If Darwin Were Alive Today...

Dawkins on CNN

2007-02-18T16:03:00.000-05:00

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.

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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.

Going Straight

2006-09-09T11:04:00.000-04:00

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.

More Sources of Information

2006-08-26T17:09:00.000-04:00

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.

Biological Information I: The Medium Is Too the Message

2006-07-09T20:39:00.000-04:00

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.

The Second Genetic Code

2006-06-28T15:41:00.000-04:00

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.

Were You There?

2006-02-21T11:02:00.000-05:00

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!"

Because...

2006-01-24T14:47:00.000-05:00

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.

Wilkins's (Temporary) Apostasy

2005-04-03T20:44:00.000-05:00

John Wikins, possibly depressed at the approach of winter in the Southern Hemisphere, has said kind things about a paper by William Dembski. Dembski's paper was a response to a paper written by Nicholas Matzke, setting forth a hypothesis for the development of the eukaryotic flagellum. Matzke's paper is fairly technical; he does provide some background for the reader.

The flagellum, of course, is of some importance to Intelligent Design. The design is so complex, and complex in such a way, that it is considered highly unlikely that it could have come about by what ID advocates consider to be Darwin's theory. There is thus, in their view, no escape from the conclusion that the flagellum was intelligently designed.

Kenneth Miller has written a refutation of the idea of "irreducuble complexity", which is the basis of the design inference. Matzke's article is more technical, referring to specific proteins.

Dembski's response, which Wilkins describes as "masterful", deals less with biology than with style. Dembski starts by listing the various screen names Matzke has used on different discussion boards. How this is relevant to anything, Dembski doesn't say. It sounds like a culture clash.

Dembski goes on to mention that Matzke, at the time a graduate student in geography at the University of California at Santa Barbara, graduated from Valparaiso University, "a Christian college in Indiana". More specifically, Valpo is a Lutheran college. I attended Lutheran schools in Fort Wayne, which is not far from Valparaiso, so Valpo was always in our minds. I thought about going there, but my mother said that my siblings and I needed to learn "that there are other people in the world besides Lutherans". After a money-exhausting year at a local college I joined the Navy, and found out in a hurry what she was talking about.

Dembski begins his argument by observing that Matzke devotes 13 pages to references and 14 to figures. Ten pages discuss prior research, three are "scene-setting". Only 20 pages are devoted to the actual argument. Dembski doesn't seem to appreciate the careful approach in Matzke's paper. Biologists like lots of references, and discussions of prior research.

In the end, Dembski grants all the biology Matzke mentions. Dembski's major objection is that Matzke's explanation is not sufficiently Darwinian. But what is "Darwinian", and why does it matter? Dembski says that

Darwinism is a theory of process. It says that you can proceed from point A to point B in biological configuration space provided that you can take small enough steps where each step is fitness enhancing (or at least not fitness detracting). The steps need to be small because Darwinism is a theory of gradual incremental change where each step along the way is reasonably probable. As Darwin put it in his Origin, for his theory to succeed it must explain biological complexity in terms of "numerous, successive, slight modifications." Anything else would cause his theory to founder on the rocks of improbability. (emphasis added)

Darwin emphasized small steps in order to stay away from saltationism, the idea that there are abrupt transitions. This was, for him, too much like creation. Darwin worked more than a hundred years ago, though, and the theory of evolution has made some progress since then. The first big jump was the development of the theory of genetics, building on the work of Mendel and Morgan. (More on this in a later post.) This led to neo-darwinism, the merger of genetics and evolution. Later still came Lynn Margulis's theory of endosymbiosis, still later developmental biology, merging genetics and embryology. Darwin didn't know anything about these areas; he based his theory on what he could see.

Dembski says

The bacterial flagellum is a marvel of nano-engineering. ... If a biotech engineering firm were required to draw up blueprints and design specifications for the construction of the bacterial flagellum, it would require thousands of pages (especially if the individual proteins that go into the construction of the flagellum had to be fully specified in terms of their structures, functions, and properties).

Besides begging the question a bit (he needs to prove that the flagellum was designed, he can't assume it), Dembksi misunderstands biology. Biological structures aren't constructed the way human structures are. There is no specification: (the previous incarnation of) John Wilkins observes that DNA is not information. Mary Ann West-Eberhard argues that the metaphor of DNA as blueprint doesn't work either. DNA and enzymes are just molecules which, by reason of their chemical shapes, allow other molecules and atoms to fall into minimum-energy relationships, with some rearrangement of valence electrons along the way. As to probability: The process that Matzke hypothesizes may have taken place over millions of years, involving astronomical numbers of bacteria. The mutations don't have to be sequential, either: Bacteria can exchange genes, in a way that serves some of the functions of sex in more-complex organisms.

Dembski says that Matzkie's model is not testable:

As for Matzke's claim that his model is step-by-step, that's trivially true -- after all, he defined the model as a series of steps. But are those steps reasonably small so that they constitute what Darwin called "successive, slight modifications." My sense is no -- getting from a type III secretion system to a bacterial flagellum in six steps seems on its face to require at least one big leap somewhere. But intuitions aside, given that Matzke's model is not detailed, there's no way to decide whether the steps are small enough to be accommodated by the Darwinian mechanism.

But cooption is in a sense a large step, maybe even qualifying as a saltation. As to detail: A hypothesis of this scope often leaves considerable room for details to be filled in.

Dembski's finale:

Two years ago cell biologist Franklin Harold published a book with Oxford University Press titled The Way of the Cell. In it he explicitly repudiated intelligent design: "We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity." And yet he continued, "But we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations." (p. 205) Is Harold, a noted cell biologist, right? Or has Matzke, a geography graduate student, disproven Harold? To be sure, stranger things have happened. But Matzke is not in the same league as the mathematician Galois, who at a tender age resolved outstanding mathematical problems that had lain open for millennia. Matzke's model, far from resolving the evolutionary origin of the bacterial flagellum and despite his protestations to the contrary, is yet another exercise in Darwinian storytelling. In this regard I commend him, because he has told the best Darwinian story to date concerning the evolutionary origin of the bacterial flagellum.

I haven't read Harold's book, but defenders of evolution learn to mistrust attackers, because it turns out too often that immediately after a damning quotation from a book on evolution the author says something like "however..." Or the attacker might leave out some important words in the quote. I'm not saying that Dembski did quote Harold out of context, just that he didn't quote enough of the passage to let us be sure.

Maybe the thing that turns scientists off most is Dembski's forgetting that the burden is on him to show that there is a design. Some ID advocates say that ID is only about recognizing design, not about identifying the designer. The most popular method of identifying design seems to be to show that something couldn't have come about by natural means. Maybe this is the only way, absent direct evidence for a designer, or a design process. The problem with this method of argument is that each year we know more about natural processes than we did last year, so saying that there is no possible way, because we can't find it this year, is not very satisfying.

Dembski forgets the difference between did and could have. Matzke gives what seems to be a reasonably possible explanation of how the flagellum could have evolved. Whether it actually did or did not evolve that way may still be open. But Dembski's argument for intelligent design requires that every "could have" argument be false, i.e. that there is no way something could have happened naturally. It is not enough that an individual "did" is false, because there might still be another possible natural way. And to call it "non-Darwinian" is not an argument for a designer. Either we can say that evolution has gone beyond Darwin, just as physics has gone beyond Newton, or we can say that Darwinism has been extended to include genetics and molecular biology. (The title of this blog suggests that I prefer the extension choice.)

Fortunately for the world of philophiles, the next spin of the earth restored John to his senses.

Beyond Ockham's Razor

2005-02-27T18:27:00.000-05:00

This essay began as a comment to a post on the Philosophy of Biology blog. The post reproduces the New York Times article by Michael Behe. My first comment was

"The fourth claim in the design argument is also controversial: in the absence of any convincing non-design explanation, we are justified in thinking that real intelligent design was involved in life."

This is an epistemological claim with an ontological implication. If we conclude that life is intelligently designed, it would seem to follow that there is/was some sort of entity doing something to move DNA molecules into positions that they had not occupied before the design was accomplished. Ockham's Razor, however, requires that we choose the alternative requiring the fewest ontological assumptions. (This is not exactly a formal requirement, but it seems like a damn fine idea.) Mainstream biology gets its ontology from observation and experiment; until ID can do something similar, we can't assume an entity out of pure logic.

A note on spelling here. William was born in the English village of Ockham, Surrey. The name of his village is often given the Latin spelling "Occam". Being a bit of a pedant, I prefer the original.

Someone replied

It's not even close to a formal requirement. Simplicity is an aesthetic criterion and should be judged accordingly. Some have a taste of "desert landscapes" and some do not.

I was absent from the fray for a couple of days, during which more comments were made. The commenters agreed that Copernicus's theory of the planets was simpler than Ptolemy's.

When I returned, I commented (slightly modified):

Ockham's Razor is not about simplicity, it is about parsimony. Latin versions of the original vary somewhat between sources, but the essence of the translation is that "Plurality should not be posited without necessity". The comment asks in effect "What does 'necessity' mean?"

These are the sorts of questions that are asked by physicists. "Do we need a fifth force, or are the traditional four sufficient?" (The answer seems to be that four are enough.) Biology takes a crisper view: The preferred explanatory principles are those that can be observed, and, preferably, experimented with outside the present experiment. As an example: In the early 20th century biologists developed the concept of the "morphogenetic field", in order to explain the development of organismic form. With the rise of genetics, the morphogenetic field fell out of favor as an explanation. In the last few decades, though, the field has made something of a comeback, now taking the form of a gradient of some signaling protein.

There is a significant ontological difference between the two concepts. Nothing much can be said about the morphogenetic field, except that there is purportedly no other way to account for form. On the other hand, the level of a protein can be measured, and the speed of diffusion calculated. The protein was discovered before it was used in the field concept; it can be analyzed in isolation. The diffusion can be manipulated, by adding protein, or by adding an antagonist. The morphogenetic field has thus become a mechanical concept, although not by that name.

Nothing of this sort can be said about any kind of designer. The only formal reason IDists can give for talking about a designer is that they feel lost without it. Biologists are more adventurous, and more resourceful.

And, incidentally, Copernicus's theory was not all that much simpler or more parsimoneous than Ptolemy's. By putting the sun in the center of the universe (partly for philosophical reaons), Copernicus was able to eliminate one layer of epicycles. He still needed them though, because he still based his system on Aristotle's idea of circular orbits.

Kepler's use of Brahe's more-precise planetary positions led him to the concept of elliptical orbits. It is one of the ironies of history that Galileo, the die-hard champion of Copernicus, never accepted ellipses, because he was not willing to go that far in contradicting Aristotle. Ellipses could be dismissed as a mathematical device, which they pretty much were. They became theoretically real only after Newton showed that his inverse-square gravitation predicts elliptical orbits. But Galileo had made his stand on the physical reality of Copernicus's theory; the Church would probably have been content if he had accepted that it was mathemetical only. So we might even consider him justified in rejecting ellipses.

In the end it comes down to what you want from a theory. If you want esthetic satisfaction, then maybe ID is for you. All you really have, though, is a morphogenetic field, something that answers only one question, and you can't even say why it answers it. If you want a description of reality, you have to buiid it one brick at a time.

And very, very few biologists put any credence in Behe's claim that they have hit a brick wall.

I'd like to go beyond what I said before. PZ Myers's article on the evolution of the jaw is an example of what argument in biology is coming to look like.

Carl Zimmer has an article about theories of the origin of language.

More about both of these next time.

Karl Haas, the Anti-Elitist

2005-02-08T07:09:00.000-05:00

Karl Haas died last Sunday. Haas was a pianist and conductor, but he was best known for his program "Adventures in Good Music", broadcast on many Public Radio stations. I heard the program only sporadically, but always enjoyed it. Haas usually had some pedagogic theme, analyzing or explaning some facet of classical music.

The New York Times obituary notes that

One listener wrote Haas in the 1960's to say that it was a "longhair program with a crew cut," a description he was happy to repeat.

He had a following among truckers and farmers.

The Times also says

Some longhairs looked down their noses a bit at Mr. Haas, but that didn't matter to thousands of regular listeners.

I knew a few of those longhairs, graduate students in music school, who seemed to think that Haas's approach was kind of infra dig.

Popularizers in science often suffer the same fate. Some scientists looked down on Stephen Jay Gould because of his columns in Natural History magazine. This disdain attached also to Carl Sagan, with his television series Cosmos.

There's a whiff of elitism here, the idea that you learn a subject by hard study, and any attempt to explain it in less-than-rigorous terms demeans the subject, watering it down. It is possible to write about a complex subject in terms that are understandable to non-specialists, but it's hard. You have to have a very good feeling for the concepts, for the vocabulary, and for your audience.

There's an old saying, "If a thing is worth doing, it's worth doing badly". That is to say, if you enjoy something, like golf, you don't have to master the fine points to get some pleasure from it. In the same way, I suggest, you don't have to know the fine points of music theory to appreciate music. The late Tibor Kozma, head conductor at the Indiana University School of Music while I was an undergrad in the physics department, was fond of saying "Unfor-r-r-tunately, mussic is an acoustical phenomenon!" (You have to imagine a slight Hungarian accent here.) This is not to say that an inaccurate presentation of a subject like classical music, or evolution, is acceptable, just that it doesn't have to be comprehensive in order for you to get something interesting out of it.

Of course you can go farther, and actually join the elite yourself. Still, it's rare to find a person who has elite knowledge of more than a few subjects. There's just too much to know. An expert is someone who learns more and more about less and less, and winds up knowing everything about nothing. But still it's possible to learn a little about a lot of things, and to be better for it. That's what Karl Haas had in mind, and why a lot of us blog.

Pigeons En Masse, Alas

2005-02-04T11:02:00.000-05:00

Looking at the first Skeptic's Circle, I remembered a tale that may be about 30 years old. It goes something like this:

An aerospace firm in southern California wanted to reduce the amount of time spent by couriers driving through traffic across the mountains to transport engineering drawings between plants. Engineers could have designed some sort of fancy telecommunications scheme, but they came up with something much simpler: Carrier pigeons, with microfilm capsules.

Nowadays, of course, engineering drawings are created by computer, and available instantly worldwide through the company's intranet. Many companies have scanned old drawings, so there is no paper storage at all. But in 1975, this seemed like a nice, simple idea, in-the-face of the complicators.

But consider the logistics of such a system:

You need a microfilm camera at each source facility.
At each destination you need an enlarger and a developing tank suitable for the largest size of drawing in the system.
You need people to do the photographic work.
The system works only in good weather. Fortunately this is usually not a problem in California.
You need lofts in which to keep the pigeons until they are needed.
You need someone to feed and bathe the pigeons.
You still need couriers to transport the pigeons across the mountains to the source locations.
Pigeons become oriented to their current location in a few days, so you need to forecast your needs, in order to have enough pigeons at each location to handle the requests. If you overestimate, you have to take some pigeons back empty. (This once doomed a suggestion to use pigeons as communication between Navy aircraft and their carrier.)
If you have more than two locations on one side of the mountains, you have to have a separate set of pigeons for each location,
Security is the killer. Your pigeons are vulnerable to hawks and hunters. Indeed, spies might station themselves along the pigeons' route with shotguns. This might be made easier due to the tendency of pigeons to follow highways. The possibility of interception is a serious problem for commercial information, and devastating for military information.

So where did such a story come from? Does anybody know for sure? Maybe like a lot of urban legends it has a nice ring until you think about it for a while.

However, there is some recent research on the subject.

This story doesn't have much to do with evolution, which is the central theme of my blog. Although, Darwin spent a long time breeding pigeons, to study variation from one generation to another. Maybe the main message here is a caution: If something seems so simple that you wonder why people ignore it, maybe it's not as simple as it seems.

Friday Cat Blogging

2005-01-27T18:54:00.000-05:00

This is Abracadabra, known to her friends as AbbyTabby. Abby is an ocicat, although she doesn't have the ocelot-like spots that gave the breed its name. Ocicats are a mix of Abyssinian, Siamese, and American Shorthair (which provides the tabby bullseye). Apparently what happens in development is that there is a reaction-diffusion process providing the rings, with a separate process that breaks the ring into spots. Abby seems to be homozygous for the recessive, non-functional form of the gene that initiates the second process.

She doesn't know she's a throwback, though. When you get past the wildness that seems to be characteristic of the breed, she's really a very sweet cat.

Who's At Fault?

2005-01-22T17:52:00.000-05:00

In the January 21 issue of Financial Times, Christopher Caldwell writes about "creationism's sly evolution", i.e. Intelligent Design. (Subscription is required.) Caldwell says that

the secular education establishment that is now trying to defend itself against an onslaught of thinly veiled biblical dogma has itself to blame for its vulnerability. Since the 1960s, teachers and administrators have pushed unpopular progressive measures into schools -- from sex education to multiculturalism -- under the guise of "openness", "multiple perspectives", and the idea that course content matters less than "teaching students how to think".

Now, Caldwell says,

evolution's defenders are in the unenviable position of being the side arguing for the exclusion of other viewpoints. Trickier still, the grounds for that exclusion are not clear to common sense. Those who have studied evolution will find it hard to imagine how biology could be seriously studied without it. But defending evolution against some of the specific objections raised by the opponents takes expertise that is beyond the reach of 99 percent of people in a democracy. Those who vote and agitate on both sides of the evolution issue do so not on a scientific basis but on a social or ideological basis. They take sides based on whether they have trust in those experts on which society has conferred its prestige. The fight over Darwin is more than a religious conflict; it is a class conflict being waged with religious terms.

Caldwell mixes up a few things here:

--The people who advocate "multiple perspectives" are not necessarily the people who are advocating the teaching of evolution. There may well be considerable overlap, but each group has its own priorities.

-- The things that students are supposed to have multiple perspectives about are attitudes, not facts. Strictly speaking, of course, mainstream evolutinary theory is a conclusion, not itself a fact; but biologists consider evolution to be,as Stephen Jay Gould said, "confirmed to such a degree that it would be perverse to withhold provisional assent."

-- I don't think that biology courses hold that "knowing how to think" is more important than content. It is important to know how scientists think about science, but content is vital. Any biology teachers like to comment?

-- Caldwell says that "[t]hose who vote and agitate on both sides of the evolution issue do so not on a scientific basis", but those on the evolution side are often the experts themselves.

He concludes

Susan Jacoby, the author of a history of American secularism, lamented recently that her country had turned away from "an accommodation between science and mainstrean religion, now a fait accompli in the rest of the developed world". But it may be that America is not more superstitious than other advanced countries, just more democratic. What Ms. Jacoby regards as an accomodation looks to the creationists like a capitulation of folk beliefs before expertise. This accommodation may be good for science and salutary for education, but there is nothing that makes it compulsory in a constitutional republic.

Is America's individualism indeed at fault? Do other cultures have more automatic respect for authority?

Or does Caldwell miss an important point? The creationists say that their views are better science than is presented by the evolutionists. I know from my experience on ARN that some people have a different standard for what constitutes evidence. I can't entirely figure that standard out, but they insist on it. Part of it is a refusal to interpolate or extrapolate based on observations, although unfettered ontological speculation is OK.

How about if the biology teacher says that Intelligent Design says that maybe there is a designer, or maybe not; in any event no two versions of ID agree, and nobody can say why their version is better. Then the schools can say "See? We already teach Intelligent Design!"

Theory and Fact

2004-11-05T13:15:00.000-05:00

One of the knocks on evolution is that it is "just a theory, not a fact!". Defenders retort that "Evolution is both a theory and a fact!" Neither of these is very helpful.

Part of the problem is that the objectors are not using the word "theory" in the sense that scientists usually use it, and defenders don't call them on it. dictionary.com has as its first definition

A set of statements or principles devised to explain a group of facts or phenomena, especially one that has been repeatedly tested or is widely accepted and can be used to make predictions about natural phenomena.

This is pretty close, but it's too much like physics and not enough like biology, especially the "predictions" part. The last definition is

An assumption based on limited information or knowledge; a conjecture,

which is more what people usually mean by "just a theory", or "I have a theory about that", or "Evolution is just a theory".

It's more accurate to say that "evolution has a theory" (starting but not ending with Darwin), and that many of the conclusions to which the evidence has led biologists are so well supported that we are justified in considered them to be things that actually happened, i.e. fact.

So what does a theory look like?

Some simple theoretical statements are:

(1) A planet moves in an elliptical orbit with the sun at one focus. (Kepler's first law of planetary motion)

(2) If mating organisms are both heterozygous for a particular gene, then approximately 25% of their progeny will be homozygous for one allele, 25% will be homozygous for other allele, and 50% will be heterozygous (a modern version of Mendel' law of independent assortment)

Now consider two more statements:

(3) (a) The acceleration of a body is equal to the mass divided by the force (Newton's second law of motion)
(b) The sun attracts a planet with a force that decreases as the square of the distance (modified form of Newton's law of gravitation)

(4) When two organisms mate, each contributes one set of chromosomes to each of its progeny.

The thing to note here is that statement (1) can be derived from statements (3a) and (3b), and (2) can be derived from (4). In other words, if (2) and (4) are true, we know that (1) and (3) have to be true. (3) and (4)4 are more general than (1) and (2), so we say that (1) and (2) are reduced to (3) and (4). More about reductionism in a future post. Also note that (4) is a statement about biology, so it is not always as simple as it sounds. More later about that too.

I used the word "gene" just now. It is common in biology to say "Genes control growth". But what is a gene? The first definition of "gene" was that it is "the unit of heredity". This is some help, but not much. It turns out that the definition of "gene" has changed, as biologists's understanding of heredity and growth have changed. This vagueness in definition has been helpful, because it allowed understanding to grow underneath a very flexible blanket. (The definition of "evolution" itself is also somewhat vague. You guessed it: More about that in the future.)

The root problem is that you can't see a gene directly. If you want to investigate the motion of planets, at least you can see a planet. You may not understand what it is, but even if you call it a god, you can still observe its motion. But the only thing people knew about genes in 1900 was that something was transmitted from one organism to its progeny. Mendel called these units "factors"; biologists started calling them "genes", to denote that these were factors for inheritance. This vagueness allowed biologists to build a concept under the bare definition. This is a sort of bootstrapping: Build your definitions in the air, then put foundations under them. It's happening today in astronomy with dark energy. Nobody knows wht it is, but they know something about how it acts.

This is similar to the concept of operationalism, which says that if you can't observe a thing directly, you define it in terms of an operation that you use to measure it. If you are talking about temperature (which is of course not a "thing", but an attribute of a thing), operationalism defines temperature as the reading on a thermometer.

To talk about an electron, in this view, you talk about an experiment, or set of experiments, in which you measure the charge, mass, and other properties of something. Then you call that something an "electron". Biologists did the same thing with the "gene". As their understanding of heredity grew more sophisticated, so did the definition of "gene". More about genes in a later post.

The theoretical part of evolution starts with Darwin. There are four major assumptions:

(1) A new generation of organisms will vary from the parents. Different individuals will vary in different ways.

(2) Some variations are heritable. That is, if one individual is larger or smaller than its parent, the offspring of that individual will tend to be larger or smaller than the grandparent. Nevertheless, the members of that next generation will vary among themselves.

(3) Some variations will tend to help or hinder the survival chances of the individual, depending on the environment.

(4) Any organism can reproduce in greater numbers than the environment can support. For example, a finch might live five or six years. Two finches can produce three of four offspring for several years, for a total of maybe more than 20. If the population of finches remains constant, then most of these offspring have to die before they themselves reproduce.

(1), (2) and (4) are simple observations. (3) is natural selection, which is based on the idea of selective breeding.

The result of all these starting points is that the average member of a population will tend to have more or less optimum characteristics for survival in its particular lifestyle. That's overly simple; I'll try to amplify it in the future.

Darwin used these theoretical ideas to interpret his very keen observations of animals and plants, and concluded that many species have descended from other species. The number of original species is something that has to be determined by observation and analysis, not by pure thought. Biologists by and large have decided that life originated only once, or at least that if there were other originations, the others have become extinct. There is a great deal of evidence that points to this conclusion, so scientists feel justified in calling this a fact.

The third thing that is often confused is the path of evolution: What is descended from what? The Tree of Life project is an attempt to gather the available information. There is sometimes controversy, and things change from time to time. That's one of the things that makes science interesting.

Aristotle and Galileo, Part I

2004-09-06T09:06:00.000-05:00

This post is a detour from the stated purpose of this blog, which is to talk about the new thinking in evolutionary biology. But I got a new book -- "Galileo in Rome", by William R. Shea and Mariano Artigas. One of the authors is an historian of science, the other is a Catholic priest. They had extensive access to the Vatican archives, which they used to chronicle Galileo's six trips to Rome.

Galileo stands at the middle of one of the most profound sea changes the history of Western thought. The change sort of starts with Copernicus, and is pretty much mature with Newton. Galileo is best known of the three, because of his difficulties with the Catholic church, and I've long had a special interest in him.

But I realized that in order to understand Galileo I would have to understand something more about Aristotle. The philosophy of Aristotle pervaded the intellectual world into which Galileo was born, second in authority only to Holy Scripture. The relationship was always uneasy, as we'll see; but Aristotle was not to be messed with.

One translator says that in order to understand Aristotle you have to read all of him. This is probably true, but I don't have time for that, and anyway I find Aristotle somewhat painful to read. His writing, as we have it, strikes me as disorganized, repetitive, and sometimes contradictory. How much of this is actually Aristotle's fault is unknowable. We have no idea what, if anything, Aristotle actually wrote. Some scholars suggest that the writings we now have may have been lecture notes, maybe by Aristotle himeself, or maybe by a student. After his death in 322 BCE, his manuscripts kicked around Europe for a few hundred years, and were finally put into their present form by Andronicus of Rhodes, in the first century BCE. We don't kow how much is Aristotle, and how much is Andronicus. There are references in antiquity to dialogues of Aristotle, but nobody has any idea about them. Still, we have to take Aristotle as we find him, because that's what Galileo' world did. So what I say about Aristotle is not comprehensive, and some of it may be significantly wrong. But I think maybe I will be able to give a feeling for Aristotelean thought.

You might want to re-read my post "History Through Its Own Eyes" for some background. But keep in mind that I've learned a lot since then.

It is usual to say that such things as that Aristotle believed that celestial bodies moved in perfect circles. This is true, but incomplete: He had reasons for saying what he did, and that's what I want to talk about here. I concentrate on his work "On the Heavens", where Aristotle sets out his theory of astronomy. He says that people will agree with him if they accept his assumptions. But Aristotle never spells out the assumptions, he just throws one in when he needs it. Maybe he spells them out in other works; in any event, a review would have been nice.

As best I can tease them out, the most significant of Aristotle's assumptions are as follows:

1. All material objects are composed of four elements, or essences: earth, air, fire, and water. This was a fairly common starting point in Greek thought. Wood, for instance, is a mixture of earth and fire. If you heat it, the fire escapes, leaving earth. (This reminds me of an old joke in the electronics industry: An integrated circuit -- a computer chip -- works because it has smoke inside. If you put too much voltage on the chip, the smoke gets out, so the chip doesn't work any more.) The essence of something is "what it is"; what we see, its appearance, is an accident. This is not entirely the way we use "accident" in English; for more, see here and here.

2. Every element has its natural motion. Air and fire are light, because it is in their nature to go toward the heavens. Earth and water are part of the earth, so their natural motion is earthward. If a substance is compounded of two elements it has the characteristic motion of the element that predominates. Presumably earth predominates over fire in wood, so the natural motion of wood is to move toward the earth. I don't know whether he addresses floating bodies. Also, he doesn't address the possibility of a body in which more than one element has an influence on the motion. I don't know what improvement this might have made, but it seems to me that he limits himself too much by doing this.

3. Motion is either in a straight line, or else in a circle. Straight-line motion is either up or its contrary, down. Circular motion has no contrary.

4. Everything is generated from its contrary, and is destroyed into its contrary.

5. A body falls with a speed that depends on the quantity of matter it has. (He really ought to say "moves with its characteristic motion".)

From these assumtions, some conclusions follow:

If there is such a thing as circular motion, there must be an element whose natural motion is in a circle. Circular motion has no contrary (as does up/down), so the element whose motion is in a circle must be different from earth, air, fire or water, and must be part of the heavens rather than part of the earth. Motion in a circle must be uniform and eternal, because a circle is perfect.

It also follows that the thing that moves in a circle has no contrary, so it cannot have been generated, thus it must be eternal. It also follows that the heavens must be perfect and eternal, and different from the earth.

This is not exhaustive, but it will, I think, give you a flavor of Aristotle's way of thinking, and of the world that Galileo found himself in.

Aristotle's view of the heavens was intellectually satisfying in its time, but it didn't do anything for the astrologers, who needed to be able to calculate the positions of the planets at specific times in the past, present, and future. In the second century CE, the Egyptian astronomer Claudius Ptolemy published a work now called the The Almagest (a corruption of the title by which it was known in its Arabic translation). Like many manuscripts, this was lost early in the Christian era, and kept alive only by Arab scholars.

The problem with constructing a mathematical model of the motion of a planet is that most planets mostly move east to west across the sky, as does the sun, but sometimes move backwards (this is known as "retrograde motion"). Mars, Jupiter and Saturn behave in this way, but Venus and Mercury always stay close to the sun. Planets move at different speeds at different times, and vary in brightness. To model this, Ptolemy started with the earth in the center of a circle. To get retrograde motion, he put the actual planet on a small circle (the "epicycle") . the center of the epicycle is what moves uniformly on the circle around the sun. With proper sizes of circles and speeds of motion, you get an approximation of the planet's motion. For better accuracy, Ptolemy moved both the earth away from the center of the circle, and also put the line to the epicycle off center. Diagrams are in this article. This fudging away from the center kind of violated Aristotle, but nobody minded much, at least at first.

In Galileo's time, Aristotle's philosophy was seen through a filter of Christian dogma. This was due mainly to St. Thomas Aquinas. Early Christianity knew only the philosphy of Plato, mainly through neoplatonism, as espoused by St. Augustine. Around the year 1100, Aristotle's writings began to appear in Europe, as translations into Latin from Arabic. Thomas tried to merge Christianity with Aristotle, with results that were not totally satisfactory. The main problem was that there were things in Aristotle that contradicted Christian doctrine. For example, Aristotle said, as we've seen, that the universe is eternal and unchanging. Unchanging is OK, but eternal is not: The Church taught that the universe had a beginning, at the Creation, and will have an end, at the Last Judgement. More serious, probably, were differences on the nature of the soul.. In 1277, the Bishop of Paris, charged by the Pope to investigate rumors of heresy at the University of Paris, condemned 219 propositions as heretical. Many of these were derived from Aristotle, some by way of St. Thomas. Many historians consider this to be the beginning of the split between theology and philosophy.

We are now sort of at the end of the preface to modern European thought. Next up: Copernicus.

History Through Its Own Eyes

2004-06-07T08:16:00.000-05:00

I want to include a lot of history in these essays. It's more a personal interest than a necessity, though. Many things, from human anatomy to the structure of U.S. presidential elections, make sense only if you know where they come from. Science, though, is not always like this. Each of the physical sciences, physics, chemistry, and astronomy, has its own set of theoretical principles. Chemistry and astronomy use ideas from physics, applied to different areas of nature. They are all to some extent the same science, though, so you have subjects like physical chemistry and astrophysics. The basic principles are often called by the name of the originator, but often the principle doesn't depend on the authority of the originator. On the other hand, the social sciences, psychology and sociology, often tend to identify with one or another individual.

Biology is somewhere in between. Darwin tends to dominate evolutionary thinking, but biologists don't cite Darwin as an authority in the same way that anthropologists cite individuals. Much of the thinking in developmental biology (our main concern here) is based on chemistry, so there is less room for individual opinion. Living things are complicated, though, and there are lots of things that biologists would like to know but can't figure out all at once. So there is room for individual opinions. Issues that involve populations of organisms are often murky; the debates over punctuated equilibrium and sexual selection are examples.

In studying the history of science we have to be careful to avoid what some historians call "Whig history". The Whigs were a political party in England (and in the U.S. until 1856). They were supporters of the English constitution, and tended to view history in terms of their own beliefs. In the history of science this view interprets history in reference to an up-to-date science textbook. Greeks who believed in atoms are heroes, those who didn't are stuck-in-the-mud. For example, Janet Browne, in her biography of Charles Darwin, talks about Charles Lyell, whose geological theory influenced Darwin's thnking:

Lyell turned history to his advantage by giving a long and cleverly argued account of the course of geological endeavour from antiquity to the nineteenth century in which everyone who held the same general idea as he did was praised and the the rest dismissed as "unscientific" in blatantly one-sided style. Like the Whig historians whom he greatly admired, he recreated the history of his subject from the position of the author, not just as one in which the past creaked panifully towards the present, but also as a story in which certain inviolate truhts of nature and liberal principles of thought (as seen by Lyell) were progressively revealed to scholars through the ages.

The problem is that nobody in the past was up to our date in all respects. All scientific thinking happens within a world view, a basic belief in what the world is and how it works. The Greeks who rejected atoms (from the Greek atomos, indivisible) believed that matter could be divided indefinitely. The others couldn't accept infinite division; they believed that there are atoms and the void. Anti-atomists couldn't accept the void, a place where there was nothing.

It is tempting to say that the atomists were on to something, and the anti-atomists were misguided. But atoms as we now know them (or think we know!) came from experiments in which chemists found that elements always combined in definite proportions, which implies that there are particles involved. (Of course we also "know" that atoms are actually divisible into elementary particles, which are themselves composed of quarks.) (The "think" and quotes will be explained next time.)

Usually the world view helps science progress, because it tells you what you can look for. Sometimes, though, it holds progress back. We'll see this especially when we get to Galileo. Occasionally somebody will challenge the world view. If the challenge is successful (which is pretty rare) we call the challenger a "visionary", if not he is a "crank".

Most historians feel that western scientific thought started with the Greek philosophers. Usually we think of Plato and Aristotle, although Plato got many of his ideas from Pythagoras and others.

The world view of the Greeks was enough different from our own that it takes a considerable effort to understand Greek thinking. Benjamin Jowett gives some of this in his introduction to his translation of Plato's dialogue Timaeus.Jowett says that one of the reasons for the obscurity of Greek thinking is that it arose "in the infancy of physical science, out of the confusion of theological, mathematical, and physiological notions, out of the desire to conceive the whole of nature without any adequate knowledge of the parts, and from a greater perception of similarities which lie on the surface than of differences which are hidden from view". Much of what will come in these essays will deal with changes in these aspects.

As one example, Greeks saw that animals move by themselves, and rocks don't. Animals are alive, so the Greeks thought that anything that moves by itself, like a planet, is alive. They also thought in terms of "nature", by which they meant "the nature of a thing". Aristotle believed that there are four elemental substances: Earth, air, fire, and water. A stone is earth, and falls because it is its "nature" to go to the earth. The nature of a rock is to be at rest. Smoke is air, so it is in its "nature" to become part of the air.

Aristotle believed that the planets are carried by crystaline spheres. They have to be spheres, because the only motion that can persist is uniform motion in a perfect circle.

Plato, following Pythagoras, held that "everything is number". This can be taken, in our time, to mean that everything follows mathematical principles. This attitude is an important part of our own world view. The physicist Eugene Wigner, for instance spoke of "The Unreasonable Effectiveness of Mathematics in the Natural Sciences". But this can be a handicap in understanding biology. Evelyn Fox Keller, in her book Making Sense of Life, talks about the ways in which the thinking of biologists is different from that of physicists. (More of that in a later essay.)

Physics and biology look at the world from different directions. Mainly, physicists want to explain the world in as few equations as possible, while biologists want to understand living things. Physicists have a powerful tool, but they pay for it in the limitation to simple systems. The motion of two bodies, for instance the earth and the moon, or the sun and a planet, is explainable. Three bodies are explainable only in special circumstances, such as the Lagrange points. Systems of many bodies can sometimes be explained statistically, as in gases.

Biology is different. All biology is local. Biologists have given up looking for top-down rules for how organisms develop; the organism will surprise you. Eventually these essays will take up these topics in detail.

Biology is organized chemistry, so it follows the laws of chemistry. Chemistry follows the laws of quantum mechanics. So biology follows quantum mechanics. The different thing about biology, though, is that there are a great many influences on a growing organism. A planet will always follow its orbit, because it has only its momentum and gravity. An organism has lots more things, which we'll get into later.

In leaning over backwards to understand the past, though, we have to be careful that we don't fall on our behinds. Some philosophers seem to argue that all knowledge is conventional, and that there really isn't any progress. But we feel confident in saying that the earth moves, and that there is no such thing as phlogiston. Again, more later.

Browne, Janet. Charles Darwin: Voyaging, A Biography. Princeton University Press, 1995.

Two Explanations

2004-06-04T10:53:00.000-05:00

I want to explain two things about this blog: The title, and the epigraph.

The title, "If Darwin Were Alive Today...", comes from discussions on ARN (see the previous entry). There is much talk on both sides about "Darwinism". But Darwin wrote almost 150 years ago. Some of his ideas are still valid, some aren't. In particular, Darwin didn't know the source of variation. His basic theory was that organisms vary in heritable ways, and that those variations that promote survival will be passed on to the next generation. (It's more subtle than that, but that's for another time.) My main (but not necessarily exclusive) topic in this series of essays will be the ongoing disoveries in individual development, and the ways in which development can vary.

This leads to a distinction between "narrow-sense" Darwinism and "wide-sense" Darwinism. Narrow-sense Darwinism is the explanations in Darwin's writings. This includes the six versions of On the Origin of Species, but also the rest of his works. In the Origin Darwin claimed that the book was "one long argument"; Stephen Jay Gould argued that Darwin continued the argument in the rest of his writing.

Getting now to the title: I suggest that, given the depth and breadth of Darwin's interests, if he were alive today, he would be intensely interested in the developments I'll be talking about. So wide-sense Darwinism includes all the discoveries of modern biology and paleontology, including things that Darwin couldn't have dreamt of.

Of course he might get into the specialization trap; see the previous post. This kind of breadth, I suspect, is for someone who already has tenure.

The second explanandum, the epigraph, is "Nothing in evolution makes sense except in the light of biology". This is a play on an the title of an essay by Theodosius Dobzhansky, one of the founders of evolutionary genetics. His title was Nothing in Biology Makes Sense Except in the Light of Evolution, arguing that biology as we see it is the result of its history, and has features that can be understood only if we understand where the features came from.

My epigraph comes from the conviction (not mine alone) that the variations that provide the raw material for evolution can be understood only in the light of the processes of developmental biology.

Beginnings

2004-06-03T13:09:00.000-05:00

For the last few years I've been a semi-regular contributor to the discussion fora on the Access Research Network, an organization for the study of Intelligent Design. (Click on "discussion forum".) About half of the participants are supporters of ID, the rest are skeptics. One of the difficulties I perceive in talking about ID vs. evolution is that there is a pervasive misunderstanding of what Darwinism is all about. "Darwin Deniers" argue that random mutation followed by natural selection ("RM+NS") is not sufficient to explain the biological world as we know it. (ID doesn't seem to offer much in the way of explanation either, but that's a different subject.) What saddens me is that "Darwin Defenders" seem to accept the RM+NS formulation.

Darwin's theory relied on variation followed by natural selection. He didn't necessarily believe that the variation was random; that was a contribution of the "Modern Synthesis", combining Darwin with the findings of Gregor Mendel.

Cutting this a little short for now (so that I have something left to talk about): Evolution today is very different from what it was only a few decades ago. The revolution is largely the result of the rise of developmental biology, which is a merging of classical embryology, molecular biology, and the enormous amount of genetic information gleaned from the study of fruit flies (Drosophila melanogaster, for the nerds). This is something of a revolution in evolution, but few people seem to be familiar with it. So I am starting this blog, in which I hope to be able to describe the New World as I see it.

My undergraduate degree is in physics, followed by education in business and in software. I am almost entirely self-taught in evolution-related subjects. Evolution is the central organizing principle in astronomy, biology, and geology (to take them in alphabetical order). Part of the problem is that in order to get tenure in any of these subjects one has to go deeper and deeper into one of the many sub-branches of just one area. ("A specialist is someone who learns more and more about less and less, and winds up knowing everything about nothing.") Stephen Jay Gould wished that paleontologists knew more biology; some developmental biologists argue that evolutionary biologists should know some paleontology. I have never had a professional need to go deeply into any of the relevant subjects, so I have the luxury of being shallow in several. I'll try to tie them together for you.

Of course I get my information from other people -- books, journal articles, even other blogs :-) -- so I will probably misunderstand sometimes. Expert criticism is welcome.

So, the adventure begins.