An Exchange on ID

UPFRONT UPDATE! Complete transcripts of the Kansas State "Science Standards Expert Testimony" have now been posted, as .pdf files (Adobe Acrobat Reader required). Thanks to commenter AR for providing the link.

Chris Hallquist wrote:

On your blog, you have a lot of posts complaining about the dogmatism of evolutionists. There's nothing dogmatic about their behavior however; they act as they do because evolution is by far the best explanation we have for observations of biology and paleontology.

The first part of evolutionary theory is something rejected by some non-scientists in the ID movement, but accepted by every scientist I'm aware of from Behe to Dawkins. It is that all life is descended from a common ancestor. It is supported not only by fossil evidence, but also by the way all life neatly fits into a family tree. Often, when scientists refer to evolution as a fact, they are referring only to this part of the theory.

Then there's the question of how the changes necessary for this took place. No one claims to totally understand them, but the evidence for natural processes like mutation and natural selection is strong. Irreducible complexity at least used to be the main claim to the contrary, but scientists have pointed out that parts of an irreducibly complex system might have formed for another purpose before coming together for the purpose of the larger system. There's excellent evidence this has happened in some cases. Behe seems to have backed off the claim that mere irreducible complexity is enough, and now often brings up systems and asks for a specific explanation, on the premise that if there are even a few such systems that remain a mystery, they must have been designed. You've noted in your blog the problem of filling mysteries with "God did it." Ultimately, what Behe's doing here is no better than UFOlogists who won't accept general explainations of why people see UFOs, but rather insist that every sighting be explained or attributed to extra-terrestrials.

Finally, the behavior of ID proponents is not always a model of scientific discovery. The theory of continental drift is not accepted because Alfred Wegener ran a political campaign to get it taught in schools. It is accepted because later discoveries turned an implausible sounding theory into one with an established mechanism (plate tectonics) that explains many observations. Scientists get justifiably agitated when ID proponents focus more on the political campaign over making discoveries.

amba relied:

Thanks, Chris. Note that I'm not a dogmatic ID'er nor do I defend everything they do and say (mainly, where are the scientific experiments??), but as someone who had naïve questions about the Darwinian theory (and a pretty good grounding in science for a layperson) before I ever heard of ID, I'm glad they are pointing out the gaps in Darwininan theory. It has become an article of faith for many people, defended with the same irrational ferocity as any other belief. A theory can be defended rationally (as you do) without such defensiveness at questions. I think it's an interesting question why some secularists get so emotional and dogmatic about it. I understand the emotional investment in religion, but what's the emotional investment in chance?! After all, there's so much we don't know. The more we discover, the more we realize lies beyond it.

My own main question about Darwin's theory (it's on the blog somewhere, but kinda lost in the sauce) is, "Is mutation completely random?" That, to me, is where an intelligence, of a kind unknown to us, might be found to operate. But I don't know how you'd test it. Take some species that mutates rapidly on a relatively small, known genome -- Drosophila? some bacterium? -- create, if you could, two identical populations, submit them to very different conditions, and . . . is there any way to see whether the mutations that arise (as opposed to those that are selected for) are non-randomly different in the two groups? Here's where my scientific naïveté kicks in -- I don't know if there's any way to do it.

Comments

[Dave]

For my money, the theory of evolution by natural selection is a beautiful idea, elgant, simple, yet totally confounding to human prejudices about the way the world ought to work. "Intelligent design" is none of these things.

"Chance" is as provisional a construct as "creation," and both are useful ways of describing phenomena, depending on the circumstances. I think it helps to remember that "chance" is responsible for a great deal of development. Consider, for example, the possible variations in form, structure, longevity, etc. for a MacIntosh apple tree, genetically idential to every other MacIntosh ever grown. Why are twins (clones) never identical? To the religious person, nothing really ever happens by chance. But this may mean as little as saying that the world is perfect as it is: a leap of faith at least as profound as any requiring intellectual assent to one or more propositions of a non-intuitive nature.

[michael reynolds]

I think a lot of people are becoming agitated in opposition to Intelligent Design because it's an easier position for them to take than overt atheism. They can argue -- correctly -- that there is simply no evidence of God in evolution, but, I suspect, they shy away from the obvious explanation for this lack of evidence.

I take the position that if there's no evidence that something exists, and if its existence would run counter to what I think I do know, then I move forward on the assumption that the thing in question does not exist. (God, leprechauns, compassionate conservatives.)

There is a mountain of evidence that is highly supportive of at least the broad outlines of Darwinism. But there is no specific evidence within Darwinism that disproves the existence of God. If you want to assume God, you can perfectly easily work him into evolution.

I don't believe you can teach leaps of faith in science classes. You can teach evidence. If -- and I don't know that this is the case -- evolution is being taught in such a way that it extends beyond the evidence, I think that's bad science. I worry that people who feel a need for a God, but cannot bring themselves to a faith in God, may turn those spiritual instincts toward science.

That having been said, I think believers are in a very weak position demanding that science cross every 't' and dot every 'i', when believers advance no evidence at all for their beliefs. You might say that they are pointing out the mote in their neighbor's eye, and ignoring the beam in their own.

Feel free to quote me on that last bit.

[Dave B.]

“I think it's an interesting question why some secularists get so emotional and dogmatic about it. I understand the emotional investment in religion, but what's the emotional investment in chance?!”

To answer your question, I believe the emotional investment of the secular camp lies in the fact that the evolution/ID debate is a proxy for the question: Who is right, believers or nonbelievers? Of course, it’s often more complicated than that, but insofar as human beings like to be right, and the two sides of the debate are really code for “there is a God” vs. “there is no God”, secularists are going to be just as passionate about this as people of faith. The credibility of both camps is at stake.

I’m with Dave that “chance” is not an easily understandable term. It is a loaded concept in the current context, and, to many people, stands for the despair and lack of meaning that await them in a world in which the hand of God is absent. To me, “chance” in the context of evolution really means “something we don’t yet fully understand.” The interesting question is not “Is mutation completely random?” but “If mutation is random, why is it so?” I think it is the possibility that the answer could be “there is no reason” that disturbs you.

I suspect that any attempt to test for the presence of design in mutation will be fruitless. Even if tests did show that some mutations were non-random, it is a big step from that to showing that the mutations were designed by an intelligent being. It could just be that there is an organizing principle at work of which we are not yet aware. That principle might be God, but I don’t think you will ever convince a nonbeliever of that, just as you will never convince a believer that God is not involved.

[michael reynolds]

I would hate to think people couldn't be convinced one way or the other on God. I was.

I've never quite understood why "randomness" equates to "hopelessness." I see my life as playing out in a sort of matrix formed by heredity, environmental influences, free will and random chance. Some things I control, some things I don't. And I am free, within the aforementioned matrix, to decide for myself the meaning of life. And despite this I manage to drag my way through my meaningless existence and, so far at least, have a fairly good time.

[Tom Strong]

I understand the emotional investment in religion, but what's the emotional investment in chance?!

Wow. Interesting question! I'm going to use it as an excuse to ramble semi-coherently!

Richard Dawkins often writes -- not unmovingly, in my opinion -- that evolution is the only theory that explains the birth of intelligence. It's basically a twist on an old skeptic refutation of ID, which goes: "If God created everything, who created God?" (C.S. Lewis, in what is frequently described by theists as his richest argument, argues the reverse: That our intelligence proves God's existence. Right now, I feel inclined to side with Kurt Vonnegut and say that our lack of intelligence, and moreover common courtesy, indicates God's lack of the same).

That said, though Dawkins uses his argument in defense of atheism, I think theists could easily use it to answer that old question: God evolved. Because while chance may be cold and cruel, it also means that eventually, something may come from nothing.

This is, obviously, an argument that freaks many people out. Depending on how you read it, it could suggest that people created God because it was evolutionarily necessary, or that people are becoming God, or that we are God, blah blah blah.

What it means to me, though, is that chance is pretty damn interesting. It can explain the existence of God, in a way that God himself can't. In this sense, it's close to old school religions, such as the Greeks', in which the gods were not creators of the universe, but rather an unavoidable result of its creation. Which, if nothing else, may explain why people like me get drawn to the work of James Hillman and company.

[Larry Kutay]

It seems to me both sides of the debate are unwilling to consider the possibility that life is genetically predispositioned to change. Darwin's theory could be used to explain such a genetic predisposition, and it would explain things like the Cambrian Explosion. On irreducible complexity, Behe's argument is best when he dicusses his forte: the cell. I disagree that one can validly argue all of the essential components of cellular metabolism (and they are numerous at the molecular level) had other uses prior to being incorporated into a single cell in the primordial soup. Run the numbers, evolution can successfully explain the formation of life forms after that event, but not the event.

[les]

A small contention; I don't think that the secularists--more appropriately, scientists, many of whom are religious--have an emotional attachment to chance, per se, but do have an emotional attachment to scientific method being generally rejected by ID, and have a strong emotional response to having the knowledge and, yes, beliefs gained in a lifetime of work and study denigrated by those who have neither worked nor, usually, studied in their areas, on the basis that its too complicated or contradicts a 4,000 year old religious text. I'd be pretty pissed myself.

[sleipner]

ID is NOT science, and can never be science, as there is no way to apply the scientific method to any of its tenets, which are totally unprovable and based on faith alone. Therefore, it has no place in any science class.

The only reason the religious right has backed away from creationism and gone for ID is that the term creationism has been linked to the loonies who think the world is 6000 years old (hmm...what about the Egyptian and Chinese civilizations that were going strong then? When did the dinosaurs live?) and that Homo Sapiens sprang fully formed from the mind of God (so much for Homo Erectus, Homo Habilis, Africanus Australopithecene and the dozens of other hominid species we have found).

The only areas that evolution has not managed to explain at least reasonably well are the process by which the initial "spark" of life occurred on this planet, and certain aspects of how large-scale speciation occurs. And there are theories about those as well - most of which can be sliced by Occam far more easily than "we're not sure how it happened so God must have done it"

It is amazing to me that this has even become a discussion in this day and age...I would have expected it about a century ago, but I would have thought people would be better educated by now.

[michael reynolds]

First, let me say that I'm very proud that we can discuss Homo Erectus without making immature jokes. Next we can take on the matter of the 7th planet from the sun.

On a more intellligent note, Sleipner is right: we began by ascribing everything we didn't understand (100% of the total) to one supernatural cause or another. Over the course of human history the supernatural cause has steadily lost ground. It has never gained ground.

We have never yet discovered an effect which had to be moved from the "natural causes" column, back into the "supernatural causes" column. We have never once had an announcement to the effect that the sun, once believed to be acting in accordance with the laws of gravity, now must be seen as subject to the actions of Apollo in his fiery chariot.

This ought to tell us something. So far in the big game of Science vs. Suprnatural, the score card is millions to zero. So place your bets however you like, but the smart money is on science.

[lynn]

What has long bothered me is this tendency for us to polarize everything into opposing camps: evolution vs. creation, science vs. God, atheists vs. believers, science vs. supernatural.
I have never understood the problem of reconciling the concepts of evolution with the concepts of God.
I think people get hung up with definitions of God and the connotations of religion. First of all, let's get rid of previous preconceptions and be a little open-minded here.
In my mind, the very principles of evolution are the essence of "God". Intelligence exists within the fabric of all living things. Laws of science, the truth of mathematics, the logical structure of music and harmony.....these are all evidence of an intelligence that has had something to do with our existence.

Let me say this in another way: wouldn't the laws of math still exist even if the earth and it's creatures did not? You wouldn't say that the laws of math have been "created", but rather that "they are".
To me, that is the essence of God. God=math; God=science; God=love.

Let's say that you had never seen a computer before, and someone gave you a demonstration of an computerized information system. Would you then believe that person if they told you the computer had spontaneously come into existence through a series of random coincidences? No, you would assume that an intelligent system was created by something with intelligence....that intelligence begat intelligence. Consider the "evolution" of the computer.

We are dangerous because we are so so arrogant. We think because we have done a couple of smart things we know all the answers. We have so much to learn about this wonderful, complex, alive and INTELLIGENT world around us.

For me, I prefer not to stuff my beliefs into someone else's pre-made box. My goal is to remain an enthusiastic inquisitor of life and above all remain open to answers as they unfold. It's when we become convinced of our own "rightness" that we become the most stupid.

[amba]

I'm with Lynn.

[sleipner]

I should clarify somewhat...I have no problem whatsoever with people reconciling their belief system with science and evolution. If you wish, that is your own choice, but do it in the privacy of your own homes and churches, but don't subject the innocent minds of other people's children to your own personal religious beliefs.

The only possible evidence for intelligent design is either thought experiments (which became passe during the Renaissance) and an ancient book that dates from the time when people thought Zeus lived on Mount Olympus and shot lightning bolts out of his butt.

Thus since there is no scientific evidence for ID, and no possibility of ever obtaining scientific evidence for ID, it is not a scientific concept and should never be presented as such, especially in any state-run organization that is supposed to uphold the separation of church and state.

Of course there's always the possibility that when the full human genome is understood we may find that a certain decryption method converts it into "Repent, Unbelievers" over and over again, but I sincerely doubt it.

[lynn]

Sleipner:
I am honestly not familiar enough with all of the tenents of the ID school of thought to proclaim myself a member. I am also not a member of any church. I am not pushing an agenda or a religion here...I simply disagree with your argument.

My point: how can you possibly say that there is no "evidence" for intelligent design?? Isn't the existence of intelligence itself "evidence"?

[lynn]

Sleipner:
I guess I wasn't finished with my comment. And I apologize for singling you out, but I am hung over and a little cranky.

What I think is ironic (and this goes back to the original point about dogmatism) is how so-called "scientists" are just as close-minded, intolerant, and judgemental as the Frists, the Dobsons, and the Falwells of the world.

How dogmatic scientists and the Religious Right are alike:
--they both think they know all the answers
--they are both intolerant to other people's point of view
--they are both arrogant and self-righteous
--because they have stopped questioning, they both have stagnant knowledge

Since we all know the abuses of religion...let's recount for a minute some of the jewels that have given to society in the name of "modern science"...which can all be found in old texts taught at schools as "scientific facts"
--masturbation causes blindness
--men are more logical than women
--black people have lower intelligence than white people
--a good cure for illness is to put leeches on your body
--electroshock therapy
--the earth is flat

In a 100 years I'm sure we will be laughing at all of the ridiculous things our society used to believe back in the old-fashioned 2000's.

So before we start congratulating ourselves for our big brains and the "marvels of modern science"....let's take a minute to realize how dumb we really are.

[sleipner]

I do not say there is no evidence, I say there is no SCIENTIFIC evidence. The evidence for ID, however, is largely either circumstantial or based on perceived (but untestable and unprovable) correlations between observation and belief.

Scientific evidence requires concrete, factual, reproduceable data that backs up the claim you are making. For evolution, there is a huge mountain of evidence from hundreds of sources and disciplines. Some examples are:

Fossils of species that appear as morphological precursors to today's species, and others that occurred before that. The diaspora of species evolution that occurred after each great extinction to fill unoccupied ecological niches. Even extinctions of species being crowded out by better competitors, such as many of the invasive species being transported across the world today is evidence of evolutionary pressures.

Bacteria becoming resistant to antibiotics. Viruses that mutate to avoid the body's immune system response. Weeds that mutate to become resistant to Roundup. Insects that evolve to become resistant to pesticides. These are particularly interesting in that generations are much faster, and hence the progress of evolution is discernable even within a few years.

Contrarily, diseases have also been shown to create evolutionary pressure. Various pandemics in the past have biased populations (both human (the plague) and otherwise) towards those members who have genetic resistance or immunities to those pandemics, and those genetic imprints are now becoming visible as genomes are sequenced.

Genetic analyses can show recent divergence of two species recently geographically separated. Mitochondrial DNA, passed down only through the mother, can show how recently two species shared a common ancestor. Other research is beginning to investigate exactly how and why from a genetic standpoint evolution can and does occur.

Studies of fruit flies and other species where environmental pressures have been artificially maintained have created entirely new species incapable of mating with the original species in a few short generations that is better adapted to the induced environment.

Lab studies simulating early earth atmosphere and conditions have caused amino acids, the precursors of RNA/DNA, to be formed out of a chemical soup. Studies of chemical signatures in ice from the outer solar system suggest complex sugars (also building blocks for life) have been created there through solar radiation-catalyzed reactions, and could have fallen onto the early earth. Though these studies are as yet inconclusive and preliminary, they at least provide concrete, measureable facts that point to possible conclusions.

The above mentioned concepts are not even the tip of the iceberg when it comes to the overwhelming mountain of evidence backing up evolutionary concepts. And I should mention that the theory itself is extremely multifaceted and complex, not the simple "God doesn't exist and we happened by chance" reduction that antievolutionists often spout.

Scientists do not claim conclusions based on their research are "fact" as the IDers do, but that they are merely possible explanations of observational results (hence the oft-maligned use of the term "evolutionary theory"). And as further studies are done, coming at the problem from different angles, and even different disciplines, a body of evidence builds up. This evidence can either support or refute a theoretical claim. If the theory is refuted, it is either discarded or modified to agree with the new research.

That is why you no longer hear of the "ether" which was once believed to fill outer space - its presence would have caused certain measurable effects to occur. Scientists devised tests, found those effects did not exist, and discarded the ether.

Evolution is one of the most successful theories ever proposed within science. It has more evidence backing it up from more diverse fields than practically any other theory. To put it on the same standing as ID, which has no scientific evidence is ludicrous.

The suggestion that merely because we are intelligent that someone must have made us that way is specious, and wholly unscientific. As a concept, it is incapable of being either tested or challenged, two requirements for any theory to be considered at all scientific. It is somewhat similar to the anthropic principle, which is a (in my opinion) circular argument that boils down to saying that we are in this universe because this universe is the only one that can support life as we know it.

With the incredibly immense size of the universe, and even of just our galaxy, the suggestion that intelligence could not occur by chance is silly. In our galaxy alone there are 200 billion stars. And the number of galaxies in the universe is estimated at perhaps 125 billion. So we have 25 sextillion (25 followed by 21 zeroes) stars...and one known instance of intelligence.

I apologize if I have been somewhat longwinded and pedantic, it is just that this is one of my big hot-button issues, mostly because I think the level of science education presented in our country is pathetic.

I should probably mention, I am a programmer, not a biologist (though I work for an environmental engineering company), most of the above information I learned merely through reading layman science magazines.

[sleipner]

Guess we were responding to each other at about the same time...just a couple comments about your last post.

I agree that scientists can be dogmatic, blind, stupid, arrogant, self-righteous, and all the rest.

However I would argue that many of the "jewels of modern science" you mention are quite dated, coming from a period when the scientific method was still in its infancy. In addition, I'm guessing most of those ideas were pushed by scientists who had either religious or political motivations for submitting them, and that their endurance despite obvious fallacy is due to the same pressures.

Of the ones you mention, black people (and hispanics) do often score lower than white people on standardized intelligence tests, but when you correct for factors such as socioeconomic status, cultural differences in testing methodologies, etc., the differences mostly disappear. Being poor is a far better indicator of low intelligence than race, and that is due to environment, not capacity.

Regarding men being more logical than women, it really depends on how you define "logical". There are cognitive differences between the ways that men and women think, and to pretend otherwise to be PC is to fall into the same trap you are protesting. In fact, recent research has suggested that men and women use completely different parts of their brains for the same cognitive tasks. I do not make any judgement about whether one is better than the other, just state that studies suggest they are different in measurable ways.

I believe electroshock therapy is still used in treatment of certain conditions, though it is being phased out as new drugs and better treatments are discovered. In the past, it was the only treatment known for many things, and for some of those it did appear to help.

The biggest advantage of the scientific method is that one of the best ways to get ahead is to shred another scientist's ideas. I would say maybe about 2/3 of science is trying to come up with new theories or more evidence for existing theories, and 1/3 is trying to kill all or part of old ones. This makes it far more likely that ridiculous or untrue assertions will last more than a few years, especially now that the internet has made peer review far easier and more instantaneous than it once was.

This is why I believe that science will eventually come up with the right answer - because it is not a single scientist, but a collaboration of minds, many of whom have contrasting viewpoints, ideologies, and/or methodologies in researching any particular issue.

Religion has no such methodology for contrasting opinions, and in fact tends to discourage any opposition to orthodoxy, in many cases by using lethal force (as in the Middle East, or by the Catholics of not too long ago).

Politics is slightly better than religion in that it has the media and the opposition party(s) to refute its illogical claims, but the difficulty with politics is that fact is rarely an issue in swaying voters - it is all in the marketing and soundbites. Few people ever listen to or understand the substance. In addition, media is easily manipulated into reporting how and what you want, as the Bush administration has proven.

One of the most concerning developments I have noticed recently is this government's attempt to manipulate science into supporting their ideologies. The scientists who agree with them get funding, positions, and political backing, while those who disagree are scoffed at and labelled as "radical extremists" or "activist scientists".

It never ceases to amaze me that the "laissez-faire" party of minimal government intervention exhibits such totalitarian tendencies when it comes to personal beliefs and behaviors, and also regarding media and science.

Sorry - yet another long-winded post. I must be really feeling my Wheaties this morning ;)

[Mike Broderick]

One thing I find fascinating (in a horrible, cant take my eyes away from the car wreak, kind of way) is how fundamentalists (of any stripe) refuse to see beyond their own perceptual box.

A few years ago I read Nonzero by Robert Wright http://www.amazon.com/gp/product/0679758941/104-7446178 2633546?%5Fencoding=UTF8&n=507846&s=books&v=glance
and was particularly struck by the idea that altruism has a survival component for the overall species (if not strictly the individual) and that cooperation may indeed be ‘hard wired’ into the structure of any collective group. “Wow” I thought, maybe here, at last, is a scientifically demonstrable basis for so called ‘natural morality’ (as opposed to something divinely imposed on the brutish masses by some unseen deity)

It should be completely obvious that this tendency for a slight bias towards cooperation over pure, “bloody in tooth and claw” competition would have an effect on natural selection. Indeed, Wright suggests that this is part of the intrinsic “evolution” of culture in the broadest sense.

The book “Sync: The Emerging Science of Spontaneous Order” http://www.amazon.com/exec/obidos/ASIN/0786868449/qid=1117817301/sr=2-1/ref=pd_bbs_b_2_1/104-7446178-2633546
also touches on aspects of this but from a completely different direction by examining the interactions of complex dynamic systems. This, I believe, is the mechanism through which the cooperative instinct plays out, irrespective of consciousness.

I strongly believe that we are starting to glimpse a deeper reality and are seeing that “evolution” is far more subtle than even Darwin himself realized.

Now ponder this. Is God (and, I mean this in the broadest possible sense) an emergent phenomenon of complex systems?

If so, there is kind of a chicken/egg problem in that if indeed we are moving closer to some ‘true’ understanding of God as our cooperative environment grows in complexity and spiritual depth it is entirely possible that we are not nearly there yet but never the less have some intrinsic understanding of and identification with the ultimate destination. In other words, God is within us all. The architect Paolo Soleri talks about this in his book The Omega Seed and I find his arguments compelling http://web.ionsys.com/~remedy/OMEGA%20SEED.htm

Recent studies in particle physics have demonstrated that information can be ‘transmitted’ over measurable distances instantaneously, transcending space or transcending time (really aspects of the same fundamental thing)

Is there some kind of ‘feedback loop’ beyond our linear conception of time, that gives rise to this fascinating tendency for mater to coalesce into life, life to coalesce into mind, mind to coalesce into God? Does our limited, linear concept of time, like flies stuck in amber prevent us from directly perceiving this deeper reality?

This isn’t just some fuzzy headed spirituality. Our experience of ‘reality’ is completely bound up in our four dimensional space but it is entirely possible there are more things in heaven and earth than are dreamt of in our philosophies

OK, Back to work now, My head hurts :p

[lynn]

Mike - I enthusiastically agree with you!

[amba]

Sleipner -- amino acids are not the precursors of DNA, they're the precursors of proteins. The components of DNA are the 4 nucleotide bases (and a 5th for RNA).

As for your examples of rapid evolution -- my question remains: ARE THE MUTATIONS COMPLETELY RANDOM? Or are they in some way "intelligent"?

[amba]

And also directed to Sleipner: you have a high opinion of the intellectual integrity and openness of scientists. The scientific method is certainly admirable in this regard in its pure, ideal form. In practice, science and medicine (being human enterprises) are dominated by establishments that preserve both their institutional power and their conventional thinking. Peer reviewed publication (or not) in professional journals is the mechanism for excluding and marginalizing new ideas which sometimes later turn out to be true, with the result of prolonging suffering for an unnecessary generation or more after the truth is discovered. The story of Semmelweis in the 18th century -- a doctor who was ridiculed and professionally ostracized for suggesting (pre-Pasteur) that obstetricians wash their hands after dissecting cadavers and before delivering babies, and whose demonstration that simple hand-washing could prevent puerperal fever was laughed at -- was repeated in the last decade when the scientist who proved that a bacterium causes most ulcers was ridiculed and ostracized by the gastroenterological establishment. Antibiotics are now part of the state-of-the-art treatment for ulcers. Many doctors still don't use them.

[sleipner]

Amba - true on the DNA vs protein question, it's been years since I read about that much. Nucleotides are made up of a sugar molecule named deoxyribose, a phosphate group, and the 4 bases, adenine, guanine, thymine, and cytosine. Three of these make up a codon that is used to create a single amino acid link of a protein.

I think the point I was trying to make is that studies have shown that it is possible to make complex molecules approaching those present in living organisms out of simple constituents, hence moving chance from an impossible to a somewhat reasonable explanation for the origin of life on Earth. I'm sure there are other studies on this subject, I just haven't done my research well enough to know the level of confidence this concept has reached as of yet.

In terms of randomness vs. intelligence on the mutations - it is impossible to tell, and most likely impossible to test. How could one differentiate between external intervention and merely an efficiently optimized cellular methodology for adaption to environmental change?

In fact, there is some evidence now that suggests even adaptions that have been excised from the genome still stick around somehow - plants in the study I read about had throwbacks to their grandparents even when neither of their parents had the gene in question. Depending on the extent to which this can occur, this could give evolution a kind of "white-out" to try something then revert if it doesn't work, making it a lot easier to mutate more rapidly.

I also agree with you that science is not the answer to every question, and that scientists are not pure, intellectual forces in the world. Many cases exist, as you mention, of people suppressing new ideas because the old ones are entrenched in the ideology of the establishment.

However, I challenge you to find any cases where politics or religion has done any better at removing old, incorrect beliefs and promoting new, better ones. They usually have far more invested in maintaining the status quo. The scientific method has its flaws, but for breaking new intellectual ground there is no other establishment in the history of the world that has come close to even matching it.

The medical establishment is probably one of the areas in which the entrenchment you mention is the worst, as pure research is a very small part of the field, and also the field is extremely complex and not as easily reduced to yes/no answers. General practitioners, insurance companies, medicine manufacturers, politics, and popularly held beliefs all can influence how medicine is perceived and which medicines/methods are chosen. In addition, medicines can act differently based on hundreds of possible factors, including genetic factors, diet, environment, historical toxin exposure, ones sex or age, and who knows what else - which can cause misleading results in studies.

Like any institution made up of humans, science is not and can never be perfect, or even close to it. However, it has self-correction mechanisms that allow it over time to integrate the data it collects into results closer and closer to the "truth". It may take a few years, or even a few generations, but it generally keeps moving in the right direction, and the pace of progress has improved dramatically even over the past 20 years.

[michael reynolds]

Hi, Guys: Realized I had something really long-winded to say, so I wrote my own ID commentary on my site.

[amba]

Sleipner, you wrote: "How could one differentiate between external intervention and merely an efficiently optimized cellular methodology for adaption to environmental change? In fact, there is some evidence now that suggests even adaptions that have been excised from the genome still stick around somehow - plants in the study I read about had throwbacks to their grandparents even when neither of their parents had the gene in question. Depending on the extent to which this can occur, this could give evolution a kind of "white-out" to try something then revert if it doesn't work, making it a lot easier to mutate more rapidly."

This sounds like an "intelligent" process in itself, not an entirely blind one. That's exactly my point. Why does intelligence have to be "external" to the phenomena? Why couldn't it be inherent in them? Note how, like most people talking about evolution, including many scientists, you wind up grammatically and psychologically attributing agency to it, animating or anthropomorphizing it. How can "evolution" "try something"? That makes "evolution" itself into an intelligent designer! As I understand it (and I don't, probably), even neo-Darwinian theory posits that mutations arise as random material "errors" or spontaneous changes in DNA without any internal or external awareness of their meaning or effect. A change in the coding for particular amino acids would happen by accident, the way a random-letter generator typing CAT would not "know" that the sequence was meaningful. Only "natural selection," a lucky fit between the "spelling error" and the requirements for survival in a changed environment, confers "meaning" on a mutation. Mutation is just a jumble of raw material that the environment shapes.

How, then, do you account for the speed and success of mutation of bacteria and fruit flies? Could random change come up with enough positive, potentially useful raw material? Isn't most random mutation deleterious?

What if mutation were a process something like thinking a new thought, trying to solve a problem? A new thought corresponds to, or results from, or causes, a material change in the brain. It's usually a variation on, a leap from, something that's already there. In the brain this process is logical, it is at least semiconscious (we may only become conscious of a new idea when it's already been made), it corresponds to something perceived in the outside world. Of course, some ideas, like some mutations, are useful and some are not. But the two processes seem somewhat analogous to me -- mutation and innovation. Then, as your language suggests, the results are "tried out."

I'm not calling this hypothetical intelligence is "God." Not giving it a name at all. I just wonder if there's any way to test for it.

[michael reynolds]

As I understand it, natural selection works like this: Ten birds. Nine are good enough at flying above brick walls that they survive to have one chick each before they make a mistake and fly into the wall.

Bird number ten has a mutation which involves an extra feather. This makes him a bit better at flying above walls. Bird number ten has two chicks who share his capacity to fly above walls. Pretty soon the well-adapted birds outnumber the less well-adapted birds. Evolution.

[sleipner]

You are right, Amba, if the evolutionary process has selected for the ability to rapidly and effectively adapt to change, one could call that "intelligent" selection.

However, if it is indeed a natural process, and part of the normal way organisms react to their environment, calling it "intelligent design" seems to attribute it to something external to itself, and is an unnecessary and unprovable extension to a theory that is whole without that addition.

It also plays into the hands of creationists, who immediately grab onto that idea and say, "Well, if it seems intelligent it has to be God that is doing it, and therefore God is scientific and should be taught instead of evolution."

More likely, mass extinctions in the past selected for those very genetic mechanisms we are discussing, because species with the ability to adapt quickly soon moved into and dominated empty ecological niches.

Michael - yes, that is a simplified description of natural selection, though in extreme environments it may be more like 1 in 10 or even 1 in 100 survive.

I wish I were more up on current research, because I know there is all sorts of interesting stuff going on in this field now that genetic sequencing has become commonplace.

I strongly recommend reading Michael's post at http://www.mightymiddle.com/ - as usual he manages to get his point across while making me LOL about 17 times during the read ;)

[AR]

The problem that many scientists would have with arguments such as those (too) frequently expressed on this blog is not that pointed questions are being raised about evolution.

Evolutionists welcome good questions. They want good questions. Without good questions, they will have nothing to do, nothing to study and ponder and think about, nothing to discover.

The "problem" is that the only people asking good questions, real questions, are virtually always biologists themselves. The great debates about evolutionary theory are the ones taking place within academia, the real questions the ones being pondered on the pages of PNAS and Nature and Cell.

The most widespread delusion in this whole ridiculous "controversy" is one that is held in particular by lay people taken in by the ID folk. And that is that the ID crowd is actually asking good (or any) questions of science, and that scientists, if they were honest, "should welcome [these] challenges and tests."

LOL. If only they were.

As has been repeatedly said here, the TOE has nothing to say about gods. Neither do most scientists.

We also do not have much to say to those who might believe that there is, say, a mystical green gnome somewhere on earth who once a year visits every child on the planet to distribute gifts. We can tell you that there is no evidence whatsoever for His Presence. We can tell you that since we do not detect any evidence for His Existence (or otherwise), that we cannot “prove” one way or another that He exists (if pressed we might have one or two things to say about the probability of either scenario). If for whatever reason believing in Him is a comfort to some, well, so be it.

LYNN, in the somewhat strange comment above says something about this. God is "Intelligence", she insists. "Music". "Mathematics". The "Laws of Mathematics".

This is an entirely acceptable exercise. One can define (a) "god(s)" in any number of ways that one finds acceptable, and derive whatever feelings one wishes from doing this. (I confess to being slightly amused with the pantheism, however; the terms are almost always idealized. Whatever happened to god=death, =needless suffering, =cruelty, =poverty, =8 million starving Africans dying horribly every year, =pus, =bacteria, =HIV, =fungi, =feces?)

And scientists would have little to say about it.

BUT.

The problem for us arises when truth – and make no mistake about it, if that word means anything at all its use is most apt here – is subverted to appropriate scientific authority to back some version of these fantasies. The truth that the planet is about 4.5 billion years old is rubbished, in favor of "somewhere between 6 thousand and 4 billion years" old. That’s the sort of dross the ID idiots, so venerated on this blog, push. The entire fossil record is rubbished, in favor of some nonsense I have had a hard time following for its inconsistencies. Geology is ignored. The data from the Pre-Cambrian, the Phanerozoic, the Paleocene, all – every last bit of a continent-load of data are ignored and rubbished. The data from genetics, molecular studies, anthropology are conveniently pushed aside or twisted in an attempt to somehow prop up a fantasy that simply cannot stand the weight of scrutiny.

People wanting to do this is one thing. People wanting to force feed this garbage to children – defenseless kids who’re being swindled of their educations – that’s really quite another.

In the face of this, when scientists justifiably react – and react justifiably angrily – we are actually termed "dogmatic". It’s a testament to how far the knowledge gap has widened that this is the case. If a group of people lobbied tomorrow to have Lynn’s kids study the claim that the earth is flat, I suspect she might react angrily – if not for the ludicrousness of the "theory" then at least for the time that will be wasted over such an exercise. Ditto claims that it is the sun that moves around the earth etc etc. What people don’t realize is that this is exactly and precisely what is happening today with biology, but the science is not well understood enough by lay people for them to see what is happening.

In a classic move, Lynn discloses her true colors when she finally asks the infamous design question. She uses computers instead of watches, bless her 21st century heart. She also asks it most amusingly, as if it has really never been considered before, as if this piercing insight of hers is really quite original, and will settle the issue once and for all – if only those clueless, unlearned scientists would sit at her feet and take in the pearls of wisdom.

The people who ask the Paley question of scientists are very interesting for what they generally demonstrate about the anti-science crowd. There is apparently no awareness of the enormous differences that exist between the two systems they propose comparing. Yet they blindly utilize the "analogy" as if it were something other than an embarrassment. Even worse, they haven't seemed to have learned how spectacularly wrong the "analogy" is in some 200 years.

There is no awareness that the computer or watch has no means of reproduction. That the computer or watch has no method of introducing variation into their (nonexistent) reproductive features. That computers and watches have not had billion-year precedents. That computers and watches have not had a constant, readily available external energy source that makes it possible to drive those reactions that introduce change.

The answer to the question "Do you think computers were necessarily designed (why simply designed – created) by an intelligent Maker?" is "Well, duh."

But what on earth has that got to do with evolutionary theory?

[AR]

In further posts here, Lynn completes the move to the Dark Side. What is most spectacular is the list of things she claims the bad, dogmatic scientists have urged in the past.

My first reaction to reading some of the things in her posts was: No way.

There’s no way this person actually means this. She’s probably a he, with a wicked sense of humor and a PhD or two in genomics or something, happily weaving caricatures and satires of creationist loonies in a lab somewhere in the wee hours of the morn.

(This reaction amongst scientist is sadly common. I think it’s a coping mechanism. We cannot allow ourselves to face the full brunt of the spectacular ignorance of some of the people calling us dogmatic idiots).

Why the suspicion? Well, the ironies are simply too delicious.

She tries to beat poor Sleipner – who is not a scientist but an intelligent well informed lay person – over the head with a couple of examples of just how horribly misguided those dogmatic, fanatic scientists have been.

She lists as evidence:

--masturbation causes blindness
--men are more logical than women
--black people have lower intelligence than white people
--a good cure for illness is to put leeches on your body
--electroshock therapy
--the earth is flat

After reading that, and realizing she’s actually not kidding, you’d probably need a little electroconvulsive therapy yourself for the severe catatonia it’s bound to induce.

Where do we begin?

The flat earth "theory" was a scientific one? Seriously, Lynn, you actually thought scientists – i.e. people who utilize the scientific method to study nature and uncover truth – are the ones who put forward the flat earth theory? Not those who passed for “learned men” in the past – who more often than not found firm support for their beliefs in that textbook of textbooks, the Bible?

Or what about this bit about masturbation causing blindness? Seriously Lynn, you have a future in comedy. I’d be very interested to know what scientific studies were conducted that showed that masturbation causes blindness. All this while I was under the impression that this was a myth propagated by the usual suspects – yes, those rational folk who’ve done so much for our understanding of ourselves and nature – the Bible thumpers, who managed to have their poison passed on by an infant medical profession still unused to using science to answer it’s questions. As in the above case, science was the cure, not the cause.

Then we have the leech business. Ah yes. Difficult to argue with this being a product of the scientific method, eh? Yeah, the multiple randomized, double blind, placebo controlled clinical trials conducted on this question are well known to every medical student today. After all, they were published in a special issue of the New England Journal of Medicine – the one that was published before the journal itself came into existence. Excruciatingly scientific, the basis for leech medicine.

And so on and so on.

If you weren’t so blinded by your own disgust (hatred?) for scientists (and their method?), Lynn, you’d be able to see that in each and every instance, the scientific method was the cure – not the cause. The idiocies that you list, and most other absurdities that have passed for “knowledge” in human societies for centuries, are almost without exception the work of non-scientists – usually your favored allies, the religious nuts. It is science that overturns the nonsense, that rights the wrongs.

You have found support from Amba, the writer of this blog. She is rather more enigmatic. Here is someone who decries scientists for their “dogmatism” – but finds no words to criticize ID, which, by definition is the purest dogma, for it has no model, no testable postulate, no falsifiable hypotheses. Here is someone who is able to point out to Sleipner that amino acids are the building blocks of proteins, not of the nucleic acids, but yet, is unable to tell Lynn what a load of ahistorical hogwash she’s been spewing on her blog (in fact, she’s “with Lynn”!). Here is someone who has some familiarity with Dawkins’ Blind Watchmaker, but yet is unwilling to point out to Lynn that her designed computer is simply no argument against evolution; indeed, that to imagine that it is, is to demonstrates a depth of ignorance about the subject so profound, it should make one embarrassed.

Why do smart people criticize a Monet with such fury, while heaping praise on a giant piece of chicken scratch?

[amba]

This exchange is a typical example of the fun and nonsense of polarization.

AR, if you'd read my blog, you'd know that I do "find words to criticize ID."

I said "I'm with Lynn" when she decried polarization and said "the principles of evolution are the essence of God," long before she -- as you are correct to point out -- absurdly attributes "flat earth" and "masturbation causes blindness" to science. I'm sorry not to be a more active participant in my own comments section; if I were, I would do nothing but blog, instead of doing almost nothing but blog.

For the record, I think (I'm resisting spending half an hour Googling and linking here) that the medical usefulness of leeches, and maggots, for certain specific conditions has now been scientifically demonstrated and that they are occasionally used in modern medicine. I know that ECT, electroconvulsive therapy, is still used for really resistant depression and that it helps people. At least one memoirist has written about undergoing it (ditto re: Googling and linking).

The polarization between "natural" and "supernatural," the notion that if there is "intelligent design" it has to operate "externally" -- that big hand reaching down from the sky to rearrange a gene -- seems absurd to me. In this I alienate myself from both the Darwinists and the IDers (who, with the warm exception of Jonathan and Amanda Witt, seem to have little interest in my blog; it doesn't serve their purposes). I wonder about the possibility of a form of intelligence and awareness intrinsic to the process of evolution itself.

[amba]

AR, you also say:

"The truth that the planet is about 4.5 billion years old is rubbished, in favor of 'somewhere between 6 thousand and 4 billion years' old. That’s the sort of dross the ID idiots, so venerated on this blog, push. The entire fossil record is rubbished, in favor of some nonsense I have had a hard time following for its inconsistencies. Geology is ignored. The data from the Pre-Cambrian, the Phanerozoic, the Paleocene, all – every last bit of a continent-load of data are ignored and rubbished."

You are lumping together young-earth creationists and ID advocates. They are not the same. In fact, some observers (Rick Heller of Centerfield, e.g.) have pointed out that by rejecting the literal interpretation of this aspect of the Bible, sophisticated IDers open the door to rejecting literal interpretation of other aspects of it, and so enter the modern world and its dialogue. Read some of the earlier posts in my "Debating Intelligent Design" sidebar. (Again I'm refusing to the temptation to go over there and spend time making links. It's all there -- plenty that will tickle your own biases, but also some that won't, if you're not having too much fun ranting to notice.)

[amba]

Sometimes I think (and the religious folk will really love me for this one) that the word "God" is part of the problem. (For its etymology go here; it's from the same root as "idol," a root which means "the one invoked or sacrificed to.") "God" just gives a capital letter to a primitive concept. This is why mystics, who have a direct experience of profound love and consciousness suffusing existence (which AR might well attribute to temporal lobe epilepsy :) ), tend to avoid giving it a name.

[michael reynolds]

Amba: I think AR is a bit more harsh than I would choose to be but his fundamental point is spot on: we have ID people who hold zero evidence, criticizing Darwinists who have several tons of evidence.

Define God however you like, there is simply no evidence that such a creature, such a force, exists. As a thought experiment imagine Origin of the Species, and the Bible, or any other mystical text you care to name, being considered for publication in a scientific journal. Imagine either being introduced as evidence in a court.

Darwin, however incomplete, is part of the reality-based community. God, in any form, is not. Evolution rests atop a mountain of evidence. God rests in imagination alone.

[amba]

Michael,

I work with a patient advocacy foundation that has teamed up with a brilliant scientist to make progress in understanding and treating a connective-tissue disorder, and I have seen how the peer-review process excludes some of the diamonds along with the junk, and publishes junk refutation of the diamonds because it suits the powers that be. So I am not quite as reverent about scientific journals as some of you guys.

Scientists simply should not forget (and the best of them never do, of course) that there's much more to "reality" than is yet dreamt of in their philosophy. And I have said that I think "God did it" is, scientfically speaking, a cop-out, a non-answer, one that closes off questioning both into "God" and into "it," which is our business here if anything is.

[Tom Strong]

Darwin, however incomplete, is part of the reality-based community.

It would be more accurate to say that Darwin is part of the material-based community. Which is why the gap between Darwinists and ID'ers, and needless to say Creationists, is so wide.

They have plenty of evidence for their beliefs. That evidence merely happens to exist in their heads and hearts -- but given that it does, is it really that unreasonable for them to look for echoes of it in the material world?

[amba]

Tom -

Thanks for making that distinction. Equating the material with the sum total of the real (rather than the measurable part of the real), and declaring that everything else is a fantasy or delusion, is "philosophical materialism." That, not science itself, is what the sophisticated ID'ers are taking aim at.

[sleipner]

AR, you're right about leeches and maggots, I had forgotten.

Leeches are now being used after surgery on areas of the body that have poor blood flow, such as the ears (too much cartilege). The leeches anti-clotting factor is better than most commercially available products, plus they cause blood to continue flowing to the area, promoting healing.

Maggots are used in cases of gangrene, bedsores that have gone bad, etc. They have the unique trait that they only eat rotting flesh, and they eat ALL of it, so they clean out wounds better than almost any other method, without taking any healthy flesh.

Though AR was perhaps a bit more harsh than I would have been, he makes a number of valid points. Personally I have no quarrel with the concept of ID, and in fact have been known to say that ID is about the only way I could ever accept any form of religion that makes claims about the origin of life/humanity.

(Of course I'm an agnostic though, I don't have the faith to be an atheist. But there's nothing a good agnostic can't do if he doesn't set his mind to it.)

I just have strong objections to it being portrayed as anything other than a religious belief system, and enormous objections to it being included in the public school system at all.

[michael reynolds]

Tom and Amba:
You guys would be on solid ground -- except for the fact that you've done exactly what I pointed out on my own site: you've placed science on the table for dissection while refusing to apply any standards of proof at all to your own beliefs. You demand 100% proof from Darwinists while providing zero proof of your own. This is taking the matter of having your cake and eating it too, a little far.

And please, no straw men. No one is dismissing the possibility of not-yet-demonstated reality. We're dismissing the intrusion of these not-yet-demonstrated fantasies into science. We're not saying that there are no Leprechauns, we're just saying maybe you don't want to count on them showing up for the swing shift.

The truth is you are (and I don't mean to sound harsh, I really don't) clinging desperately to a series of beliefs you are secretly convinced are untrue. You want badly to believe. And to that end you engage in bobbing and weaving, dodging and evading debate where you refuse absolutely to apply to yourselves the standards you fiercely demand be applied to everyone else.

Either you believe that the scientific method is meaningful -- and since you attempt to use it to attack Darwin, it seems that you do. Or you believe that reality can be defined in terms of whatever notion pops into your head. If the latter then I would point out that we can, like you, simply fill the holes in evoluton with whatever pops into our heads. Magic pixie mutarons explain all your doubts about Darwin. Ta da!. Case closed.

The problem with the idea that one can declare real whatever "feels" real, is that you cannot then deny the feelings of a madman, a psychotic, a racist, an anti-semite. The voices in the head of the madman telling him to kill, kill, are every bit as real as your "evidence." If your version of God can simply be wished into existence then I guess we'll have to hope to hell no one gets the idea of wishing Huitzilopoctli into existence.

Mystics imagine that they are creating a better, more wondrous, more accepting world. Nice fantasy. But not true.

[AR]

Michael Reynolds is quite right to suggest I was quite sharp. It's the reaction that one is propelled to when making a defense where one perceives all sense of proportion has been lost. You feel you're forced to be firm because the situation is just incredible.

Reynolds also puts the point more succintly than I did: when you're comparing a scientific theory with so much evidence from so many disparate fields of human study, to a caricature of belief that actively tries to bend truth to serve its religious ends, some awareness of this should suffuse the discussion.

If it did, you're likely to find that the scientist can admit to a deep spirituality. For example, the experience of realizing - from something you just discovered in your own lab - what an epic story ours is, is so profound that to describe it as spiritual or holy is as good a use of those words as any.

Tom Strong says:

They [ID'ers & Creationists] have plenty of evidence for their beliefs. That evidence merely happens to exist in their heads and hearts -- but given that it does, is it really that unreasonable for them to look for echoes of it in the material world?

That's a creative use of the word "evidence", but I suppose you have to use something - and I understand what you're trying to say. However, your claim that these folk are only looking for "echoes of it in the material world" is painfully untrue.

If one had a firm belief in the existence of Yetis, and sought to find "echoes of it" by claiming for instance that enlarged footprints in melted snow were really evidence of Yetis, and then fought to have all children, whether they believed in the Yeti religion or not, be forced to learn this as "science" in their classrooms...

AMBA, I know that these people each pick and choose different aspects of their mythologies to advocate, or believe in. I am not expert at the distinctions. However, it is not true that ID supporters don't subscribe to YEC. In the recent circus in Kansas, a number of them informed the hearings that they believed Earth was between a few thousand to a few billion years old.

(That bit of sophistry has a mine of humor going for it. It was wonderfully funny to read of the confidence intervals they each expressed. From "6 thousand to 4 billion years old," indeed. I'd love to know their methods for arriving at that CI, and exactly how much worth they place in something with a CI that large).

As for Lynn's leeches, there is FDA approval for them for a specific use (and yes, maggots too). Lynn however is probably referring to the old practice of using them for bloodletting (she wrote, "a good cure for illness is to put leeches on your body."). Bloodletting is seriously bad medicine, of course, and to suggest that the practice was backed by the use of the scientific method is wholly incorrect.

ECT is an example of a treatment that has received a whole lot of undue bad press. It has an established place in the treatment of severe depression unresponsive to meds and for catatonia. I have seen it used twice - once in each of the above scenarios - and it's the sort of thing that makes you feel really sad with the damage the media can do. ECT is actually a life saver.

You make several criticisms of the institutions of science. These are principally concerned with how new theories and conjectures and hypotheses are received. Some of your criticism is on the mark (occasional abuse of the peer review process), some inaccurate (Semmelweis and the OBs at Vienna General Hospital, Marshall and Helicobacter pylori). They all suffer from the failure to acknowledge that inherent to the very nature of science is its natural propensity to push the truth out, whatever non-scientific forces stand in its way (whether these are religious bigots as in the past, or personalities within scienctific establishments today that behave non-scientifically). Marshall is of course the perfect illustration of this.

The most serious point here that I would like you, Amba, to answer is the following. You repeatedly criticize science and its institutions for being resistant to theories that are in opposition to its central, widely held theories and Laws.

You make this criticism not as a philosopher of science, but in the context of a debate about creationists and "ID'ers." In making this criticism, you use as examples scientists who made new scientific discoveries that changed old ways of thingking.

But, what in creationism and ID do you feel are valid theories that have been closed off by scientific institutions?

Do you see why your criticism of the scientific establishment's initial (and extremely short-lived) resistance to Barry Marshall's findings, for example, has absolutely no relevance to the resistance to creationist disingenuity?

[AR]

And please, no straw men. No one is dismissing the possibility of not-yet-demonstated reality. We're dismissing the intrusion of these not-yet-demonstrated fantasies into science. We're not saying that there are no Leprechauns, we're just saying maybe you don't want to count on them showing up for the swing shift.

Michael,

You write really well, and you have a gift of getting to the core of an issue effortlessly. The above para cuts right through to a central issue in philosophical criticisms of science.

The only thing I would caution is ascribing beliefs to Amba that I'm not sure are apparent. She has a propensity for finding fault with scientists, and an amazing willingness to get in bed with a lot of (what most scientists would consider) spectacular kookiness, but she has not declared her personal beliefs one way or another, as far as I know.

[amba]

Michael -- talk about straw men! Tom Strong and I are not exactly true believers. The true believers would not recognize us as such!

[amba]

AR: If you actually read my blog, you would see that I am not an apologist or propagandist for ID. I don't think it has done anything yet except remind us of the gaps in Darwinian theory. I got interested in it because I had my own very specific question about Darwinian theory, which was, "Is mutation completely random?" Nobody seems to have even heard this question, the volume is too high.

By bringing up flaws in the peer review process, I did not mean to compare that to science vs. ID. It was just a way of explaining that while I revere the scientific method --surely one of the greatest advances in human history, and responsible for all our material progress, relief of suffering, lightning communication, etc. -- I don't revere the scientific establishment. Many of the people who have made major breakthroughs were initially rejected by it. And I don't revere philosophical materialism. The fact that the material is almost all that science can currently measure and explain (although it starts to get seriously weird with quantum physics and cosmology) should not lead to the belief that the material is all that's "real" or all there is.

My personal "beliefs"? I'm an agnostic, obviously. I am comfortable with saying "I don't know" when I don't. To "believe" is to give a hope, a hunch, a speculation, or a hypothesis the status of fact. I know someone who claims to have had a personal experience of abduction by aliens. I haven't seen any aliens myself, so I don't "believe in" them. But neither can I make myself dishonestly more comfortable by deciding that they cannot possibly exist and that this person is either a liar or crazy. I simply don't know. If and when I see one, I'll let you know. Similarly, I've had experiences in which uncanny things seemed to be happening for a purpose, beyond chance, or in which I felt warmly cared for and protected by . . . what? I am not going to decide for sure that these experiences are either wishful thinking or proof that somebody up there likes me. They make me feel that the universe is meaningful, aware, and friendly. I hope it is, but I don't know.

[amba]

To make that more clear, I'm not saying nothing can be proven. The germ theory of disease is proven. That the earth revolves around the sun is proven (as even the Catholic Church now admits). Parts of Darwinian theory are pretty well proven, and parts are not -- they are speculative extensions, which, if taken as "true," have become articles of faith.

[sleipner]

I hesitate to ever call anything "proven" outside of mathematics. There is always one exception to the rule, one situation in which the theory doesn't work exactly as one would expect it to.

Of course this does not disprove the theory (as the creationists would say), it just creates additional questions for scientists to investigate, yielding a deeper understanding of the universe. Quantum mechanics is a huge area in which Newtonian physics breaks down, but one doesn't discard Newton just because he doesn't always work.

I appreciate your question regarding whether evolution is totally random or not, but in the larger scheme of things, I would have to ask, does it matter? I mean, if it isn't totally random, but there is no way to determine the source of the nonrandomness, then how can one attribute it to anything in particular?

I personally believe that natural selection, over innumerable generations and multiple extinctions, has come up with organisms that are particularly good at adaptive evolution.

Another point I had meant to mention earlier but forgot is that there are quite a few examples of symbiotic species that cannot live without each other, which are examples of how rapid evolution might occur. In some cases it is a bacteria and an insect, in others it is a plant and an animal of some sort.

In some of those cases, it is obvious that the two species are merging and becoming a single species, and the symbiosis gives us clues to how some of the various systems within our own bodies may have come into being in the ancient past.

I think bacteria and viruses are huge agents for evolution that are largely overlooked, and were perhaps the largest players in the biological history of this planet.

[AR]

AMBA,

I have little objection to most (but not all) of what you wrote in the final two comments.

With respect to your question on mutations, one cannot provide another with a biologic education in the comments section of a blog, but perhaps I can point you in the right direction.

Firstly, I would not use the word "intelligence" when referring to mutation. Intelligence usually connotes a cognitive process with neuronal matter as its anatomic substrate (unless one is talking of the intelligence of (a) God(s), in which case science has nothing to say about it). The thing I think you are looking for is the phenomenon known as adaptive mutation.

A basic principle of classical genetics is that mutations occur independently of their phenotypic consequences. This is indeed usually the case, and is the reason why we call mutations a random process (Strictly speaking, as mutations have definite, well-understood physical causes, they are not perfectly random events; with respect to the outcomes of mutations, however, they are).

However, in the 1980s scientists began to notice some curious phenomena in E coli. A guy called Shapiro noticed that mutations could occur in this bacterium when they were nondividing and subjected to a stress that favored the resulting mutant. John Cairns did a lot of work on this too, and found essentially the same thing. There was some speculation at the time that only selective mutations specifically favorable to the stressed environment would occur, but this has since been shown to be untrue. This is now a widely studied field, and the best understood system is the E coli lac frameshift system.

The details of this stuff are quite technical, but if you wish I can point you to some papers (below). I do not see how adaptive phenomena might be advantageous to a ID worldview, and I would suggest anyone who thinks it does does not understand it, to say nothing of the difficulty these folk would have explaining other systems of mutability. However, they are as always welcomed to try.

Shapiro, J. A. Observations on the formation of clones containing araB–lacZ fusions. Mol. Gen. Genet. 194, 79–90 (1984).

Cairns, J., Overbaugh, J. & Miller, S. The origin of mutants. Nature 335, 142–145 (1988).

Cairns, J. & Foster, P. L. Adaptive reversion of a frameshift mutation in Escherichia coli. Genetics 128, 695–701 (1991).

Rosche, W. A. & Foster, P. L. The role of transient hypermutators in adaptive mutation in Escherichia coli. Proc. Natl Acad. Sci. USA 96, 6862–6867 (1999).

Godoy, V. G., Gizatullin, F. S. & Fox, M. S. Some features of the mutability of bacteria during nonlethal selection. Genetics 154, 49–59 (2000).

[AR]

Amba, one last thing. If you believe this,

I don't think it [ID] has done anything yet except remind us of the gaps in Darwinian theory.

you are mistaken. Like I said earlier, the interesting stuff in evolutionary theory is happening inside academia (unsurprisingly - that's the way it is in every science). The ID people are not doing anything except advance a religio-political agenda by taking advantage of most lay persons' unfamiliarity with science.

[Seth Chalmer]

I like amba's tone. It's a tone of humility in the face of an amazingly large and complicated universe. Amba is unwilling to claim or defend unproven knowledge.

Amba may be an agnostic, but to me, that's the proper tone for religion!

My favorite theologian, A.J. Heschel, said that true religion can only begin from an attitude of awe. If you're not in awe of the miracle of the universe, you're not paying enough attention.

I know it's been said before, but the universe really is amazing enough for both science and faith. Indeed, God's creation is so amazingly huge and complex, that all the science in the world and every faith in the world will never get us near perfect understanding of it. And we need it. We need it all. Genesis, logic...Who can afford to give up a bit of it?

In response to your mutation question, amba, let me say this: that there has been a series of mutations that led to the brain of even the dumbest human alive is a miracle. God did that. And to those who say chance did that...sure. God made chance. Chance, and every other concept. The thought of chance and God being opposed underdefines God.

Science classes should teach logical evidence only--Darwinism and its gaps both. They should leave out religion and God's Creation not because it isn't true, but because it is more true. Too true and too big and too awe-inspiring to define.

[michael reynolds]

AR: Yes, one must be cautious when stalking the wily Amba.

On the larger philosophcal question Amba and others have raised, I don't get why it would make us all feel warm and fuzzy if we learned that an intelligence guided the universe. Of course I see the obvious hangover from childhood -- a need to believe that a Mommy and a Daddy are taking care of life's problems.

But I personally find the idea of an intelligence that would create, or supervise the evolution of, the Ebola virus, or tapeworms, or for that matter this d----- cold I can't shake, appalling. If someone is running this show he's doing a rather poor job of it. There are more species extinct than alive. I'm hardpressed to imagine how that record points to a benign intelligence. If it points to intelligence at all, it's a blundering, incompetent and malicious one. Is it someone's happy thought of the day to meditate on the Great Designer who cooked up childhood leukemia?

Which brings me back again (sorry, I'm a fiction writer) to motivation. Since all agree that there is a mountain of evidence supporting the theory of evolution, and since we all agree that there exists no measurable evidence to suggest the existence of god (however defined), I am left to wonder why people reach so desperately for a creature or a concept which, if it exists, serves to confirm that the universe is stupid rather than random, and malicious rather than indifferent.

[amba]

AR: That is such cool stuff, about the role of bacteria in evolution. I have read that our cells' mitochondria may be bacteria that formed a symbiotic relationship with primitive cells.

I will struggle to read some of those papers about the possibility of non-random mutation in e.coli.

Michael - on the contrary, I think the reaction you describe (if there's a god, he's a sonofabitch for making Ebola, etc.) is the human reaction of the petulant disappointed child. We expect "god" to be omnipotent the way little kids expect their parents to be. If there is "god" it probably has an awesome but more limited role than we would like. Starts creative processes in motion but does not govern their every ramification. Cannot protect us from suffering but can inspire us to endure and find meaning in it -- and work to conquer it. I would guess God is related to negentropy. No mythology says God created chaos -- death and disease are the dues creation pays to chaos. Something like that.

[michael reynolds]

I prefer to whip out the razor (Occam brand, available at Walgreen's) and slice away the unproven, the improbable, and the superfluous. And there goes God down the sink.

Oddly enough what's left in my world is amazing enough, sufficiently fascinating to fill a million lifetimes with questions and answers and new questions. And I don't have to pull any muscles straining to keep alive a silly, and not terrribly interesting idea devoid of support.

And again, Amba, you've sidestepped my question on motive. You presumably don't go around adopting every unprovable notion, why the God idea in particular?

[Tom Strong]

Michael Reynolds,

You guys would be on solid ground -- except for the fact that you've done exactly what I pointed out on my own site: you've placed science on the table for dissection while refusing to apply any standards of proof at all to your own beliefs.

I've done no such thing; actually, my beliefs are quite similar to yours on this issue. I'm certainly not defending ID, which I think belongs in philosophy classes, not biology classes. (Though it is worth wondering: why exactly don't we teach philosophy in high school, except as an elective at more prestigious schools?)

I am making a single, rhetorical point: that scientists who think they can paint evolutionary theory as "reality" misunderstand their opponents, who insist on seeing the spiritual as the basis of reality. While I think this view is wrong -- particularly when it insists on refusing mountains of physical evidence -- it is both common enough and varied enough that I can't say it's crazy.

Let me give you a clearer idea of where I'm coming from. I worked in anti-domestic violence movement for a spell, and a key text that I read then was The Politics of Reality by Marilyn Fry. Fry's last essay in that book makes a trenchant point: The original meaning of "reality" is "the king's land." He who determines reality is sovereign. As a result, we open a big can of worms in any democratic society when we start telling other people what their reality needs to be.

This is a divide that you simply cannot cross with evidence. It doesn't matter that many scientists are religious, or that they regard darwinian theory as open to informed criticism. A large section of the public has already gotten used to equating darwinism with dogmatic atheism and materialism, and they will simply tune out any argument that overturns their sense of what is real.

AR,

However, your claim that these folk are only looking for "echoes of it in the material world" is painfully untrue.

Perhaps a little understated, but truer, I think, for the ID'ers than it is for out-and-out creationists.

[michael reynolds]

Tom:
I apologize for mischaracterizing your position. Obviously I did not read as carefully as I should have.

My only excuse is that I am three weeks into the cold-that-will-not-die. And frankly, I have to say, I have received nowhere near the amount of pity appropriate for such a terrible affliction.