About this Author
College chemistry, 1983
The 2002 Model
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: email@example.com
May 6, 2010
If you're looking for some ammunition in a creationist argument, evolutionary biologist John Avise of UC-Irvine has provided plenty in a new PNAS article entitled "Footprints of Nonsentient Design Inside the Human Genome". He goes over a number of not-too-intelligent-looking kinks in our genes.
This same point has occurred to many other people before, of course (I went on about it a few years ago here), but Avise has done a real service by collecting the arguments in one place in a clear and concise way. Exons and introns, spliceosomes, disorders of gene transcription and regulation, the unreliability of mitochondrial DNA, duplicons, pseudogenes, mobile DNA elements - they're all here, and all (to my eyes) much better explained by random, nonsentient tinkering than by thoughtful design.
Avise tries at the end to propose evolution as a helpful adjunct to religon, but I don't think his argument is going to fly with the people who might be most in need of it:
Evolution by natural causes in effect emancipates religion from the shackles of theodicy. No longer need we agonize about why a Creator God is the world’s leading abortionist and mass murderer. No longer need we query a Creator God’s motives for debilitating countless innocents with horriﬁc genetic conditions. No longer must we anguish about the interventionist motives of a supreme intelligence that permits gross evil and suffering in the world. No longer need we be tempted to blaspheme an omnipotent Deity by charging Him directly responsible for human frailties and physical shortcomings (including those that we now understand to be commonplace at molecular and biochemical levels). No longer need we blame a Creator God’s direct hand for any of these disturbing empirical facts. Instead, we can put the blame squarely on the agency of insentient natural evolutionary causation. From this perspective, the evolutionary sciences can become a welcome partner (rather than the conventionally perceived adversary) of mainstream religion
No, we're not going to get rid of theodicy that easily. The people whose beliefs most draw them to creationist and ID arguments tend, I'd say, to see life (and most especially intelligent human life) as one of the most important parts of Creation. Humans are, according to the Bible, the absolute peak of the entire process, and are thus the deserving subjects of continuous special attention from the Deity. Very few people with these foundations to their beliefs are willing to allow random evolution to share the stage.
+ TrackBacks (0) | Category: Intelligent Design
June 2, 2006
Razib over at Gene Expression dropped me a note about a petition titled "Conservatives Against Intelligent Design". I know that many of my readers don't necessarily share my political views (and this blog isn't explicitly political in nature, anyway). But anyone who'd like to help point out that many people who lean right actually think Intelligent Design is untestable and untenable can sign here.
We now return to the ASCO-centric world the blog will inhabit for the next few days (see the post below, and to come).
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February 9, 2006
Over at Pharyngula, I find that there's a bill in the Wisconsin state legislature which would ban the teaching of Intelligent Design in science courses. Since I've commented on this issue several times, I thought it would be instructive for me to say what I think about this proposal.
It's an awful idea. Just awful. As tempting as it might be at first, this is truly the wrong way to deal with ID in the classroom. Its advocates already enjoy themselves no end complaining about the rigid, dogmatic Darwinists trying to suppress Intelligent Design's brave, pathbreaking dissent - y'know, like Galileo, right? This will just hand them a wonderful party favor.
And besides, this isn't the way to settle these issues. One of the main things that drives scientists crazy about ID is that it sets itself up as some sort of equivalent alternative scientific explanation (while offering nothing close to what a legitimate challenge to evolution would have to bring). If we're going to have a fight about what's science and what isn't, then we should settle it by debating the evidence and the logic, not by getting someone to change the rules for us.
I can hear the protests now: "But isn't that what happened in Dover? You people got the court to throw ID right out of the schools!" Ah, but it was thrown out after loads of testimony from both sides, after cross-examination of everyone's expert witnesses, in an opinion by a judge who sat down to weigh the evidence. That's what torpedoed the ID side in Dover: careful, rigorous examination of everything they had to say. And it'll work every time.
So I hope that this Wisconsin idea dies before ever being brought to a vote. Don't do us scientists any favors, guys - we can handle this on our own. I have a great deal of contempt for the Intelligent Design movement, and I want to see it given the drubbing it deserves in open debate, over and over again, until it goes away.
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December 22, 2005
I was driving last night and listening to NPR, when they broadcast a commentary by Joe Loconte of the Heritage Foundation. This was bemoaning the Dover decision tossing Intelligent Design out of the local Pennsylvania school curriculum, and I'm afraid I ended up adding some loud and vulgar commentary of my own while hearing it.
Loconte's analogy was to the Big Bang theory in cosmology. He claimed that when the theory was proposed, that some of the objections to it were because of its similarities to the creation account in Genesis. I wasn't aware that the Big Bang was considered too religious, but it seems that this was the case for some physicists. That's quite an irony, though, considering some of the religious objections to it now. (Here's a rundown from everyone's favorite creationist web site, Answers In Genesis, certainly the first time I've ever linked to them. Hours of entertainment await you there, though, I have to admit.)
And you can see where the rest of the commentary went. We should make room for seemingly heretical theories in science, even if they seem to have religious overtones, because the orthodox dogma of the scientists can indeed be overthrown, yea verily, just as it was with the Big Bang theory. Loconte has sounded this note before, many times - see this CNN transcript where he goes on about the "high priests of evolution" and the "divergence of views within the scientific community" on the issue.
But Loconte neglected to mention that Big Bang cosmology won its case by providing empirical evidence, and plenty of it. And this was done completely within the framework of scientific discovery - making testable predictions, for one thing.
And that's where the analogy with ID breaks down. If Intelligent Design has made any testable predictions, I've missed them. If it's advancing due to further research, I've missed that, too. Loconte has made the error, which is unfortunately common in those with no scientific background, of assuming that ID is just another scientific theory because it claims to be. "I can't see how something this complicated could have happened except by God doing it" is not a basis for scientific discovery. For that, you want something like "I can't see how something this complicated could have happened. Let's look at all the evidence we can get and follow it no matter where it leads."
+ TrackBacks (0) | Category: Current Events | Intelligent Design
December 20, 2005
The last time I touched on Intelligent Design around here, things were pretty lively, and I promised not to return to the topic until the Kitzmiller decision came down. Well, here it is (PDF).
Good luck getting that link to load today, though. I think that this one from the York Dispatch is working better. From what I've read so far, Judge Jones has completely hammered the ID case flat:
". . .The Board contacted no scientists or scientific organizations. The Board failed to consider the views of the District's school teachers. The Board relied solely on legal advice from two organizations with demonstrably religious, cultural, and legal missions, the Discovery Institute and TMLC. Moreover, Defendants' asserted secular purpose of improving science education is belied by the fact that most if not all of the Board members who voted in favor of the biology curriculum change conceded that they still do not know, nor have they ever known, precisely what ID is. To assert a secular purpose against this backdrop is ludicrous. . .Defendants have unceasingly attempted in vain to distance themselves from their own actions and statements, which culminated in repetitious, untruthful testimony. . .
. . .Those who disagree with our holding will likely mark it as the product of an activist judge. If so, they will have erred as this is manifestly not an activity Court. Rather this case came to us as the result of the activism of an ill-informed faction on a school board, aided by a national public interest law firm eager to find a constitutional test case on ID, who in combination drove the Board to adopt an imprudent and ultimately unconstitutional policy. The breathtaking inanity of the Board's decision is evident when considered against the factual backdrop which has now been fully revealed through this trial. The students, parents, and teachers of the Dover Area School District deserved better than to be dragged into this legal maelstrom, with its resulting utter waste of monetary and personal resources. . ."
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November 7, 2005
[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.
+ TrackBacks (2) | Category: Current Events | Intelligent Design
November 6, 2005
Friday was the end of arguments in the Kitzmiller v. Dover Area School District trial on the teaching of "intelligent design" in the local 9th-grade biology class. We won't see a decision in the case for a while (perhaps by the end of the year), and no one knows how broadly the judge in the case might be inclined to rule.
I don't see how there could be much uncertainty in my position on this matter, but just in case: I think that "intelligent design" is pernicious nonsense. I understand why some people believe it, but the argument from incredulity doesn't do much for me. If I threw up my hands at everything that seemed to complicated for me to explain, I'd be out of a job, and rightfully so. My scientific predecessors kept trying to explain mysteries - good for them! - and I'm not going to stop looking for answers, either.
Since the organization defending the ID position has said that they want to "use the courts to change the culture", here's hoping that they get an enormous bucket of cold water poured on them. I was a college student in Arkansas when Judge Overton ruled in McLean v. Arkansas, an attempt to mandate the teaching of "creation science", and his opinion still makes fine reading. It put the brakes on that whole approach to ridding curricula of evolution, but eventually such selection pressure led to the spread of this latest mutation. "Intelligent Design" is clearly the scion of "creation science" - try as I might, I don't see how anyone but a fool can believe otherwise. If it too gets struck down, we can all expect yet another variation in another few years as the anti-evolution forces continue to evolve.
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August 7, 2005
Note for new readers: I don't talk much about politics on this site, since there are more than enough blogs to cover every political position imaginable. But once in a while we veer off course. . .
The uproar over President Bush's support for "Intelligent Design" seems to have died down a bit. (You can find commentary all over the blog world, naturally - My fellow Corantean Carl Zimmer was, understandably, dismayed. For some cries of distress on the pro-Bush side, try Sissy Willis, Jane Galt, and this roundup at Instapundit.)
I wasn't too thrilled myself. I have no time for the ID folks. I think that the best of them are mistaken, and the worst are flat-out intellectually dishonest. But I wasn't that surprised by Bush's statement, either. It wouldn't surprise me to find out that he doesn't know enough biology to know how silly his support (wishy-washy though it was) makes him sound to people who do.
But I also think that, as a politician, Bush made a back-of-the-envelope calculation that saying this sort of thing wouldn't do him any harm, and (within error bars) it probably hasn't. I'm not sure how much of a slice of the electorate people like me represent (voted for Bush twice, convinced that Intelligent Design is pernicious), but I'll bet it's not too big. And other issues, which frankly - though I hate to admit it - I find to be more pressing, still leave me not regretting my vote in the last election. If Bush goes further in promoting ID teaching, I will of course oppose that in any way I can think of, in the same way I opposed his steel and textile tariffs. That doesn't mean I'm cheerful about the situation, but there's no possible President who wouldn't tick me off about something or another.
I would expect most Presidents to outsource their needs for any knowledge of evolutionary biology, anyway. It's not a job requirement. Now, I know that being smart enough to see problems with Intelligent Design would seem, on the other hand, to be a job requirement, but it depends on what a person turns their attention to. And a review of Presidential history suggests that performance is not well correlated with intelligence, anyway. If anything, the distribution is a bit U-shaped. Dullards like Franklin Pierce and Warren Harding failed, but on the other end of the scale, academicians like Woodrow Wilson failed in different ways.
Aaron Haspel's discussion of "Chet" - friendly, hard-working, well-adjusted, riotously well-paid Chet - is worth reading in this context. And I'll let James Branch Cabell have the last word, in a famous passage from Jurgen, when he meets that fantasy's nearest thing to God:
". . .And of a sudden Jurgen perceived that this Koshchei the Deathless was not particularly intelligent. Then Jurgen wondered why he should ever have expected Koshchei to be intelligent? Koshchei was omnipotent, as men estimate omnipotence: but by what course of reasoning had people come to believe that Koshchei was clever, as men estimate cleverness? The fact that, to the contrary, Koshchei seemed well-meaning, but rather slow of apprehension and a little needlessly fussy, went far toward explaining a host of matters which had long puzzled Jurgen. Cleverness was, of course, the most admirable of all traits: but cleverness was not at the top of things, and never had been."
I'll try to talk a bit about Chets (and George Bushes) as I've experienced them in the drug industry in an upcoming post.
+ TrackBacks (0) | Category: General Scientific News | Intelligent Design
May 23, 2005
I haven't commented on the controversy about including "Intelligent Design" in school curricula, but I don't want that to be interpreted as any kind of approval. On the contrary - until it offers some testable predictions, which would seem an unlikely thing to hope for, I don't see how ID even rises to the level of a preliminary theory, much less one that can compete with the level of evidence backing up evolution. Many of ID's advocates, to a greater or lesser degree, strike me as intellectually dishonest.
Intelligent Design proponents are fond of arguing about "irreducible complexity", the idea that some structures are too complicated to have been generated through stepwise evolution. They argue this on the anatomical level, which I don't buy, but I'm not going to debate that one in this forum. (Allow me to refer the curious to my fellow Corantean Carl Zimmer, who's had plenty of run-ins with these folks, and his fine introduction to evolution. Those interested in the latest news on the ID/evolution battles should check out The Panda's Thumb. For sheer mockery, often irresistible in these cases, try this.)
But when they start making arguments at the chemical level, the what-are-the-odds stuff about proteins and DNA, well, that's when I come out of my lair. A paper in the latest issue of the journal ChemBioChem got me thinking about this today. (If you have access to Wiley journals, it's here as a PDF.) It's an update of the analytical work still being done on the Murchison meteorite (a href="http://www.publish.csiro.au/?act=view_file&file_id=AS03060.pdf">PDF), which fell in Australia in 1969. The more than 100 kg of recovered Murchison material have been attacked over the years with just about every instrument of the constantly shifting state of the art in analytical chemistry.
Why all the interest? Well, a short answer is that the pieces of this meteorite reek. Even now, they smell like low-grade gasoline, and they had a powerful odor indeed when they were freshly collected. The Murchison fall is a wonderful example of a rare class of meteorites called carbonaceous chondrites. Many people don't realize how much organic gunk is floating around out in space, but there are surely millions of tons of this stuff wandering around our solar system alone.
What's in the Murchison pieces? The list continues to lengthen. We're up to at least 500 different soluble compounds, but much more of the material is dark polymeric asphalty stuff that's hard to analyze. Most famously, the meteorite contains many amino acids. Save glycine, those come in left- and right-handed isomers, and a major find is that the Murchison material is slightly biased toward the left-handed ones, which happen to be the ones that life on Earth is built around. This is an important point: the chemicals that life as we know it is composed of are not at all odd or unlikely. They're all over our solar system, they're in interstellar clouds, and there's every reason to think that they're smeared and splatted all over the universe.
And more of the stuff is being made all the time. In 2002, several research groups took icy mixtures of water, methanol, ammonia, HCN, carbon dioxide and carbon monoxide (just the sort of mixtures that you see in cometary ices and the above-mentioned interstellar clouds.) They irradiated them with ultraviolet light - as would come from the Sun or untold billions of other stars - at cold outer-space temperatures, and obtained over a dozen of the most common amino acids - here are some more details.
So, here's another key point: the really big step is between making random chemical combinations and having carbohydrates and amino acids as inevitable products. Believe me, the molecules of life are an infinitesmal sliver of all the possible backbones of up to ten or twelve carbon, nitrogen, and oxygen atoms. But organic chemistry, with no active hand on the controls, turns out uncountable heaps of them. Compared to that, the gaps that need to be filled in on the way to living systems don't seem so large.
This, to me, is one of the major stories of the last few decades. Starting hundreds of years ago, astronomy gradually moved the Earth out of its supposed spot in the center of the universe and placed it in the huge (and hugely strange) context of the universe that we now know. Now chemistry is moving us away from the view of life as a strange and precious anomaly - granted, perhaps, by a divine being? - to something that could be everywhere and may well start of its own accord. The building blocks are ubiquitous, and if you give them half a chance they start to stack themselves up.
For better or worse, the presence of an active Designer does not suggest itself. That may not seem right to some people, for many different reasons. But if there's one thing that science has been showing us, it's the the universe doesn't much care what we think about it.
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