNA. (As with just about everything in biology, it's a little more complicated than that.) The tRNA transfers its amino acid to the string of amino acids that's already attached to the ribosome. The ribosome moves the mRNA three letters on, ready for the tRNA that matches the next three-letter group.

DNA doesn't know anything about three-letter words (or about amino acids, for that matter); it's only at the ribosome that the word size becomes important. The correspondence between tRN and amino acid comes from an enzyme known as aminoacyl-tRNA synthetase. There is one synthetase for each combination of tRNA and amino acid; the synthetase attaches the proper amino acid to the proper tRNA.

A more technical explanation is here. This correspondence between mRNA, tRNA, and synthetase is sometimes known as the "second genetic code".

Or is it the first genetic code? RNA has lots of uses, and does most of the work in forming proteins; DNA just sits there. Maybe RNA came first, then DNA came along as a better way to simply store the information, leaving RNA as the user. This seems consistent with the RNA World hypothesis.

The relevance to the evolution of a more efficient DNA code is that any change in the length of a DNA word would have to be reflected in the tRNA, the ribosome, and the synthetase. If the pioneers of molecular biology had found that each tRNA included some sort of indicator of how far the ribosome needed to move the mRNA, then we might be a bit more receptive to an inference of design.

Tuesday, February 21, 2006


Were You There?

Ken Ham, a founder of Answers in Genesis, gives kids his Genesis literalism straight. When a teacher talks about the time of the dinosaurs, the kids are supposed to ask, "Were you there?" The teacher will sheepishly admit that, no, he wasn't there. The kids then say "I know someone who was there! And He wrote about it in his Book!"

Actually the teacher, if she or he actually knew it, is being thrown into the briar patch. This is an excellent opportunity to give the students some of the basic reasons why scientists started about 200 years ago to believe that geological evolution is basically true.

Ask the kids if they have seen the TV show CSI, which stands for Crime Scene Investigators. Most of them have; I understand that the show has made forensic science a popular career ambition. The investigators look at all sort of clues, then use their knowledge of science to try to figure out what might have happened to leave such clues. Often (or, in fiction, always) they can arrive at a scenario such that there is no other way that all these clues could be the way they are.

I don’t suppose many crimes are solved by geological principles, but a lot of historical puzzles can be solved. Consider a river flowing to the sea. The water will carry dust and sand, and may have enough energy to push gravel and stones along the bottom. As the water arrives at the ocean the path widens, so the water slows down. Now it no longer has enough energy to move the stones, so they collect near the shore. Eventually they harden into the sort of rock called conglomerate. Farther from shore the water is moving slower, so the sand falls out, eventually to harden into sandstone. Farther still, the dust settles toe the bottom to form shale. Far from the river mouth the water is quiet, and plankton grow in the upper few meters. As the plankton die, their calcium carbonate skeletons drift to the bottom to form a calcium muck that eventually becomes limestone. (This doesn’t take all that long, as geology goes. People have found limestone containing bottle caps.)

The interesting part starts when the land starts to sink, or sea level starts to rise. Now the river mouth is farther inland, so the near-shore conglomerate is also farther inland. When the sinking goes far enough, the sand will settle out over the conglomerate that was deposited earlier.

More sinking leads to shale over the sandstone, then to limestone over the shale. If the land now starts to rise, you see the reverse sequence: shale over the limestone, sandstone over the shale, and conglomerate over the sandstone. Now some of the layers will be out of the water, subject to erosion.

A lot of this happened in forming the Grand Canyon in the U.S. A detailed description of the major layers is here. Actually, each of the major layers has lots of sublayers, hundreds in all. Note the sequence from the Tapeats Sandstone to Mauv Limestone. This is classic. Other layers seem to be out of sequence. Geologists explain this as a result of the rock not being underwater at some time, maybe with upper layers eroded away. Creationists will cry “Fudging!”, but often the surface below the “missing” layers will show footprints, and maybe actual evidence of erosion. As almost always happens in places where there are many layers of rock, different layers have different fossils, and the sequence of fossils is much the same in the Grand Canyon as in other locations.

This just explains the rock layers, though. The canyon itself was carved by the Colorado River.

This page gives lots more history of the Canyon. What geologists mean by "history" is a story about what might have happened in the past in order to produce the sequence of rocks that we actually see. There is sometimes considerable debate in cases where there is more than one possible explanation; geologists then look for more details, maybe comparing these rocks to comparable rocks in other parts of the world, where maybe there are more layers that can give more detail.

Another source of controversy is an explanation that doesn't correlate with anything else. This is known as an "ad hoc" argument, and is widely regarded as feeble. Things should hang together. The earth has only one history, although conditions vary from one place to another.

Ken Ham relies on "someone who was there". But lawyers know that eye-witness testimony can be highly unreliable. Tests and actual cases have shown that witnesses get faces wrong, and sometimes get sequences of events wrong. Written accounts are particularly unreliable, if you can't cross-examine the witness. (Try casting doubt in a public school classroom on the credibility of Sacred Scripture. ) On the other hand, geology offers physical evidence, just the sort courts like best. Blood samples and ballistics are the hard-evidence stuff of court cases, just as rock layers and fossils are the evidentiary stuff of geology.

Some creationists claim to have scientific explanations that lead to young-earth conclusions, but geologists aren't convinced.

So when a student asks "Were you there", you can reply "No, but the rocks were!"

Tuesday, January 24, 2006



I've neglected this blog for more than a year because I was busy posting at the Access Research Network, a hotbed of “intelligent design”. I stopped posting there because I got fed up with the same old tired arguments. (To be sure, though, they got fed up with my tired arguments.)
I learned a lot, though. There are a number of actual scientists there, who make good arguments based on good science. There are also a number of people who are advance vociferous arguments that range from misguided to bizarre. I think of some of these as “conceptual whetstones”: dense and abrasive, but useful for sharpening. In trying to counter some of these misconceptions, I've gotten a deeper appreciation for some of the basic ideas of evolution. Nobody over there seems about to change their minds, so I decided to leave, and get back to my own blog.

This post was inspired by one of my antagonists claiming that I had confused cause and effect . Because causality is an interesting and subtle concept, I'm starting out with that topic. I had pointed out changes in a popoulation are caused by variation followed by natural selection, which prompted him to say that “a 'variation' is an effect, not a cause.

Discussion of causaliy goes back at least to Aristotle, who identified four Causes. These are usually given as Material Cause (the stuff of which a thing is made), Efficient Cause (the process by which it is made), Formal Cause (the shape into which it is made), and Final Cause (the purpose for which it is made). The traditional example is a statue: the Material Cause is the marble; the Efficient Cause is the action of the sculptor; the Formal Cause is the shape of the statue; the Final Cause is the desire to have a statue.

Marc Cohen, of the University of Washington at Seattle, gives a more nuanced view: The word we translate as “cause” is better rendered as “explanatory factor”. Aristotle's example of Final Cause is “Why is the man walking around?” “For his health”. The Final Cause of the statue may be that the sculptor needed money.
Efficient Cause can be elaborated:
  • The Efficient Cause of the statue is the wedging of the blade of the chisel into the crystal structure of the marble.

  • The Efficient Cause of the moving chisel is the motion of the sculptor's hand.

  • The Efficient Cause of the motion of the hand is the contraction of the arm muscles.

  • The Efficient Cause of the muscle contraction is electrical impulses from motor nerves.

  • The Efficient Cause of the electrical impulses is thought patterns in the sculptor's brain.
Some considerations:
This last step sort of merges Efficient Cause with Formal Cause.
The electrical impulses are filtered through synapses, which reflect the sculptor's practice
with chisel and marble.
The muscle contraction involves several mechanisms that I left out.

The Scottish philosopher David Hume changed people's notions of causation:
Hume sums up all of the relevant impressions in not one but two definitions of cause. The relation -- or the lack of it -- between these definitions has been a matter of considerable controversy. If we follow his account of definition, however, the first definition, which defines a cause as "an object, followed by another, and where all objects similar to the first are followed by objects similar to the second", accounts for all the external impressions involved in the case. His second definition, which defines a cause as "an object followed by another, and whose appearance always conveys the thought to that other" captures the internal sensation -- the feeling of determination -- involved. Both are definitions, by Hume's account, but the "just definition" of cause he claims to provide is expressed only by the conjunction of the two: only together do the definitions capture all the relevant impressions involved.
We have to be careful here, though. It might be that the two objects have a common cause, rather than one being the cause of the other. (We might have to use a different definition of “cause” in order to make this work.)

In 1948, the German philosopher Carl Hempel presented his “covering law” model of causation, which starts with one or more natural laws, then derives causation from law and conditions. (But how do you discover natural laws before you have an idea of causation?)

This is still not final, though. Some philosophers are broadening the idea of causation to go back to some of Aristotle's ideas. If someone asks “Why is the porch light on?”, a natural-law answer like “Because electric current is flowing through the filament” would be considered either non-responsive or smart-alecky. An acceptable answer might have the form “Because I am expecting company”, or “Because I forgot to turn it off”. “Expecting company” is a Final Cause; forgetting assumes that there was a reason for turning it on in the first place.

All of this is incomplete; what I want to do is come to a brief discussion of causation in biology. Consider one of the steps in the evolution of the jaw. An embryo of a vertebrate has a number of arches in the pharynx. In a lamprey, a jawless fish similar to an eel, the first arch develops into the lips of the mouth. In a jawed fish, one of the growth factors is expressed at a slightly different place, with the result that the arches grow into jaws. Biologists have been saying for decades that pharyngeal arches evolved into jaws, and creationists denied it. This is direct evidence of how it happens.

But why does this shift happen? Is this a cause or an effect? Going back to the Efficient Cause of the statue, it seems that this is both an effect and a cause, that is, it is a link in a chain of causes. The mechanisms of controlling gene expression are known in general terms; I suspect that somebody is trying to figure out specifics for this pathway.

What about Material Cause? In the case of the statue, the marble is completely passive; the chisel does all the work. The creation of the statue would be much the same if the material were wood or clay. The situation is much different in biology. Here the shapes of the molecules control what happens. The Efficient Cause is the chemical attraction between molecules. Two hydrogen atoms and an oxygen, at a high enough temperature (which is the same as kinetic energy), will form a water molecule. When one or more molecules interact with an enzyme, the shape of the enzyme interacts with the shape of the molecules in order to bring about the chemical reaction.
So in sculpture, the Material Cause is largely irrelevant; Efficient Cause is (almost) everything. The tools might vary somewhat, and the fine motions of the hand will be different, but for a sculptor experienced in several media, there is little difference. In biology, by contrast, Material Cause is everything, while Efficient Cause makes no difference.

Formal Cause in biology might be treated as an example of emergence.

I suggest that the difference in Material Cause and Formal Cause is what marginalizes the analogies with watches and automobiles that the creationists and their “intelligent design” brothers like so much. Watches and cars are like the statue: Material Cause is irrelevant. Clocks used to be made of wood. You can make a car out of plastic as well as steel. It will perform differently, but the assembly process is much the same. A biological entity constructs itself, based on the shapes of the constituents.

FOLLOWUP: While this post was fermenting in my Drafts section, this post at the Philosophy of Biology blog discusses another aspect of Aristotle's philospophy. Be sure to read the comments.