Wednesday, December 21, 2005

Evolutionary Biology and Charles Darwin

There will probably be another court case in the United States, perhaps two. Michigan and Kansas are looking like real possibilities. Then there are the other countries (Australia, Great Britain and South Africa, to name a few) where intelligent design is gaining some ground. I will be devoting some electrons to the court cases and the intelligent design movement in the time ahead as well as what the entire "Intelligent Design vs. 'The Theory of Evolution'" controversy is really about: the relationship between religion and science. However, at the same time, I would also like to devote this blog primarily to the discoveries in Evolutionary Biology.

There is a great deal which is going on, and the pace promises only to pick up. In 1990, they begun the Human Genome Project. This was completed in 2003. From what I understand, with the technology of today, the same project could be completed within a matter of weeks. With the same technology, we are analyzing the genomes of other species, and thereby coming away with a clearer understanding of the phylogenetic relationships which exist between them, or for that matter, a better understanding of the role of various genes and regulatory DNA. Moreover, there are the many different theories within Evolutionary Biology and even entire new branches of science, such as "Evolutionary Developmental Biology," which is usually called by its shorter name "Evo Devo." (There really isn't any "The Theory of Evolution" anymore -- when someone uses that phrase, the most charitable interpretation usually is that they simply don't know what they are talking about.) There is also our deepening understanding of the role of viruses (particularly retroviruses) on the evolution of life itself, and our growing understanding of how life itself originated.

However, it seems appropriate at this time to honor the fellow who started this all, so I will be adding a link to The writings of Charles Darwin on the web."

Links on Kitzmiller v. Dover

He beat me to it!

Wesley R. Elsberry has posted Waterloo In Dover: The Kitzmiller v. DASD Case links to major resources regarding the case at Panda's Thumb. They are in a sidebar. The main post itself begins with the conlusion to the decision handed down by Judge John Jones III. I will undoubtedly be reading the whole thing (139 pages) over the weekend, but from what I have seen so far, it is both unsparing and definitive.

One of the earlier articles to appreciate the historic importance of this decision appeared overseas in the Guardian Unlimited (UK):

"Yesterday's verdict concludes a trial that was seen as the most important legal review of science and religion since the 1920s. It arrives at a time when the teaching of evolution is under attack in school districts from Georgia to Kansas and when the school district in Dover was seen as the cutting edge of a new effort by the religious right to inject its views into America's state school system.

"Judge Jones's verdict was ambitious in scope, dealing not only with the actions of the Dover school district but also with the very notion of 'intelligent design', an idea which surfaced 15 years ago following the failure of earlier efforts to introduce traditional biblical creationism in public schools."

US judge bans intelligent design from science lessons
Suzanne Goldenberg in Washington
Wednesday December 21, 2005

For a good overview of why the trial turned out this way, you might try:

Kitzmiller et al versus Dover Area School District
a report by Burt Humburg & Ed Brayton
Date: December 20th, 2005

Tuesday, December 20, 2005

The Kitzmiller vs. Dover Case, 20th of December 2005

The decision in the Kitzmiller vs. Dover Case is out.

If you are unfamiliar with the case, Dover Area High School administrators would read aloud, at the beginning of biology lessons on evolution the following statement stating that evolution is only a theory, not a fact:

"The Pennsylvania Academic Standards require students to learn about Darwin's theory of evolution and eventually to take a standardized test of which evolution is a part.

"Because Darwin's theory is a theory, it continues to be tested as new evidence is discovered. The theory is not a fact. Gaps in the theory exist for which there is no evidence. A theory is defined as a well-tested explanation that unifies a broad range of observations.

"Intelligent design is an explanation of the origin of life that differs from Darwin's view. The reference book, 'Of Pandas and People,' is available in the library along with other resources for students who might be interested in gaining an understanding of what intelligent design actually involves.

"With respect to any theory, students are encouraged to keep an open mind. The school leaves the discussion of the origins of life to individual students and their families. As a standards-driven district, class instruction focuses upon preparing students to achieve proficiency on standards-based assessments."

This task fell upon the administrators because it was something which the teachers refused to do.

One of the more important highlights of the trial was the uncovering of the fact that the intelligent design textbook "Of Panda's and People" had been a scientific creationist textbook until the Edwards v. Aguillard in 1987 which ruled that scientific creationism could not be taught -- soon thereafter, the words "scientific creationism" were replaced by "intelligent design" almost as if by a word processor. This came to light in the discovery phase. During the trial, this was a key part of Barbara Forrest's testimony.

In today's decision, Judge Jones stated that the key issue is, "whether Intelligent Design is science," and, "we have concluded that it is not." Speaking of Intelligent Design, he said, that it "cannot uncouple itself from its creationist, and thus religious antecedents."

For the entire ruling, please see:

Friday, December 16, 2005

Panda's Thumb on Abiogenesis

Mat Brauer at Panda's Thumb has brought up a subject yesterday which is especially close to my heart: abiogenesis, that is, the origins of life. (Carl Zimmer has covered aspects of this before, particularly with reference to recent experiments relating to the RNA world. I am including links to the Zimmer articles below. Similarly, I will include a link to a post from evolgen which is closely related to the Zimmer articles.) A fairly good conversation has ensued discussing various aspects of the problem of the origins of life. I will no doubt be mining some of the references for additional material, but for the time being, if this is something which is of interest to you, please check it out.

Incidentally, you might also want to look at the following:

Abiogenesis from EvoWiki

What Came Before DNA? DISCOVER , JUNE 2004 by Carl Zimmer

Getting Closer To Life's Dawn, by Carl Zimmer September 02, 2004

On the origin of life, by RPM at "Evolgen," March 09, 2005

Life's Origins Were Easier Than Was Thought, September 16, 2005

Project on the origins of life launched
Harvard joining debate on evolution, By Gareth Cook August 14, 2005

NSF Grant Awarded to SFI to Study How Life Emerged on Earth, October 18, 2005

Wednesday, December 14, 2005

Recent News on Human Evolution

Subject: new material on human evolution at The Loom, Evolgen, and Panda's Thumb!

Before getting to the really interesting stuff, I should let you know that I plan on doing essays, and typically they will be somewhat long, maybe 1400 words or so. I started off with three different essays, and I will try to keep it to perhaps one a week, will try to insure that each essay will have some real gems for links. Oh, and if you are looking for some ideas for some of your own essays, you might check out the links on the right side of the main page of Evolving Perspectives.

In any case, there has been a fair amount of news regarding human evolution recently. (I am not going to cover the brain at this point, but simply the evolution of the human species.)

One of my favorite authors is Carl Zimmer. Just today he put up a new essay entitled Tree or Trellis. He just attended a panel by the American Anthropology Association on the topic of "Updating Human Evolution," and "Tree or Trellis" focuses on some of the recent results. Did humanity spread out in several waves emanating from Africa as far back as nearly 200,000 years ago, as Allan Wilson suggested back in the 1980s, or did humanity only begin to spread out much more recently? Well, if what you are looking at are the mitochondria which we inherit only from our mothers (as part of the cytoplasm), then it appears that all of humanity can be traced back to a woman living approximately 200,000 years ago. However, if one looks at the male Y-chromosome which men inherit only from their fathers, then it appears that all men can be traced back to a man who lived only 59,000 years ago. (Why is there such a difference? You may want to check out one of Carl Zimmer's earlier articles: Adam and His Eves. The clue, of course, is in the title.) But different genes will tell you different stories, and while none of them lie, none of them are telling you the whole truth, either.

More recently, we have come to know that humanity branched off from a common ancestor with the chimps and the bonobos approximately 6,000,000 years ago. Through further genetic analysis, Alan Templeton has been able to bring forth evidence there was a wave of humanity which left Africa much further back than what Wilson's team had suggested: 2,000,000 years ago -- but there have been other major waves -- and our genomes have a very rich story to tell us once we learn how to listen to them. To give another example, by analyzing the retroelements in the human genome, scientists have more recently uncovered evidence that human evolution has undergone several periods of rapid expansion. You may wish to check
'Punctuated' evolution in the human genome, or if you are interested in the technical details, perhaps "Periodic Explosive Expansion of Human retroelements Associated withthe Evolution of the Hominoid Primate" (pdf).

Yet there is more: in "Hooray for Humanzee" RPM tells us that only recently scientists have begun to discover not simply what kind of story the human genome has to tell about human evolution, but what it has to say about evolution in general, and the nature of mutation in particular, both in terms of the fusion of two chromosomes, and in terms of rearrangements of the genome itself which exist in humans today. Mutations -- it seems -- aren't nearly as harmful as creationists might wish you to think.

And this just in: there is a great deal more to find regarding the role of retrotransposons in mammalian, primate and particularly human evolution at the Panda's Thumb today. See: Human Evolution: It’s all in the testes. And yes, there is a very good reason for the title of the Panda's Thumb piece! (Hint: where do retrotransposons come from?)

In any case, you may wish to check out "The Loom" by Carl Zimmer, "evolgen" by RPM and The Panda's Thumb. In fact, you might want to link to their main webpage -- like I have from my main page!

commenting and trackback have been added to this blog.

Tuesday, December 13, 2005

... Deja Vu All Over Again!

On December 15th, the decision that the "evolution is a theory, not a fact" stickers were an unconstitutional violation of the Separation of Church and State will be revisited. For anyone who might have missed the original trial, check the CNN story: Judge: Evolution stickers unconstitutional (Friday, January 14, 2005 ) . However, is this really that original? Nick Matzke at Panda's Thumb began to wonder, then did some digging into the newspapers from more than seventy-five years ago...

Thoughts on the Intelligent Design Inference


One of the more psychologically powerful arguments against evolution by supporters of intelligent design and other creationist groups is based upon the so-called "design inference." Simply put, the idea is this: if one looks at a given organism, in certain respects, it resembles a machine in which the parts work together to perform some function. And just as we can look at a machine and infer that there was someone who either made or designed that watch, so we should be able to infer that there was an intelligence (God, or if we wish to be more vague, "the intelligent designer") who made the organism. As such, this is an argument from analogy.

Part I: Design and the Appearance of Design

For example, Young Earth Creationist Kent Hovind will often bring up the subject of his Casio watch. He will rattle off a list of its functions, which include storing 150 phone numbers, acting as a calculator, and performing the function of a countdown timer. Thus when he visited Japan, even though he never met the individual, he was "pretty sure" that there was someone in the country who had "made" the watch, then by analogy argue that the complexity of life could not have been the result of any natural process, but had to be created by God.

Likewise, he and other individuals who appeal to some form of the design inference would argue, if one takes a look at the eye, the heart, or the hand, these have the appearance of having been designed. For example, the eye has a lens with which to focus light, a retina which acts like film in receiving light, a mechanism exists for focusing on objects both near and far (in this case, muscles which adjust the shape of the lens), and the iris acts as a mechanism for adjusting the amount of light which the retina receives. So in various ways, the eye is comparable to a camera, albeit one that has developed as part of a living, growing organism, rather than being constructed by someone who makes cameras.

However, Michael Behe typically prefers to apply this argument at the molecular level:

"The resemblance of parts of life to engineered mechanisms like a watch is enormously stronger than what Reverend Paley imagined. In the past 50 years modern science has shown that the cell, the very foundation of life, is run by machines made of molecules. There are little molecular trucks in the cell to ferry supplies, little outboard motors to push a cell through liquid." (Michael Behe, "Design for Living," NYT February 7, 2005, Late Edition - Final, Section A , Page 21, Column 1)

But as many evolutionary scientists would argue, the appearance of design can be deceiving. For example, when Perceval Lowell looked through his telescope, he thought that he saw canals on Mars. And more recently, one photo of a rock formation on Mars looked almost unmistakably like a human face. Yet upon closer examination, the "canals" were simply geological patterns in the surface of Mars, and the apparent face on Mars looked nothing like a human face when viewed from another angle. In response to what Behe describes in terms of the internal workings of a cell, such scientists could easily argue that Behe is stretching the use of analogy well into the realm of metaphor.

For example, "trucks" do not walk around on two "legs," but this is precisely what myosin -- one of the transport mechanisms within the cell -- does -- while transporting intracellular supplies along suspended "fiber" highways of actin. Nevertheless, analogies between the artifacts of man and the organisms of nature seem warranted -- yet they immediately raise the questions of what sort of analogies should be drawn, and what sort of conclusions arguments from such analogies can properly support. Indeed, a better analogy for myosin would be that of workers carrying supplies while walking around under water on two legs, wearing magnetic boots which adhere to the suspended sidewalks they follow -- but I doubt that such an analogy would take us in quite the direction that Behe might want.

There are of course times when something clearly looks designed. To take an example which both Hovind and Behe are particularly found of, if someone looks at Mount Rushmore, even without knowing any of its history, one can "see" that it was designed. It in no way looks like it could have been the product of volcanism, plate tectonics, or erosion. It is a sculpture -- which was clearly made and designed by someone. But making this judgment in the absence of actual knowledge of its history, we would be relying upon our knowledge of other sculptures, statues, or wood carvings. We would be relying upon our knowledge of what humans are capable of doing, and would be able to suggest the means by which they did these things. This contrasts sharply with the so-called Intelligent Design theory which prefers to remain silent on the actual nature of their "Intelligent Designer" and the means by which he (it?) brought into being his designs. Yet this is exactly the sort of explanation that any scientific theory of "intelligent design" would be required to give.

Part II: A Division of Tasks

When Hovind cites Mount Rushmore as being analogous to a living organism in requiring someone to make it, there is already one problem simply in terms of Mount Rushmore itself: while it had a single designer, it did not have a single maker. There were teams of individuals who carved Mount Rushmore out of rock. There was a division of labor, albeit of a relatively simple sort. And if oblivious to this fact, one were to posit a single human maker, he could not be any ordinary human in possession of the technology which existed at the time. Either the technology being used by such a human would have had to be very advanced, or the human would have had to be some sort of superhuman -- with an extended lifespan or the ability to work very, very quickly. But this would be by no means the simplest solution which fits the facts: positing a team of sculptors using the technology available at the time (including dynamite) would -- and indeed, this is what we know to be the case, given historical records and personal accounts. Mount Rushmore is the product of a division of labor between ordinary human beings in possession of technology which was quite common place at the time of its construction.

There is another argument which both creationists and proponents of Intelligent Design will often make -- that expecting random evolution to arrive at a living organism or cell is like expecting a tornado ripping through a junkyard to produce a commercial passenger jet. But this argument is flawed on several levels. First, it omits any consideration of the actual pathways which produce proteins, cells, or living organisms. Second, it is an argument which assumes that evolution must finish its job in one miraculous fit of action, rather than performing things incrementally, over time. And third, while recognizing the role which evolution grants to random mutation, it completely ignores the role played by natural selection.

When mutations occur in living organisms, one should expect only those mutations which have little effect or a beneficial effect to get passed on to the next generation. And most genetic mutations have no effect. In omitting the role of natural selection, opponents of evolution set up a straw man who by design won't fight back. (Interestingly, when Behe tried to write an academic paper purporting to demonstrate the inadequacy of evolution, one of the first criticisms leveled against it by a peer was that it omitted the role of natural selection.)

Looking back at Kent Hovind's watch, he would be hard-pressed to find its maker. The problem is similar to that involving Mount Rushmore: just as there wasn't any one person who made Mount Rushmore, there wasn't any one individual who was responsible for creating Mr. Hovind's Casio watch. There was a division of physical labor, with some people being responsible for the shaping the metal which went into the casing, others being responsible for the glass, others being involved in the creation of the wires, and still others being involved in the creation of the silicon computer chip. Then there were the many groups of individuals responsible for mining and processing the raw materials which went into each of the components that ultimately went into the production of the watch. And along the way, there were many machines which were themselves the product of a great deal of physical labor and still other machines used to produce them. In the modern world, if one were to try and trace everything that went into making a single watch, the web of products, services, and people may very well extend out until it includes a significant fraction of the global economy itself.

But of course, there wasn't just a division of physical labor in the production of the watch, but a division of cognitive labor as well. There was the individual who designed the watch. There were individuals who knew how to run the machines and create the various components, and there were individuals who designed the components, and there were still other individuals who designed the machines. Thus when a Young Earth Creationist or proponent of Intelligent Design theory tries to argue for the divine creation of things in the biological realm by analogy with products created in a modern economy, if one follows the analogy through, it begins to lead in a direction which they would likely find undesirable.

For an individual to create a modern, industrially-manufactured watch, such an individual would have to have talents far in excess of those possessed by anyone alive today. Simply in terms of all of the knowledge which ultimately goes into design of the machines which are involved, such an individual would have to be a genius the likes of which this world has never seen. But even in the absence of anyone remotely fitting such a description, watches get made, for a modern economy breaks up the tasks which go into the creation and design of its products into manageable units and then assigns these tasks to people who are capable of performing them.

Part III: Running the Watch Backwards

One should also remember that the modern economy isn't something which simply sprang into being like Athena, fully-formed from the head of Zeus: the modern economy is the product of a long history of evolution, beginning with various primitive barter economies, then growing with the extension of trade, specialization, and innovation stretching across nearly ten thousand years of human civilization. At each point in which economic progress was made, the physical and cognitive labor was divided into manageable units, and there were individuals who were equal to the physical and cognitive tasks required of them at the time. Thus some people designed sundials and abacuses, later others designed mechanical watches and slide rules, and still later others designed early electronic watches and calculators, and along the way, many other needed technological improvements were made. Similarly, those who design or use the machines employed in the manufacture of various products must be viewed as largely products of their time and consequently of times past, having available knowledge accumulated over centuries. For example, those who design pieces of electronics are may very well be making use of algebra, calculus, principles of electrical engineering, chemistry, the theory of electromagnetism, and perhaps even quantum mechanics, where each of these fields no doubt had a great many contributions from a great many of other minds scattered throughout the centuries.

Now imagine that one were to gradually break-up the cognitive and physical labor even more finely in space and time. The tasks which people would have to perform would become increasingly dull and monotonous. But the more one broke up the tasks, the less that would be required, both physically and intellectually of the people performing the tasks, until at some point, no intelligence at all would be required anywhere within the economy at any point in its history. At some point, instinct might be enough, but breaking it up a little further, perhaps only autonomous functions. Breaking it up even further, all that would be required is simple trial-and-error, with errors getting eliminated by natural selection. Simple "innovations" which fail become dead-ends, and those which succeed live until the next minute or day. At this point, we have something which is in many ways quite analogous to the history of the evolution of life on earth -- with the main difference being that in the case of biological evolution, there is typically no distinction between the worker and the tools which the worker employs, and the central purpose of the worker's actions is not to earn money at some business, but to live until the next day, month, or year -- and ultimately reproduce.

There exists between many of the things which are the result of biological evolution in the natural world correspondences to things which are the result of technological evolution in the human world. An eye resembles a camera, and likewise, many of the mechanisms within an organism or cell often resemble machinery. These are cases of parallel evolution, much like dolphins and fish, birds and bats, or in the human world, the nearly simultaneous invention of the phone (by Alexander Graham Bell and Elisha Grey) or discovery of calculus (by Isaac Newton and Gottfried Wilhelm Leibniz), or the sonar employed by bats, dolphins, and submarines. In arriving at solutions to the problem of survival, nature is faced with many of the same sets of engineering problems faced by human engineers who design machines. And given the similar sets of problems and design constraints, one can often expect similar sorts of answers. Looking inside the cell, we see a kind of nanotechnology which is still several years or decades ahead of what we can accomplish. But given the design constraints, when our technology becomes more advanced in this area, we should see even more similarities between our nanotechnology and what nature has already achieved.

In Conclusion: The Design Inference -- Properly Understood

When someone argues by analogy that just as the complexity a watch implies a watchmaker, so the complexity of life implies either the existence of a god or more vaguely, an intelligent designer, there are many who will find such an argument fairly compelling. However, the analogy upon which this argument is based immediately breaks down for a number of reasons. First, we know that watches do not reproduce -- they are not biological organisms. But biological organisms do reproduce. Second, we know that humans exist, and that humans make these sorts of things. But we do not know that there exists anything which makes living organisms -- unless it is by means of reproduction. And if by "make," the individual who is putting forward the argument means something other than by means of reproduction, then his argument begins to look suspiciously circular.

However, there are even more problems with this argument once one begins to carefully examine how a watch is specifically made -- even before one gets to any kind of analogy. The analogy itself is intended not simply to argue for the existence of someone who made living organisms, but who is also exceedingly intelligent. But virtually any manufactured good, if created by a single individual, would imply an intelligence far greater than anyone who has ever lived. Nearly any manufactured good that one can think of is in one way or another the product of a division of physical and cognitive labor, and in this sense, is properly viewed as the creation of not one maker or designer, but of a long list of individuals stretching across the globe, and back to the dawn of civilization -- and even before that. And given this division of labor, while some of the individuals involved were undoubtedly geniuses, all of them were quite human. Moreover, one would in fact be hard-pressed to suggest a human artifact which is simple enough to have been designed by an individual without employing the division of physical and cognitive labor.

The complexity of a watch or other manufactured good which the arguer casually explains by reference to its maker or designer is itself the product of two fairly interdependent evolutionary processes: the growth of human technology and the growth of human knowledge. And just as a division of labor reduces the degree of intelligence required of anyone involved in the production of a manufactured good, so may a further division of labor reduce the degree of intelligence even more in the production of something exceedingly complex -- even to the point at which no intelligence would be required anywhere at all. Those who make use of the design inference to argue for an intelligent designer also seek to deny that the complexity of life can be explained by means of evolution, but when properly understood, their argument strongly suggests the very opposite is the case.

Monday, December 12, 2005

Religion and Science

The religion vs. evolution debate has broken out once again, and certain groups are trying to get their religious views into high school classrooms -- this time in the thinly-veiled form of "intelligent design," a broad tent where young earth creationists, old earth creationists, and people who simply prefer to remain more abstract can join together in common cause. In an online discussion devoted to the issue, one individual said that he couldn't really understand what the controversy was about. He argued that if God is omniscient, omnipotent, exists outside of the world He creates, and expects us to believe in Him through faith alone, then surely He would not have left any traces in His creation which would provide an empirical alternative to that faith. Viewed this way, the world discovered through science -- including evolution and the big bang -- is simply the divinely opaque means through which God created the world we now see.

I agreed. Properly understood, there is no conflict between religion and science: each deals with different human needs (and for some people, philosophy may satisfy the same needs that religion serves for others). The realm of empirical knowledge belongs to science, whereas religion ministers to the need for normative guidance. The question of whether or not God exists lies beyond the realm of empirical science, and properly belongs to religion and philosophy. Many scientists (including a good number of evolutionists) are in fact religious -- they simply do not let their religious views interfere with the quest for empirical knowledge. (For one example, see the "Science and Religion" interview with Kenneth R. Miller.) Properly, scientists will respect these beliefs of their religious colleagues, realizing they may very well provide those colleagues with the moral guidance which makes them better scientists. The importance of moral guidance, and, more specifically, the moral courage to deal with the ever-present possibility of failure in both the existential and cognitive realms, is not to be underestimated.

In the existential realm, religion properly provides the individual with the moral courage to act despite the possibility of failure, where failure can sometimes mean the possibility of actual death, and the fear of failure itself can often be experienced as such. Likewise, the fear of being mistaken -- where being mistaken may threaten our beliefs about who we are -- is at times experienced as a threat much like death itself. Here, too, there is need for moral courage, although of a somewhat different kind. Properly, religion encourages in its own way the view that while recognizing one's mistakes may be experienced prospectively as a form of death, the act itself brings a form of rebirth and self-transcendence, giving one the courage to revise one's beliefs when confronted with new evidence.

However, when people attempt to mix the realms of religion and science -- attempting, for example, to use science to promote a given religious or philosophic view -- in the long run, given the very nature of the relationship between religion and science, the results will be the reverse of what is intended, and may end up damaging what in fact they hold most dear. For example, a proponent of science who believes that faith in God is absurd in the age of Science may end up creating a religious backlash against science itself among those who take a different view. But properly, empirical science cannot speak of the metaphysics of that which lies beyond the empirical realm and the ontology required by its naturalistic explanations.

Alternatively, those who attempt to use science to prove the existence of God will end up with a God susceptible to empirical criticism, when belief in God should be a matter of faith. A religious view rooted in science will be grounded in the shifting sands of scientific discourse, placed in constant threat of being uprooted by the newest scientific discoveries. For the better among those who initially accept this substitute for true faith, such a view will at first seem intoxicating, but will soon prove poisonous to their religious beliefs.

For others, the proper religious stance becomes transformed, and the proper intellectual courage to revise one's beliefs when confronted with new evidence is transmuted into its polar opposite. Intellectual "courage" becomes the will and the power to challenge, doubt and deny any body of empirical evidence or knowledge whenever it comes into conflict with their religious or political beliefs. At this point, one of the most fundamental ethical virtues -- honesty -- has itself become undermined, and with it all the virtues which would normally be encouraged and taught through the moral guidance of religion. Properly, religious leaders who understand what is at stake will oppose "empirical" faith both for the contradiction which it embodies and as the antithesis of the true faith they seek to protect and nourish.

When properly understood, this unnecessary conflict between religion and science will be consigned to the oblivion it so richly deserves. Yet more could undoubtedly be done so as to avoid such misunderstandings and consequent conflicts in the future. Science has been and continues to be responsible for a great deal of humanity's material and intellectual progress. Religion is responsible for humanity's moral and spiritual guidance. The roles they serve are complementary and to a significant extent in today's world, interdependent. Religion and science each have their own inner dynamic, but religious and scientific communities share a common concern for humanity as a whole. If religion and science are to perform their proper functions in human society, they must remain separate, with their fundamental natures respected. But still there can be dialogue.

Some time ago, Pope John Paul II visited with biologists to discuss evolution and then ended official Catholic Church opposition to evolutionary theory. This was a good beginning, but unfortunately there wasn't much follow-up. If a dialogue were to begin between the religious and scientific communities, one born out of mutual understanding and respect, such a dialogue could serve the interests of both communities and perhaps even the interests of humanity as a whole. As one interesting possibility, a scientist of the same denomination as a given church might occasionally make a good guest speaker, particularly if he were to discuss the role that religious belief has played in his life and work, and he were to share a few of the more interesting, recent discoveries in his particular field.

In a sense, such religious scientists might serve as bidirectional ambassadors between the two communities, and would deserve honored places within both. If properly promoted, such guest speakers might help to boost church attendance, particularly if they are good speakers. And perhaps when church services are not being held, churches could make available rooms where scientists could discuss their work with the public, and even their concerns for some of the problems which currently face humanity. This could also serve as good public relations for the religious and scientific communities as a whole. I myself do not know where a dialogue between these communities would lead -- this would be up to the participants. But I have little doubt that it could become quite interesting and enlightening for everyone involved.

Sunday, December 11, 2005

In Defense of Evolutionary Science

(I wrote the following on Saturday in response to a creationist opinion piece in the newpaper "The Ithaca Journal." His letter is fairly typical of what you will often find in newspapers.)

This is in response to Harry Lockwood's "Evolution isn't Science" of Dec.10th, 2005.

The process of evolution is one of the most well-established discoveries of science today. Our knowledge of this process was originally built upon the existence of a hierarchy of categories of animals classified according to their similarities, the fossil record and embryology (all of which involve the "systematization of knowledge derived from observation") but, unlike stamp-collecting, reaches beyond what has simply been observed to arrive at causal explanations, make predictions, and meet the test of experience as empirical science always must.

Given the similarities which exist between fish and reptiles, reptiles and birds, and reptiles and mammals, land mammals and whales, transitionals were predicted which would show a mixture of attributes from the older, more ancestral form to the latter. In each case, a series of transitionals existing at different steps in the right chronological sequence along the suggested paths were found, including a creature which was half way between having a reptilian jaw and a mammalian jaw (something creationists declared impossible) -- bearing a double-jointed jaw which worked.

Today we are able to observe the evolution of viruses and bacteria. We are able to modify their environment and see how species evolve in order to adapt to it, how they acquire resistance to antibiotics. In the mid-1980s, Hall removed three different genes from a single bacterium which were necessary for the digestion of lactose, whose descendants then re-evolved genes for such digestion through a process of stress-induced hypermutation and natural selection. A similar process of hypermutation and natural selection is involved in our own adaptive, B-cell based immune system which responds to new pathogens. Those who declare evolution through mutation and natural selection impossible owe their very lives many times over to the simple fact that such a process is possible and that it works.

Lockwood invokes the Second Law of Thermodynamics (without naming it) which tells us that the disorder within a closed system will never decrease. What he does not realize is that the earth is not a closed system. Order may rise out of chaos like a storm growing at sea. Organisms can grow and multiply, and species may evolve and branch into new species -- because this increasing order is more than balanced by the energy released in the process through which the sun consumes itself.

He argues that virtually all mutations are harmful, failing to realize that such harmfulness can occur in degrees and is relative to the genes which already exist in genetically diverse populations due to earlier mutations and genetic drift. Natural selection will eliminate the more harmful mutations, and what may have been slightly harmful in one context could be quite beneficial in combination with other genes or within later environments. Natural selection does not eliminate all but the fittest, but acts like gravity upon a fluid pool of genetic diversity which has the capacity to flow somewhat randomly due to the local currents of genetic drift, but in the general direction of greater adaptation.

Evolutionary biology is a strong yet growing branch of empirical science supported by a vast body of evidence which is growing at an ever-increasing rate. For example, we are able to identify the proviruses left by retroviral infections tens of thousands or even tens of millions of years ago in the genomes of many different species (30,000 in the human genome alone). When we compare the vast genomes of different species, we find that closely-related species have the same retroviral insertions at the same exact points.

This isn't random: the insertions are at the same exact point because the insertions occurred in their common ancestor. Moreover, the diagrams which are constructed strictly on the basis of such insertions match the diagrams based upon the evidence which existed prior to any knowledge of viruses or DNA. Nevertheless, such insertions provide us with far more precise and detailed knowledge than was available before. Similarly, closely related species will often share the same broken genes ("pseudogenes") which are broken in the same way -- such as chimps and humans whose ancestors lost the ability to produce their own vitamin C.

The persistence of creationist beliefs in the face of such overwhelming evidence stands as a monument to an educational system which fails to prepare students for an increasingly scientific world. It stands as a testament to the willful ignorance of those who would prefer Ptolemy's geocentric vision of the solar system over the Copernican if they realized that it conflicted with a blindly literal interpretation of the Bible. Those who wish their children a better future should insure that their young minds are not enslaved by such senile, dogmatic fundamentalism, see to it that the educational system is repaired, and that such well-supported science receives the focus which it deserves.