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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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November 7, 2005

Intelligent Design, Molecule By Molecule

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Posted by Derek

[Update: reading this post, I can see that I was in a pretty testy mood when I wrote it last night. Intelligent Design does that to me. So if you're not in the mood to be ranted at, come on back tomorrow and I'll see what I can do for you. . .]

Further update: comments have now been turned off, to keep this one from rising from the grave. No doubt I'll post on ID again eventually, so everyone will have another opportunity to ventilate their opinions.

OK, one more on this topic, and then we'll try to give it a rest until the Dover school board decision comes down. (The comments to the yesterday's post are still rolling right along, though, as you'd expect from a debating ground like this one). The article by Jerry Coyne I linked to yesterday gives some good anatomical arguments against intelligent design. But I wanted to zoom down to the molecular level for a minute, since after all, I am a chemist.

DNA is a wonderful molecule, no doubt about it. And to someone like me, who believes that the evidence for evolution is overwhelming, it's also a fine illustration of how it works on a molecular level. Others, though, no doubt see in its intricacies the hand of a creator. What, I wonder, are we then to make of the degraded remnants of old viral DNA in our genome? Designed in there, or not? Or what about the long stretches that seem to do nothing but repeat the same few base-pair letters over and over - dozens, hundreds, or thousands of times? Doubtless the Designer would have his reasons, but perhaps some of these would have been better implemented with repeats that aren't so prone to breakage and mismatch. Hundreds of terrible diseases result. (That page is only the barest sample. It's an awful topic to research). It's almost as if these things persist as the residue of ancient random choices or something.

Moving on to what are supposed to be the normal genes, we find entire books can be written on the horrible consequences of tiny changes in the genetic code. Take the so-called Swedish and Dutch mutations in the amyloid precursor protein. Switch the DNA a bit, and you get a new amino acid in the protein. Get the wrong one, and you die, most terribly, from early and rampaging Alzheimer's disease with complications. Those particular mutations have been in families for hundreds of years now - we've tracked them through the generations. They're still with us because the people involved live long enough to have children - many of whom are destined to die the same terrible way - before the underlying disease finishes them off. It's almost as if the consequences of a mutation were more severe when it affects reproductive fitness.

Mysterious ways, mysterious ways. No doubt that accounts for why we (and guinea pigs, and Peruvian fruit bats) can't make our own vitamin C, the way the other mammals can. Or why our livers respond to the excess of free fatty acids in type II diabetes by. . .making more sugar, which is exactly what the body doesn't need. There must surely be a reason, too, a good well-designed one, for autoimmune diseases: having our bodies tear themselves to pieces on a cellular level; I can't wait to hear why that feature was built in. It's almost as if once we've had children, just about anything can happen to us.

I'll stop there. I could go on for pages. Suffice it to say that when I look at the biochemistry of living systems, I see an amazingly complex system, wonderful to behold. And it's held together with duct tape, chewing gum, and weathered pieces of wood - whatever was handy, and whatever worked. It's almost as if it's just been tinkering along for a billion years.

Comments (133) + TrackBacks (2) | Category: Current Events | Intelligent Design


COMMENTS

1. peej on November 7, 2005 10:48 PM writes...

Derek- maybe you have hit on the "not so intelligent design" theory.

Personally, I think your observations just give credence to my explanation that all life is being designed by a bunch of competing 14 year old boys in some giant sim game. Multiple Not-So- Intelligent designers, as it were.

Now I just have to convice a school board to include this in the curriculum for fair balance.

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2. biohombre on November 8, 2005 12:02 AM writes...

Hmmmmm. Duct tape, chewing gum and pieces of wood? With over 100 genes (http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/D/DNArepair.html) involved in maintaining the fidelity of DNA, (or over 500 proteins involved in DNA replication & maintenance; Nature 409, 860-921 ) it strikes me as just a bit more elegant and just a bit less jury-rigged than you imply! I do not know if it has a failure rate to satisfy rigorous 'sigma six', or better self-maintenance than Mac OSX (10.4.3), but I suspect it may do better than some manufacturers of our commodity electronics!

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3. Clark on November 8, 2005 1:01 AM writes...

Friend of mine is a born-again microbiologist. Was a creationist for a long time. Is now an IDer of the flavor of God giving an occassional nudge. Is this so bad? It led him to 'predict' that all the junk DNA was not junk but actually useful in ways we hadn't yet determined. (And this is turning out to be a lot more true than was apparent 10 years ago. As an example, the viral fragments may be useful for jumping genes) It did NOT cause him to stop looking for the evolutionary things (remember he believes that only the occassional nudge is necessary). While I think it is a violation of Occam's Razor, it is largely a harmless bent that actually provides a different (and thus useful) perspective as long as not taken too far.

If what is bad about ID is the camel's nose, then we should be honest and say so.

Clark

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4. David on November 8, 2005 3:57 AM writes...

The ID movement, as articulated by the Discovery Institute and its associates, denigrates the hard work of scientists and makes a mockery of the process of scientific discovery. By actively attempting to defecate on evolutionary science for purposes of suplanting good science education with religious dogma, the "ID movement" of the Discovery Institute (DI) positions itself not at the nose, but in the heart of the camel's bowels. One wonders whether the ID proponent who favors "God's occassional nudge" can be left unscathed by the foul fumes of the DI approach. Where is the line between a "harmless bent providing a different perspective" and a religious zeal that would, through distortion and faulty reasoning, joyfully violate your freedom of religious choice and that of your children?

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5. daen on November 8, 2005 4:37 AM writes...

biohombre, DNA copying and repair mechanisms certainly do ensure remarkably high fidelity. Except when they don't. There are diseases which affect these repair mechanisms (for example, the XRCC and xeroderma pigmentosum disease genes), and certain DNA polymerases are lower fidelity than others.

If one in three copies of OSX spontaneously developed an electronic cancer, I wouldn't consider that a "six sigma" result.

If there is a Designer, then He is not entirely right in the head. Or He really doesn't like us very much.

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6. qetzal on November 8, 2005 8:00 AM writes...

Clark,

I fail to see how ID adds anything useful. How does ID lead one to predict that most non-coding DNA has a function?

That said, I have no objection to anyone pursuing the scientific implications of ID as they perceive them. In fact, I wish more ID proponents would do exactly that.

The problem with ID is not the camel's nose. The problem is that most major ID proponents claim that there is significant evidence for ID, when there is not. Many ID proponents claim that evolution is a 'theory in crisis' or some such. Also untrue.

A great many ID proponents want high school instruction in evolution to be watered down or subject to special caveats (evolution is 'just a theory'). A significant subset want ID taught as an alternative 'theory.'

The reality, of course, is that there is virtually no scientific evidence that supports ID. There is certainly no scientific theory of ID. In most cases, ID isn't even formulated as a testable scientific hypothesis.

Despite all this, some people want to force the teaching of ID in public science classes. And it's quite clear that they want this because it furthers their religious goals. This is a perversion of science and a perversion of public schooling.

Adults who choose to believe in ID (despite lack of evidence) are not the problem. The problem is adults who want to teach kids that ID is well-suppported science, when it clearly isn't.

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7. Tom Bartlett on November 8, 2005 8:52 AM writes...

I wish we were intelligently designed. Except, I'd be out of a job. But, I guess I'd be able to throw away my eyeglasses.....

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8. SteveSC on November 8, 2005 9:13 AM writes...

The issue of a creator, whether a 'nudger', 'clockmaker', or raging Zeus, is properly the realm of religion. We don't have enough knowledge to know whether, in a probabilistic universe, there is some 'intelligence' who is loading the dice.

The problem in the public schools is that the religious zealots are rising up to battle the 'anti-religious' zealots. Intelligent design is a tactic used to oppose those who believe that freedom OF religion is freedom FROM religion and teach kids that evolution 'proves' there is no god.

When zealots of one stripe want witchcraft, astrology, mysticism, and various "man is the source of all destruction to Gaia" tenets taught in the public schools, and oppose teaching the Bible as literature, or even Shakespeare, it is no wonder that zealots of another stripe rise to oppose them. To be credible, scientists that oppose ID should be just as energetic opposing ALL the pseudo-science in the public schools.

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9. Derek Lowe on November 8, 2005 9:32 AM writes...

Steve, I'm ready, willing, and able. Anyone who wants to point out organized efforts to teach voodoo or the like, please do. (As an amateur astronomer, you can imagine how much time I have for astrology, for example).

And I regard much current environmentalism as a religion. (I remember the first time I came across that idea, in a speech by Michael Crichton. It was disconcerting, because there are a lot of things about Crichton that I don't like, but when I read that, I thought "Yeah. . .of course. . .")

Fuzzy Gaia-ism is probably the biggest load of rubbish in the school system, measured by volume. But as far as I can see, Intelligent Design has the highest muzzle velocity these days.

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10. Tom Bartlett on November 8, 2005 10:04 AM writes...

I think "freedom FROM religion" is pretty much my most cherished aspect of the Bill of Rights. And it pisses me off every time I hear some demagog politican invoking the Deity to sell soap, or justify bombing civilians or any other Christian purpose.

I agree with Derek that fuzzy Gaia-ism is rubbish, but I would also argue that global warming, whatever your political leanings may be is THE most critical issue facing humanity this century.

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11. PandaFan on November 8, 2005 10:22 AM writes...

If we are designed, not only did the designer not let us synthesize vitamin C, said designer left a nearly functional gene for the process behind (which looks suspiciously like the functional ones in other mammals, save the function destroying mutation).

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12. fool on November 8, 2005 11:07 AM writes...

Derek

The underlining assumption of your critique of the "unitellegent design" is that the creator's intention was to let man live forever disease free.

It was, untill sin entered. Remember what the God of the bible said:"but of the tree of the knowledge of good and evil you shall not eat, for in the day that you eat of it you shall surely die. Genesis 2:17” And when Adam did, God said "“ Cursed is the ground for your sake; In toil you shall eat of it all the days of your life. Both thorns and thistles it shall bring forth for you, and you shall eat the herb of the field. In the sweat of your face you shall eat bread till you return to the ground, for out of it you were taken; for dust you are, and to dust you shall return.”

Obviously, a dramatic change at the DNA level was brought about with that curse, whcih would explain the things you mentioned regarding DNA and just human pain and suffering in general.

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13. Timothy on November 8, 2005 11:16 AM writes...

Apparently that God fellow is a real jerk.

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14. fool on November 8, 2005 11:29 AM writes...

With all the voodoos out there in this world, it can be mighty confusing...well it actually is! You all are rigthfully skeptical and should be at anything that sounds like a fairy tale.

But I submit to you that the Bible and the God of Israel can hardly be compared to the other voodoos, with thousands of years of researchable history and countless scientists of all fields behind it. I have a humble suggestion to all of you skeptics. Assume the biblical account of origin to be true, and use ITS account (not your own version) to examine it against the facts and see if it makes sense beyond reasonable doubt.

Like I said before Kurt Wise and Ken Ham (www.answersingenesis.org) are excellent references.

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15. Derek Lowe on November 8, 2005 11:32 AM writes...

Fool, I can see why you recommend Kurt Wise, since you seem to be on the same wavelength. I really can see why, if you stipulate at the beginning that the bible is the inerrant word of God, why you come to the conclusions that you do. It's just that I don't (and can't) start from that premise.

But that leaves us no room, in the end, to discuss anything. Anything the scientists think that they can explain? They're wrong. God created it to look like that. And the things that the scientists can't yet explain? They can't, because God did them. How do we know that? Because it says so here in his book. And how do we know it's his book? Because it says that it is. We have God's word that it's the Word of God.

Case closed, for those with enough religious faith to take all that in. Case not closed, for those who align with the system of thought that has built the technology we're now using to argue these points.

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16. Jim on November 8, 2005 12:24 PM writes...

Here's an interesting question (at least I think). Do we know more about the universe than we do not know? Surely we know much more about the universe than we did 4000 years (or yesterday for that matter) ago but do we know more about it than we don't know? Likewise, do we know more about the simplist living organism on earth than we don't know? With every question we answer don't we create 3 more? I think we (as scientists) often have an extremely arrogant view of things. We act as if we have it all figured out (as compared to our ancestors thousands of years ago) when in fact we do not. To be sure, science constantly moves forward and it provides the basis for the advance of civilazation in many respects but we are not even close to having all the answers. Is ID science? That's a tough question. Is an archeologist or anthropologist sifting through a pile of rocks looking for primative tools practicing science? Is natural selection by random mutation truely random?

Should we teach our kids it is truely random and that this is an irrefutable fact?

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17. jim on November 8, 2005 12:29 PM writes...

Just so there's no confusion, the idiot "Jim" above me is not, well, me, the "jim" of yesterday's posts. I wouldn't want my rep soiled by this vegetable who can't tell that ID isn't science.

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18. RKN on November 8, 2005 12:55 PM writes...

  Suffice it to say that when I look at the biochemistry of living systems, I see an amazingly complex system, wonderful to behold.

Me too, but...

  And it's held together with duct tape, chewing gum, and weathered pieces of wood - whatever was handy, and whatever worked.

With all due respect to you, Derek (and I mean that), I loudly disagree.

I would invite inlookers to take a gander at this and then decide for themselves if it looks more like duct tape, gum, and driftwood, or rather more like a printed circuit board.

Does this provide evidence for the design[ER] or in any identify who it is? ABSOLUTELY NOT. Does it infer design? I think any intellectually honest person would have to say it does. Could it have self-assembled via the preferential selection of accumulated mistakes? That thought experiment is left to the reader.

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19. qetzal on November 8, 2005 1:10 PM writes...

Jim (not jim) asked:

Should we teach our kids it is truely random and that this is an irrefutable fact?

No. But we should teach our kids that evolution is the best and only scientific explanation for the diversity of life on Earth. It is the only explanation that is well supported by scientific evidence. It's the only explanation that has repeatedly made successful predictions about what we should expect to observe in appropriate contexts.

Does that prove that it's correct? No. Does a lack of scientific evidence for a designer prove one doesn't exist? No!

If there really are public school teachers who routinely claim that science disproves God and that the universe is irrefutably undesigned, they should be firmly corrected or fired. However, I suspect this is largely a strawman argument. I don't know of any recent cases where parents felt compelled to sue schools for teaching atheism. Contrast that with the many recent controveries involving inappropriate attempts to slip religion into science class: Dover PA, Cobb County GA, Kansas State Board of Education (more than once now), ....

To be clear, I'm just as opposed to teaching atheism in public schools as any other religious tenets. But I'm also skeptical of SteveSC's implication that this is a major overt problem.

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20. Nathan on November 8, 2005 1:47 PM writes...

Listen people, it's all very simple:
Teaching that the universe was "created" (or designed) is a RELIGIOUS statement.
Teaching that the universe was "created" from nothing by chance is also a RELIGIOUS statement.

Either teach both or teach neither.

The vast majority of nonscientists understand the simplicity of this. Why do so few scientists?

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21. Derek Lowe on November 8, 2005 1:52 PM writes...

RKN, those metabolic pathway charts are always impressive-looking. (Until recently there was an older version taped to a wall downstairs from my office). But I can just as easily look at it and see two billion years of "whatever worked". Our imaginations seem to run in different ways.

Earlier generations of humans looked at the cathedral-like complexity of cave formations and clouds, the fine structures of snowflakes and crystalline outcrops, and the curved and carved patterns of eroded rocks, and decided that these things must have been built.

And built they could have been, if you believe in a God that set up the physical laws involved and sat back to see what they could do. I have no problem with such a Deity. I do have a problem with one that could faked everything to make it look as if such laws were in operation, though.

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22. jim on November 8, 2005 1:55 PM writes...

Nathan,
For something so "simple", you sure misunderstand it. The theories you think you have a problem with DON'T require that the universe was created from nothing by chance.

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23. fool on November 8, 2005 2:06 PM writes...

Derek

I find it perplexing that highly educated people would believe without such faith that, as complex as life is, there can simply be one explaination--evolution and a God cannot have designed all this.
Do you really have that big of a faith to believe billions of years plus NOTHING will give rise to one single cell, let alone humans?

RKN
I have to say you're among the most intellectually fair-minded persons on this board. No offense to anyone else.

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24. fool on November 8, 2005 2:10 PM writes...

jim

"you sure misunderstand it. The theories you think you have a problem with DON'T require that the universe was created from nothing by chance."

Please give your insights on how the first atom (or whatever) came to exist without invoking God or something like God.

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25. jim on November 8, 2005 2:20 PM writes...

An interesting question, fool, and one currently being addressed through ACTUAL RESEARCH. While you may find it hard to get your head around, I also don't have a problem with the thought that "God" or whoever got the ball rolling. My point in this case was that this in no way invalidates Darwinian (or neo-Darwinian, really) evolution and natural selection, and vice versa.

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26. fool on November 8, 2005 2:22 PM writes...

"I do have a problem with one (God) that could faked everything to make it look as if such laws were in operation, though"

I'm not quite sure what you meant by that. But it'd certainly make sense to me that when God created Adam, he didn't make a baby Adam and allow the "physical laws" to make him a grown man just so that years later people like you and me can make sense of our carbon dating. He surely would've made a grown man to begin with. And the same goes for the rest of the creation.

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27. Nathan on November 8, 2005 2:28 PM writes...

Jim,
Of course "God" doesn't invalidate Darwinian evolution. The two can be absolutely compatible. However, I don't want it to be taught that chance mutation (biological universe) or chance collisions (physical universe) created what we see and know. By saying this, scientists are essentially making "chance" thier creator. I choose to have "God" as the creator, not chance. Both are RELIGIOUS viewpoints and either both or niether should be taught in schools.

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28. David on November 8, 2005 2:33 PM writes...

This fear-mongering about school teachers using evolution to teach that “God doesn’t exist” – where does it come from? Have there been any published studies of this? How many public school teachers are stupid enough to think that science has an answer to the existence of God question, and how many live in a social context that would allow them to make such a bold public statement without being called on it? Really folks, kids do talk to their parents and real cases of “God-denial” would stand out like a fish out of water.

The problem rather is that many parents and “community leaders” PERCIEVE that evolutionary science threatens their beliefs about God – especially those who subscribe to biblical literalism. This of course is the reason behind the “ID movement” which effectively argues “my God doesn’t exist and my moral standards don’t mean anything, if evolution is a fact, and current evolutionary theory is an accurate representation of the history of life”. Never mind that evolutionary theory is not considered the “ultimate truth” but rather the best explanation consistent with the mountains of evidence. Never mind that it is tentative and revisable. People threatened by evolutionary science usually haven’t taken the time and energy to understand it, but there is also the complication that deep belief systems are often difficult to reconcile with reasoned and reasonable views of the evidence and the scientific processes that develop and support scientific theories.

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29. jim on November 8, 2005 2:49 PM writes...

I couldn't have said it much better than David. Can anyone provide evidence for this supposed concerted campaign by science teachers to impose atheism on their students?

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30. fool on November 8, 2005 2:54 PM writes...

David

"Never mind that evolutionary theory is not considered the “ultimate truth” but rather the best explanation consistent with the mountains of evidence. "

I'm not so sure about that. What you have is a mountain of evidence being interpreted as for evolution which is also consistant with creation. And there's also another mountain of evidence against evolution, such as the gaping gap in fossil records for transitional species.

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31. fool on November 8, 2005 2:57 PM writes...

jim

"An interesting question, fool, and one currently being addressed through ACTUAL RESEARCH. While you may find it hard to get your head around.."

Indeed that's beyond what my mind can fathom how one can create energy/substance out of nothing. Not only will these researchers shut people like me up, they will also solve our energy crisis!

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32. Derek Lowe on November 8, 2005 2:57 PM writes...

Fool writes:

"I find it perplexing that highly educated people would believe without such faith that, as complex as life is, there can simply be one explaination--evolution and a God cannot have designed all this."

Science forces us to deal with the evidence we have in front of us, whether we find it comforting or not. The evidence I have in front of me is tha evolution occurs right now (as in bacteria, for example). The speciation found on isolated islands and such cases strongly suggests that it has occurred to produce a variety of other living species in the same manner. And the fossil record strongly suggests that it has occurred in the past, in the same manner. And the biochemical record (DNA analysis) strongly suggests that it occurred in the past, too, leaving thousands and thousands of clear traces and clear connections between species.

All of these lines of evidence agree with each other in degree, in kind, and in timing. They point the same way, and at the same thing. What I find perplexing is how all this can be ignored or brushed aside, and why I am supposed to do likewise.

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33. jim on November 8, 2005 3:12 PM writes...

fool,
It's amazing that you can even find ways to selectively quote a three-sentence paragraph. Is that stuff in the ID handbook?

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34. fool on November 8, 2005 3:17 PM writes...

Derek

As a scientist myself, I'm all for examining the facts. What I have been trying to get across is these facts could be interpreted differently according to one's onw world view.

jim

I didn't quote your entire post to save space. And the quote was NOT out of context. Just answer my previous question if you want to.

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35. jim on November 8, 2005 3:30 PM writes...

Actually, grammar commander (fool), it WAS out of context. The part I thought you would have trouble understanding was my ability to allow for the existence of a god (even one that created existence itself) without rejecting well-established science.

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36. Timothy on November 8, 2005 3:36 PM writes...

Fool: it sounds like you've been reading too much Kuhn.

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37. David on November 8, 2005 3:40 PM writes...

fool: “What you have is a mountain of evidence being interpreted as for evolution which is also consistant (sic) with creation. And there's also another mountain of evidence against evolution, such as the gaping gap in fossil records for transitional species.”

My case substantiated by “fool”, who apparently knows little or nothing about 1) geological time; 2) the processes whereby fossils are produced 3) the probabilities for a full series of graded transitions to be preserved, 4) the probabilities for fossils to remain unchanged over geological time, 5) the probabilities that fossils would have been discovered given the effort to date and 6) the plethora of transitional forms so far discovered showing grades of evolution in such animals such as horses, whales, etc. Negative arguments from ignorance seem to be the fuel for the ID fire.

While on this tirade, I’d like to comment on the misconception so often pushed by ID proponents that feeds into the frenzied backlash against evolutionary science taught in schools. It speaks to the random origins issue so problematic for some in this discussion.