Mechanical

Evolving Human Stupidity

I'm not going to talk about intelligent design proponents. I'm going to call a spade a spade and refer to them as creationists. Let's just get this straight: there is no "intelligent design". There are creationists who explicitly embrace God and ID proponents who lie and pretend that religious zealotry is not what's behind their campaign of deceit. Of course, I'm sure that God doesn't mind a little intellectual dishonesty to prop him up, right? Clearly the ID folks have realized that faith ain't enough, praise the Lord!

This is not to say that all who believe in Creation are liars. There are many well-meaning people out there who sincerely and devoutly believe in the story of creation and there are more folks who are swayed by the creationists arguments because the creationist campaign of lying and their very selective use of information has created a propaganda machine that politicians can only envy. However, when you look closely at the creationist claims, most of it boils down to one thing: evolution supporters don't know everything, therefore they're wrong, praise the Lord!¹

It's tough to find a better example of how far we are willing to go to lie to ourselves. It's tough to find a better example of the self-deceit we are willing to engage in when we can accept such a specious argument. And it's tough to keep a straight face while listening to it. So I won't. Praise the Lord!

The Evil, Mad Scientists Are Out to Get You!

First off, let's make one thing clear: science is not evil. Science is just people asking why things work. That knowledge is used often used to help people. That's all it is. Yes, some of the knowledge we have attained has been used for evil, but to use that to claim science is evil is to claim that religion is evil because many evil things have been done in the name of religion.

You would not only not be reading this if it were not for science, you would probably not be alive. I would have died as a baby were it not for a complete blood transfusion when I was a few days old. I would have died as an adolescent due to my asthma. I would have died as an adult due to a cholesteotoma. Carl Sagan once recalled a dinner where he asked his assembled guests how many of them were alive only because of science. All of the guests raised their hands. Evolution instills in us a sense of self-preservation. If you think it's OK that we die, kill yourself. Let me know how it turns out.

Everyone Knows the Earth is Flat

One of the most ignorant "rebuttals" I hear about evolution is an attempt to refute the weight of the vast majority of scientists who accept evolution. The basic argument is something along the lines of "yeah, but everyone once believed the earth is flat." That is not true. In all probability, the vast majority of folks likely didn't give the issue any thought, but for anyone who cared to pay attention, it was abundantly clear that the earth is round.

Long before Christ, Greeks realized the earth was round due to the spherical shadow it cast on the moon during lunar eclipses. Many of them even came up with fairly accurate estimates of the earth's circumference. Anyone watching ships sailing to sea would notice the hull disappearing before the mast. In other words, once humans had the technology to consider the situation, the truth became apparent. Even today, many folks erroneously believe that Columbus sailed to the Americas to prove the earth was round. That's not true. He knew the earth was round, he simply argued that it was smaller than most others believed.

Arguing that "just because many people believe something doesn't make it true" is certainly correct. Many people believe in the Christian god and many people do not. One of those groups is certainly wrong (with many shades of grey in between). However, that means that if the truth of a proposition is important to us and we are disinclined to believe the massive amounts of researchers who cite anatomical, genetic and geological evidence for evolution, then we need to consider this evidence ourselves. So let's do that.

The Stupid Watchmaker

So you're standing in a warehouse and there are parts of a Boeing 747 lying around. All of a sudden, a huge wind whips through the warehouse, picking up the parts and miraculously assemble them into a 747. This, clearly, is so highly improbable as to be viewed as impossible. In fact, this very argument is used repeatedly by creationists. They claim that this argument refutes the Big Bang theory. They claim that complexity doesn't arrive by random chance. If you find a watch on the ground, you can reasonably infer the existence of a watchmaker.

Sounds compelling, doesn't it? This is basically a retelling of the Irreducible Complexity argument. The basic argument has two points, one ostensibly following from the other. First, some things are so complex that they cannot be broken down into simpler things. Second, if something is irreducibly complex, it must have been designed.

Now as it turns out, the first point is rather tough to prove or disprove. It's clear that we can design things which appear to be irreducibly complex. Whether or not such things occur in nature is the sticking point. As it turns out, scientists frequently agree that organisms with irreducibly complex features exist. A perfect example stems from the pesticide pentachlorophenol (PCP). This pesticide, created in 1935, is highly toxic. However, several bacteria were discovered which had developed the ability to break down this chemical and consume it. One of the most famous, sphingomonas chlorophenolica, uses three enzymes in succession to break down PCP. Remove one of those enzymes and the PCP kills the bacteria. Thus, we have one of many irreducibly complex systems found in nature. Praise the Lord!

Unfortunately for the creationists, it's already well-understood how this irreducibly complex behavior could occur naturally. As it turns out, the enzymes necessary for breaking down PCP already served other roles. Their adaption for breaking down PCP was fairly straightforward.

Ah, but that's not fair! If the pieces were already there, that's cheating, right? Well, let's take a look at the number one claim for irreducible complexity that creationists like to use: the bacterial flagellum. They beat this to death. They proudly cite this as an example of why creationism (ahem, ID) must be taught in the classroom. They use the flagellum as a logo on their web sites. They write books about it. The flagellum, they proudly claim, is the death knell of evolution.

The argument works like this. The flagellum is comprised of three part, the motor, the rotor, and the paddle. None of these parts functions without the others and unlike the enzymes which break down PCP, none of these parts serve any other purpose. Given how complex all three of these parts is, it's inconceivable that they would spontaneously appear via random chance. Thus, evolution cannot explain the flagellum.

Being wrong doesn't mean they're right

Before I deal with the creationist misconception about the flagellum, it's worth stepping back a moment and looking at the big picture. If, in fact, the creationist arguments about flagellum are true, does this prove there is a god creating and guiding life? As it turns out, no. Proving that evolutionists are wrong about one point does not mean that their conclusions are false. Let's use a simple syllogism as an example.

  1. Premise: all cats are fish.
  2. Premise: all fish are animals.
  3. Conclusion: all cats are animals.

This is one of the first forms of syllogism we learn when we study logic. All A are B. All B are C. Therefore, all A are C. This form of a syllogism is considered valid. That is to say, the premises necessarily lead to the conclusion. In this particular case, the conclusion happens to be true. However, the first premise is false. Therefore, while the premises necessarily lead to the conclusion, the fact that the first premise is false means that we cannot use it to support the conclusion, though few would argue that cats are not animals.

This is a very important point to keep in mind. In fact, it's just as fair to point out that if creationist premises turn out to be false, it does not mean that there is no god or that this super being does not have a hand in the creation of life. In fact, I always wonder why creationists are willing to accept that some invisible super-being is easier to accept than the idea of self-organizing systems -- the latter of which we can observe -- but that's a discussion for another day.

The main crux of the creationist argument is the flagellum is irreducibly complex. Remove any part of the flagellum and it ceases to function. As it turns out, this is not true. One of the fascinating aspects of evolution is how things which are used for one function are often co-opted for another. Remember the enzymes which break down PCP? They're a classic example. In the case of the flagellum, it turns out that the basal body (the "motor") is closely related to type III secretory systems (TTSS -- discovered in 1994). TTSS allow bacteria to inject proteins into cells. With relatively little modification, we have a relatively simple portion of the flagellum serving a completely different role. The complexity of the flagellum does not appear to be as irreducible as creationists claim.

Regrettably for creationists, further research in flagella evolution is providing more evidence that it's not as irreducible as first thought. Amusingly, after discovering that the flagella are not irreducibly complex, some creationists are now arguing that the components which comprise the "irreducibly complex" systems are themselves irreducibly complex and therefore biologists have an even more systems to explain. It's turtles all the way down, baby!

Before we turn away from the irreducible complexity argument, there's a final point to make. So far we've found many supposedly irreducibly complex things which, upon further inspection, are reducible. But what happens if we find something that is irreducibly complex? Interestingly, we have, but not the natural world.

In the early 1990s, a scientist named Chris Adami decided to create a system which could test how evolutionary processes worked. He devised a system which basically rewarded digital creations for how well they could perform basic math operations. In the process, this software has been used to examine irreducible complexity.

The researchers set up an experiment to document how one particularly complex operation evolved. The operation, known as equals, consists of comparing pairs of binary numbers, bit by bit, and recording whether each pair of digits is the same. It’s a standard operation found in software, but it’s not a simple one. The shortest equals program [Charles Ofria, the director of the Digital Evolution Laboratory], could write is 19 lines long. The chances that random mutations alone could produce it are about one in a thousand trillion trillion.

One in a thousand trillion trillion. Think about that. One in a thousand trillion trillion. How many years would a thousand trillion trillion seconds be? A trillion seconds is 31,688 years. A thousand trillion seconds is far, far older than the age of the universe. Initial results had 23 out of 50 trials able to produce "equals". In later experiments a researcher decided to limit the resources available to the "organisms". Limited resources, of course, force greater competition for those resources. In these experiments, not only did all trials develop the ability to produce "equals", they did so much faster. Creationists were not happy with the results and have tried to find flaws with the methodology. They've actually done a great job of finding bugs in the software and improving it.

Does this prove evolution? No. Instead, it shows that the math works. Ridiculously improbable things somehow become probable with evolution. Read the article. It's fascinating.

The software, by the way, is open source and available for download. Have fun with it.

Chaucer the Creationist

Like Chaucer intimating that gap-teethed women were sexually promiscuous, so too do creationists somehow think that gaps in the fossil record are somehow meaningful. Wouldn't it be fun to point an AK-47 at one of them and say "hey, you can't see the bullet, therefore it's not there"?

Regrettably, fossils are somewhat harder to come by then bullets. You don't have to wait for a bullet-beast to die, get covered in mud or sand, and slowly have their bone replaced with lead and get stumbled across millions of years later by some right-wing militia nut. No, we're not so lucky. Organic matter has a nasty habit of decaying. Seriously. Sacrifice a puppy to your God, leave it on your kitchen counter and tell your friends to check on the corpse every few million years. It helps if you don't tell 'em where the kitchen is.

This creationist argument is so silly that it's almost a waste of time to refute it. Plenty of evolutionary steps in mankind have been found. The archaeopteryx is a classic example an intermediate step between dinosaurs and birds. We even have fossil evidence suggesting that whales indeed were land animals which returned to the sea. Of course, evidence is not proof and whenever researchers uncover more evidence, the creationists either deny it or demand more.

Ignoring the links

One key piece of evidence that creationists have been oh so smug about is the lack of clear evidence of the first water-dwelling creatures evolving to live on land. Despite the existence of lungfish, amphibians, and plenty of other creatures today which seem to have crossover characteristics, the creationists have demanded even more evidence. Well, once again it appears that scientists have found it, even though they weren't specifically looking for it. The recently discovered tiktaalik appears to have lived over 300 million years ago. Despite apparently having gills and being a fish, it also appears to have had lungs and functional limbs, right down to the wrist joint. There were several fossils of tiktaalik discovered, thus giving scientists plenty of evidence to work from.

So have creationists been persuaded by the presentation of yet more evidence they've demanded? Of course, not. John Morris of the Institute for Creation Research says it's just a variety of fish. Curiously, said institute's Web site is strangely silent on the subject of tiktaalik. I would think that if Mr. Morris knew enough about the subject to dismiss tiktaalik as "just a variety of fish", he'd be happy to trumpet that news on his Web site. I expect a curious article on the subject soon.

And since we're on the subject of John Morris and his institute, why don't we read what he has to say about missing links:

If you still don't know what a missing link is, don't worry. No one knows what a missing link is, because they are missing! We've never seen one. They're still missing. Evolution depends on innumerable missing links, each of which lived in the unobserved past and have gone extinct, replaced by their evermore evolved descendants.

So you can see their basic strategy. If a missing link is found, deny that it's a link. Then point to gaps and say "see! It's missing!" I wonder if he makes this stuff up with friends at late-night beer fests. They have to be laughing their asses off.

Conclusion

Of course, an entire book could be written on this topic. When stuff like this is written, if creationists stumble across it they often point out that while A, B, and C are covered, the author didn't cover D. "What about D, huh? Huh?" Or they'll go toe to toe and try and pull out more research which seems to contradict a point or two. That's their strategy: change the subject or resort to a death by a thousand cuts. They'll deny that the fossil record presents any serious evidence. They'll deny statistical DNA studies which support evolution. They'll deny anatomical features support evolution. They even sometimes claim that more and more scientists are abandoning evolution (they aren't). They ignore the fact that there's broad scientific consensus about the overall basics of evolution and instead pick on niggling little details where scientists disagree. They misuse and misunderstand how science works and they prey on our scientific ignorance and overwhelm us with anecdotes which they claim support their beliefs.

All things considered, it's the anecdotes which worry me. There is so much evidence in support of evolution that there are naturally tons of gaps which we haven't filled. There are little bits and pieces that we can't make fit. The creationists stand in front of the evidence and point to the gaps. This dishonesty is astounding and if there is a God, I'm sure he's hanging his head in shame.


1. I suppose I could reply with "Creationists don't know anything, therefore they're wrong", but I'm a better man than that. Barely.

(Here via my beloved, da_lj.)

You might find it pleasant to read the decision in Kitzmiller, the "intelligent design" trial (I absolutely refuse to write that phrase without scare quotes) last fall. I can't think of an afternoon in the last year that was more professionally satisfying to me (I'm a bioinformaticist) than the one I spent reading it.
I read that. It was absolutely wonderful. I really appreciated how the judge dealt with it. I almost cited that in this post, but it never quite fit.
Fair enough...

Are you living in the UK now (D. occasionally mentions things about you, since I've been interested by the posts of yours he's pointed me at in the past)?

[Oh, and you might be amused to know that Dembski is now writing his own program to show why programs to imitate evolution are of course all wrong, wrong wrong. *sigh* Self-parody just doesn't begin to describe these people.]
No, I'm still in Portland. I'm just waiting for the paperwork to go through before I can move. It's frustrating because my stepmother died and her funeral is in the UK but there's some question about the validity of the work permit if I'm in the country when it's issued. As a result, my father and I have agreed to take no chances and I'll simply visit him when I get over there.

Dembski is writing his own program? Do you have a link for that? I'd be fascinated to read it. I've done a bit of work with artificial life and I know that it's very difficult to do correctly. I'd be curious to know more information about Dembski's approach.
Geez. That sucks--I'm very sorry to hear about your stepmom.

I don't have a link. (Oddly enough, there are no peer-reviewed publications about it. I'm sure you're completely surprised, no?)

The first I heard of it was in Jeff Shallit's extremely cogent, and only somewhat nasty, dismantling of Dembski's credentials as a "mathematician", which was an expert submission in the Kitzmiller case; you can find it on the NCSE site. I think the project is called something like "MESA"? If you're willing to tolerate the smell, you could check his blog.
I've probably read 75-80% of the testimony in the case (given what I do for a living, it was pretty important...).
My Third Side
(Anonymous)
Personally, I have a problem with both of them. Creationists (in the christian term) use ID to prove they're right. As I understand it, ID displays the possibility(!) of some form of intelligence that is findable in the universe. For me, this doesn't say anything about a god or the truth of a creation. It just says that some form of intelligence participated in the past. It could even be existance itself that brings some form of intelligence through it's complexity. So ID in my opinion does not even rule out any kind of evolution. But I might have a pretty abstract view of it.

On the other side, the scientists today. Some if not most of them for me today *are* evil, in some sense of that word. Many of are sceptic about anything but their own field or sciences. Science in my eyes should question itself more often. And it should never begin seeing it's models as truth. The greatest lack of science today is the ignorance on the issue that their wisdom is based on experience, not on reality. I don't speak for all scientists, as there are still very good ones and great minds out there.

Well, that's my opinion, in short :)
phaylon
(Anonymous)
I am not quite sure after reading your first paragraph if you don't believe that there are some that find the story of Adam and Eve a bit silly but still believe in intelligent design or that you just aren't addressing them. For instance, are you lumping scientists like Newton, Einstein, and Davies into this category or specifically excluding them for a more narrow group within the weak/strong anthropic principal group?

I guess it doesn't really matter. People are entitled to their opinions. Opinions are like ass - everyone has one and most people's stink (mine included).

Ok - not all God fearing folk think science as bad and a large number of scientists believe in God in one form or another. History favors the winners and by and large the gnostic camp lost. Ok - good thing I don't have to fear judgement from the winners (being a Christian myself) but that doesn't mean that they hold the only opinion on the matter.

I am a Christian, I believe in evolution. I believe that the next stage in human evolution will be a spiritual one (the ability to communicate the ineffible).

As far as the airplane paragraph goes. You should really read the Symbiotic Universe by George Greenstein. I am not saying that the fact that an electron's charge is exactly opposite a proton is proof of God or that without quantum tunneling heavy elements would be impossible or that water floating when it freezes unlike almost everything else is proof that the universe was designed to make life possible. I just think that the chances against a randomly created universe producing life are so small one SHOULD be wondering if there is intelligent design.

Ok, I didn't finish reading your post. I am don't think you were addressing people that think as I do. If you really want to read a quack-pot - you should read the Physics of Immortality by Frank J. Tipler. Here is my take. Frank was a mathematician and a strong atheist. He has a mystical/spiritual experience one late night lost in his numbers and it has such a profound effect on him that he can't shake it. He ends up setting out to prove God exists through math by equating him to a super-computer.

*shrug*

The Anthropic Principle
I am not saying that the fact that an electron's charge is exactly opposite a proton is proof of God or that without quantum tunneling heavy elements would be impossible or that water floating when it freezes unlike almost everything else is proof that the universe was designed to make life possible. I just think that the chances against a randomly created universe producing life are so small one SHOULD be wondering if there is intelligent design.

This is known as The Anthropic Principle and this sums up the problems with it. I would highly suggest reading their argument, its short and well formed, but I'll amply the major point of their rebutal here.

While it may seem the universe and our planet are tuned for life, the same outcome results if life is tuned for our universe and our planet. Voltaire parodied the Anthropic Principle by stating that noses are designed for glasses and feet are designed for shoes. Look how they fit together so perfectly. If the nose were shaped differently glasses would be useless!

It is true that life as we know it would be unlikely not be possible if the universe wasn't tweaked exactly so to a (seemingly) improbable degree. One can then conclude, as you do, that the universe must be tuned for life. This is not necessarily so. The statement only applies to life *as we know it*, not all possible life. Since we barely even understand our brand of life we cannot say what other radically different forms life might take in a universe with radically different physics. There's nothing which says life cannot form in a universe where, for example, ice sinks in water. There's nothing which says life requires DNA or must use evolutionary mechanisms or be carbon based or rely on water.

To state that no intellegent life could exist under a different set of physics ignores that we're not even very good at predicting the conditions that life as we know it will flourish. We find life where we do not expect it in conditions we thought to be detrimental to all life: clinging to hot sea vents; deep underground; on glaciers. To state that ours is the only possible universe to support intellegent life is hubris and an argument from incredulity. Just because we cannot conceive of it doesn't make it so.
I think a big problem with most creationists is that they feel creationism and evolution are mutually exclusive. I've never seen a study that suggested that.
See, it's not a matter of studies that suggest anything for the Creationists. They deny that evolution could ever occur because for them, 'evolution' involves the Big Bang, solar disk accretion, lunar formation impact, dinosaurs, descent in common with modern apes (strawmanned as descent from monkeys or 'goo-to-you') and therefore it denies a literal-as-possible reading of Genesis.
Which is to say, scientific studies, or studies of any kind, means jack - and - all to them.
The same people that tell you when the bible says the earth was made in 6 days it really was made in 144 hours. That's a good point.

I guess I always felt people could look at it like this (can't we all just get along?)

A) God created the big bang
B) the big bang created man
C) God created man
Well thought out...
(Anonymous)
I would point out that the OT of the Bible clearly states that the earth in round. "The LORD sits on the circle of the earth" or some such.

I have personally always wondered where the material for the BIG BANG came from...?
Where da matter at?
I have personally always wondered where the material for the BIG BANG came from...?

Prepare to be sorry you asked.

Before I jump in, keep in mind that cosmology is weird. It works on the very, very big and very, very small. The very short lived and the very old. Little in human experience prepares you for the way things work on those scales. Common sense often doesn't work and just gets in the way.

One set of hypothesises (I don't believe their well formed enough yet to be called as theories) says that the total energy of the universe is 0 (just so we're all on the same page, matter and energy are interchangable: e=mc^2). This neat bit of cosmological accounting answers the question "where did the universe come from" with "nowhere". What you say? If the total energy of the universe is 0, what's powering my laptop? I'll try to explain one of these hypothesises. Keep in mind that I barely understand this stuff myself. There will be lots of hand waving and all sorts of specifics will be wrong (I'm pretty sure my uses of "entropy" and "work" are not accurate).

Two ways of looking at the potential energy of a system are gravitationally and work potential. When energy is all spread out evenly entropy is maximized and no useful work can be done. When its concentrated lots of work can be done. The classic example being gas in a room. If its all squeezed into a corner its at low entropy, there's an imbalance and the gas can do work by expanding to fill the room. It has a high potential. Once it fills the room at reaches equalibrium it cannot do any more useful work and thus is at maximum entropy. It has a low potential.

Gravity is the opposite. When things are all spread out gravity causes them to fall into each other, clump, heat up, spin, spiral, form stars and planets and all sorts of interesting things. Spread out matter has high gravitational potential. Once its clumped together its potential is low. A black hole is the ultimate in low gravitational potential.

The early universe was compressed down to a point. Zero gravitational potential but a huge potential for work. As it spreads out, gravitational potential increases and its work potential decreases. If you view work potential as positive energy and see gravitational potential as negative energy they cancel out. Net energy of the universe, zero. All sorts of localized imbalances make the universe interesting. Those imbalances may be generated by echos of gravity waves from the preceding universe... but that's way outside what I understand.

Like I said, I've probably got it all wrong and even if I did get it right cosmologists are still in the early phases of noodling around with this sort of thing. But it does offer a possibility for a universe without some Intergalactic Cable Guy to throw the switch.
Separate school and state. Please.
(Anonymous)
It seems to me that most of your beef with Creationists would disappear if democracy had not evolved a structure (pun intended) for indoctrinating children, the compulsory schools, over which factions in the democracy will fight eternally for the right to give kids the "correct" indoctrination. I have no interest in forcing creationism or intelligent design into schools. I simply want to acknowledge the liberty of these little people by recognizing their right not to be compelled into anything (http://www.sepschool.org/).

Here's where many evolutionists get disingenuous, because secretly they believe it is really important that they get other people's kids aside to teach them why creationism is wrong, so that their parents don't subvert them. It's as if they think their arguments won't stand on their own once those children are independent adults, so they are really fearful of allowing people to have true liberty.

You can't have it both ways. As long as creationists don't bother anybody, it ought to be okay to believe whatever you want. I use the same reasoning for why I believe gay marriage should not be illegal. (How often do you hear that from a fundamentalist?) Don't force anything on me or my kids, and we won't force anything on you or yours.
I've only got about halfway through your post - mainly because I've been clicking all the links and getting far too curious about everything - and thus run out of time and need to help capture a cat to take to the vet. ANYWAY, I thought I'd post on the strength of what I've read so far, more about the personal uneasy coexistance of the two theories. I'm not sure how appropriate it is :/

When I was really young my mother brought me up with lots of bible stories and going to Sunday School and a Church primary school. Creationism wasn't exactly pushed on me but Genesis was referenced a lot and there was nothing really on the curriculum which made mention of other theories explicitly. I did, however, read a fair few books which told me about the Big Bang thory and dinosaurs and evolution and Darwin while I was on my own. Somehow I came to believe both. There seems to be a part of my brain that tells me "Yup, God, world, creating, fair enough", another part is equally content with "Dinosaurs, evolution, mutation, matter - well done universe!"

I can sort of pick an explanation depending on context and be equally ok with it. Maybe God created the dinosaurs, maybe man evolved and created God. For whatever reason it seems to be a dualism that hasn't caused me a theological crisis and I was perfectly happy to study biology at secondary school until I was 18 as one of my chosen subjects. I think I was lucky that Creationism wasn't forced upon me, though. I do think it ought to be explained as a theory but only insofar as all the other theories are given time.

I will return later to finish reading!
Nicely put. I like your style.

Interestingly, I do have a very intelligent geek friend who believes in some kind of creator god. Not due to any religious background, but because he spent years working on self-evolving algorhythm programmes and concluded that evolution simply does not work the way folks say it does...

My feeling is that he is overestimating his own skill as a programmer, and mistaking the virtual world of his artificial life-forms for the real - and vastly more weird & complex - world out here. Just because it didnt work for him, in his virtual simulation, does not necessarily have any bearing on the outside world. Its just an analogy, not a proper simulation...
Agreed. Evolution is very difficult to simulate. Probably one of the best counter-arguments is that mutation rates in genetic algorithms are much higher than they are in nature because otherwise things can't get done in a reasonable amount of time.

And while we're on that topic, did he have structures analogous to DNA? If so, what sorts of mutations were involved? Base-pair mutations? Frame-shifts? Sequence mutations? What about sexual recombination? For mutation, was single-point or multi-point crossover used? Did he properly understand the role environment plays, such as restricting resources, isolating populations and altering the "physical" environment from time to time? (the last part may not be strictly necessary)

Hell, we can get more basic. Did he start from scratch or did he seed the world (abiogenesis versus creationism)? If he seeded the world (probably), how far along life's path did he start? What implicit biases may have crept into the work?

Evolutionary and genetic algorithms are still a relatively young field and anyone who is going to make sweeping claims based upon them must be careful. Claiming that because his computer programs didn't work the way he expected evolution to work is a dicey thing. This isn't to say he's wrong -- I've never seen his work and I wouldn't be the best person to evaluate it -- but it's a huge leap to go from watching programs misbehave to asserting there is a god.
I guess my last post should have been summed up as: what assumptions were made in his software? I could have been a wee bit more concise :)
Hehe. I think he made a whole bunch of assumptions (as one must) when setting up the program. It was not from scratch. His observation was that *evolution through mutation and natural selection* did not work as commonly claimed. My argument with him was that he was extrapolating from his simulation without sufficient evidence, because his simulation was *not* the real world...

He *has* talked to me about the finer details, but tis not my field, and they kinda washed over me...
Punctuated Equilibrium
With regard to "gaps in the fossil record," see also punctuated equilibrium. The first paragraph of the Wikipedia entry is actually very succinct:
Punctuated equilibrium (or punctuated equilibria) is a theory in evolutionary biology which states that most sexually reproducing species will show little to no evolutionary change throughout their history. When evolution occurs it happens sporadically (by splitting) and occurs relatively quickly compared to the species' full duration on earth. Punctuated equilibrium is commonly contrasted against the theory of phyletic gradualism, which hypothesizes that most evolution occurs uniformly and by the steady gradual transformation of whole lineages (anagenesis). Punctuated equilibrium is the currently favored theory for the fluctuating patterns of evolution observed in the fossil record.
—Theory
lichtkind
(Anonymous)
dear Ovid with full respect and acknowledgment of your good and free cgi course and your long time perl contributions, this post from you is in my POV fully biased, uninformed and misleading. even if i like the part with: "science is just..." that i not agree with, i dont even think you can understand this matter in any deeper form at current time. so why im bitching here?

I dont want defend creationism because as far i know they are partly right by accident, not because there bright, or insightful, they only defend their beliefs and refuse to approach in knowledge which is mostly also true for science. there are not only some holes there are plenty artefact contradicting nearly every theory in evolution which are ignored since decades in archology the situation is even worse. dont need to debate that there are enough written about and who wants to understand, will do it, the point i want to make is that this entire battle science vs beliefsystem is just waste of time because both are full of shit.

just look at the gab between what darwin written and what is teached, most student are shocked by darwin, then listen to well respected genetic scientist Mae-Wan Ho about how is this young sience driven in a very bad direction, because once bigger inventions are fade more in the past history is often revised. once you grok this pattern of bluring knoledge you will find it in physics (gap between early works of maxwell faraday and the things that came later, gab between different inventions of einsteins pal bose) medicine (far too many examples most of them today called quacks) and other science like biology and expecially evolution theory.

the whole picture is too complex to be rolled out in a sentence but to answer to your arguments:

1. yor not right in your assumption that you can find out the earth is round because the ocean. gravitation ist constant and there are several holes and mountains in the sea. every seaman knows this, so just my appearance of an sailing ship you cant shurely conclude that earth is round.

2. your right that greeks did know about round earth but as far i know they calculated it from the shadow of a pile at noon on locations with different longitudes. and your conclusion that this was also known in europe by this time is absolutely false, maybe some free masons did know but the average monk (most others couldt read anyway) did not because since the great disputes in 13 century the readings of aristoteles and others was restricted, and free speach in some areas tightly controlled so most didnt know. it was over 100 years after kepler and only with the credibility of somebody important like sir isaac newton that could touch this matter and bring it to more public atention.

this things have not changed. most of the really interesting and importend, viewchanging things are still well published but very well hidden from a wider attention. for instance the existance of ufo's are one of the best documented facts several times better documented to be absolute certain(military witnesses in 40ies, dr greer, billy, etc. etc.), but most people think this is silly x-files stuff. there is the main problem, no matter what knowledge we talking about.

hope i bored you not too much
blessings (sir_lichtkind on use.perl)
Ignorance
I'm not going to talk about intelligent design proponents. I'm going to call a spade a spade and refer to them as creationists.

Except ... no. The only way you can reasonably get away with saying ID == Creationism is if you redefine Creationism so that it resembles something that people who have traditionally called themselves Creationists fundamaentally disagree with. Come on, how useful is that?

Dembski, perhaps the most prominent ID proponent, explicitly disagrees with a young Earth, with creation over six 24-hour days, and so on. He believes in an intentional, guided natural selection and evolution of species (though he believes that humans were "specially created").

Creationists disagree with all of that (except the part about humans being specially created).

So you're obviously wrong. But at least you feel strongly about it, and that has to count for something!

You get into the bulk of your post with a stupid straw man attack: ID proponents have nothing against science. I won't belabor this further there's no point: your attack is nonsense.

You then say, The basic argument is something along the lines of "yeah, but everyone once believed the earth is flat" ... except, of course, that the prominent ID proponents do not use this form of argument. They do point out that just because scientific consensus believes something does not make it true: for example, Newtonian physics. But they do not say that because it could be wrong, that it is.

Also, you fall into a serious logical trap yourself: that just because some arguments that some ID proponents use are false, therefore ID is false. Hell, even if all ID proponents offered those arguments, it still would not prove ID is false, because ID does not essentially rest on those arguments. Much of what Darwin said was proven false; does that mean his theories are false? Of course not. You'd have to attack the essential statements of ID in order to prove ID to be wrong.

Of course, you cannot do that, because the essential statements of ID are not disprovable. But that's no excuse for attacking ancillary claims of ID propnents and pretending your assault actually harms ID itself.

Finally, you write: This dishonesty is astounding and if there is a God, I'm sure he's hanging his head in shame. Oh right, because nothing you've ever done is as bad or worse than giving arguments that someone else thinks are stupid and dishonest? Seriously, you need a serious dose of perspective.

-- pudge

Re: Ignorance
The only way you can reasonably get away with saying ID == Creationism is if you redefine Creationism so that it resembles something that people who have traditionally called themselves Creationists fundamaentally disagree with. Come on, how useful is that?

Many ID folks identify themselves as creationists and vice versa. For example, one of the primary email address of intelligentdesign.org is Cre8ionist@intelligentdesign.org. Even brief research on the Web will reveal many more instances of this.

Many creationists do not believe in a young earth and many freely acknowledge evolution within a species (though they deny that one species can evolve into another). So just as you obviously feel that my sweeping generalization about ID proponents is limited, so to is your "creationists disagree with all of that" comment. Creationists are far more varied in their outlook than you suggest and, as a result, you do them a disservice. If you trust Wikipedia, they go into more detail about this.

For most folks reading what I wrote, I think they understood exactly what I meant by equating ID with Creationism: it's the "God did it" theory. The modern ID movement just tends to publicly eschew the word "God" in hopes that they can snow the public into thinking that they're some form of science. ID is merely an aspect of religion. As such, there's nothing wrong with it. It's the rank hypocrisy of its proponents which offends me.

Also, you fall into a serious logical trap yourself: that just because some arguments that some ID proponents use are false, therefore ID is false. Hell, even if all ID proponents offered those arguments, it still would not prove ID is false, because ID does not essentially rest on those arguments.

You're putting words in my mouth. I did not say that ID is false. In fact, I specifically wrote In fact, it's just as fair to point out that if creationist premises turn out to be false, it does not mean that there is no god or that this super being does not have a hand in the creation of life. I wrote this to point out that some of the more common attacks ID proponents use are fallacious. I did not attack ID, though I confess was rather harsh towards some ID proponents.
Re: Ignorance
Many ID folks identify themselves as creationists and vice versa.

This is true, and irrelevant. Many Perl programmers consider themselves to be Christians -- even its author! -- but that does not mean Perl == Christianity.

So just as you obviously feel that my sweeping generalization about ID proponents is limited, so to is your "creationists disagree with all of that" comment.

I was a bit sneaky here in that I was specifically referring to "people who have traditionally called themselves Creationists." All such people believe in the Young Earth. Old Earth Creationism is a new deal (and has more in common with most ID proponents, but is still different, for example, in that they do not acknowledge evolution from one species to another, as most ID proponents do).

I did not write that to be sneaky, but to point out without getting into detail that it all depends on how you define Creationism.

If you trust Wikipedia

Not on this issue I don't. :-) I generally distrust Wikipedia on any controversial issue, especially in how to define the issue.

For most folks reading what I wrote, I think they understood exactly what I meant by equating ID with Creationism: it's the "God did it" theory.

I know a lot more than most folks about ID and Creationism, and I didn't understand it that way at all.

Regardless, nothing you said dented that theory.

The modern ID movement just tends to publicly eschew the word "God" in hopes that they can snow the public into thinking that they're some form of science.

Some people do this, yes. Certainly not all major ID proponents do.

And some in the modern Darwinist movement -- e.g., Richard Dawkins -- say that evolution shows evidence for lack of God's hand in our existence, which is also entirely false and dishonest. But I guess since he doesn't believe in God, he doesn't have to worry about shaming God. :-)

You're putting words in my mouth. I did not say that ID is false.

I'm sorry, I took there is no "intelligent design" to be a statement that the view was false, rather than saying that there is no distinction between ID and Creationism. I see now I was in error. However, that statement still is false, because as I have sufficiently demonstrated, Creationism != ID.

I did not attack ID, though I confess was rather harsh towards some ID proponents.

No, you were harsh toward all ID proponents, which is my main problem with what you wrote: you said all IDers are Creationists, which is false, for any commonly accepted definition of "Creationism."

Sure, if you water down "Creationism" to mean "God acted intentionally to cause man's creation," then ID, essentially, is Creationism. But that also means that many, if not most, scientists (in the U.S., anyway) are Creationists, including the ones who full-throatedly believe in natural selection and the evolution of species from other species, including man, as there is nothing in that broad statement of God acting intentionally to preclude any of that. So your use of "Creationist" therefore becomes quite meaningless.