Tuesday, April 17, 2007

Dr. Egnor and the Evolution of a Definition

Michael Egnor is whining again, this time that some "Darwinist" has "airbrushed" out his favorite bits of the Wikipedia article on Reverse Engineering -- the part that defined science as a type of reverse engineering. John Pieret + commenters have amply fisked Egnor's quasi-paranoid evocation of Soviet-style censorship, as well as the odd logic of taking a few sentences from Wikipedia definition as "evidence". But the good doctor never fails to provide ample material such that there are always a few scraps left over for further gleaning. Consider this part of his complaint:
The biological reverse engineering analogy was part of the original definition, and had been present until the day that I linked to it in my post. Someone (perhaps a Darwinist?) went to work with an eraser.
I wonder if it occurred to Dr. Egnor to wonder how that "original definition" got there in the first place? It's not present in the first version of the article, dating from 3 October, 2001. It remains absent until 17 December, 2005, when a user called Wernher (as part of a general expansion) adds the single sentence:
A telling analogy of RE is that the research of physical laws can be seen as reverse-engineering the world itself.
I don't know what Wernher thinks the analogy "tells" us, but this early form does begin the theme that science is a type of reverse engineering -- over four years (and dozens of intervening edits) after the "original definition".

On 13 September, 2006, a transitional form (though close to the modern form) appears, from a user called, who replaces Wernher's version with:
Reverse engineering is essentially science, using the scientific method. (Conversely, engineering could be thought of as 'reverse science'). Sciences such as biology and physics can be seen as reverse engineering of biological 'machines' and the physical world respectively.
This is getting close to the version Egnor liked so much. It only remains for user (what's with all these users called by IP addresses, anyway?) to delete the text in red to reach the modern form

So: Egnor's "evidence" that science is a type of reverse engineering consists of the fact that someone called thinks it does.

Some evidence.

When this whole l'affaire Egnor started, I figured that, whatever goofy ideas he may entertain in his spare time, he's still probably a competent doctor. However, after witnessing the continuous torrent of fallacies and ignorance -- many IMHO completely inexcusable in an educated man -- I've decided that, should I ever require brain surgery, and am given the choice between Dr. Egnor and this, I'll choose the robot. At least I can expect it to behave logically.

Wednesday, April 11, 2007

Pope Benny on Evolution: Sounds Too Familiar

So, I innocently surf up the TV listings to check what time CSI is on this week, and the headline that catches my eye is: "Evolution can't be proven: Pope Benedict". It seems His Holiness has written a book giving his take on the Creation/Evolution controversy. I'm not about to run out and buy the thing -- too busy reading some real philosophy of biology to waste time on what some guy in a funny hat says his god thinks about it -- so until the reviews start appearing I'm stuck making my assessment via news-outlet sound-bites. (Not that I personally care either -- but Benny's words do carry some weight with a certain largish segment of the public, and the state of public discourse on this subject does concern me).

Reportedly, Benny's book endorses Theistic Evolution, ie. accepting that the facts of natural history are as modern science says, only that God guided the process in some way. However, that "in some way" allows a lot of wiggle room, from positions in which theology is just so much superfluous (if poetic) window-dressing on science, to ones which verge on some flavour of ID or creationism. John Pieret at Thoughts In A Haystack seems to take the optimistic view, but I'm not so sure. From the ctv.ca article (emphasis mine):
"The question is not to either make a decision for a creationism that fundamentally excludes science, or for an evolutionary theory that covers over its own gaps and does not want to see the questions that reach beyond the methodological possibilities of natural science"
"But it is also true that the theory of evolution is not a complete, scientifically proven theory."

Benedict added that the immense time span that evolution covers made it impossible to conduct experiments in a controlled environment to finally verify or disprove the theory.

"We cannot haul 10,000 generations into the laboratory," he said.

Where have we heard those phrases before? The complaints about "gaps", "methodological naturalism" and "not proven"? Pope Benedict may have verbally rejected Intelligent Design along with crude creationism, but he has qualified his acceptance of evolution using boilerplate straight out of the ID/creationist movement's own phrase book. I'm not convinced. Is it possible that Theistic Evolution -- spun hard in a creationist direction -- could become the next stalking horse in the assault on science?

OTOH, my misgivings could just be the result of sloppy reportage.

Sunday, April 8, 2007

Hallelujah! Rocks are Designed by God!

Unlike many creationists I don't consider engineers to be scientists, so I don't always have a lot to contribute to the science/pseudoscience discussion. But every so often, the ID/Creationists stray over the line into my territory. Like when a doctor starts saying silly things about both science and engineering.

About a month or so back, a new star appeared in the Intelligent Design firmament: Michael Egnor, professor of neurosurgery at SUNY, and with an impressive record as a practicing physician. It started (more or less) with his post at the Discovery Institute blog on why evolution is useless in medical practice, which begat a flurry of rebuttals from medical bloggers like Orac. Additional fun and games ensued as Egnor replied to his critics, or issued fresh pronouncements, resulting in a blizzard of blog posts that I won't even try to select from (Google Is Your Friend). Along the way, Orac issued Dr. Egnor a challenge (summarized here):
  1. Explain, specifically, how the design inference is "of great value" in medicine.
  2. Explain, specifically, how the design inference has been of "enormous help in scientific research in general and medical research."
This week, Dr. Egnor replied to Orac's challenge. The gist of his reply is that Watson and Crick's discovery of the structure of DNA is an example of "reverse engineering":
To untangle the structure of DNA, they inferred design, not chance. They reversed-engineered DNA. They collected physical data about the structure of DNA (X-ray diffraction studies, Chargaff’s rules, the physical chemistry of nucleotides, etc), and then they designed a model of the molecule to understand its structure and function.
Egnor seems to base much of his argument on the following Wikipedia entry (bolding is Egnor's, red text is mine):
Reverse engineering... is the process of discovering the technological principles of a device or object or system through analysis of its structure, function and operation…Reverse engineering is essentially science, using the scientific method. Sciences such as biology and physics can be seen as reverse engineering of biological 'machines' and the physical world respectively.
The Wikipedia entry has since been edited to remove the text in red -- a change with which I heartily agree. Yes, there is a conceptual similarity between the work of reverse engineers and that of research scientists. Both groups start with a "black box" (the externally-observed behaviour of their study system), draw inferences about what might make it behave that way, and then find methods of literally or metaphorically "looking inside the box" to elucidate its inner workings. But, really, the resemblance ends there. To apply the term "reverse engineering" to both activities is to illegitimately impose a concrete term from the one domain on to the other, on the basis of an abstraction properly seen as underlying both.

However, it gets worse.
Apparently, doing this kind of "reverse engineering" of the natural world implicitly invokes the concept of "design" (presumably by You Know Who):
Much of modern biological research, and most research in molecular biology, is reverse engineering. Some scientists infer design explicitly. Some use the design inference implicitly, even if they disagree with its philosophical implications. We can’t do modern biology, at least at the molecular level, without using reverse engineering, which is the inference to design.[emphasis mine]
This simply compounds misapplied terminology with confused logic. What on earth does Egnor mean here by "inference to design"? In reverse engineering, we know that the system under study is designed and built by humans -- it's not an inference, it's part of the background knowledge we start with. (As an aside, that piece information is often useful in the reverse engineering process: knowledge of human psychology and standard practices can inform our investigation into the study system. This stands in contrast to IDists, who claim that one can study design while knowing nothing about the nature of the designer(s)[1]). But in the case of natural-world research science, we don't know in advance that the object of study was designed -- that is the very "inference" the IDists want us to make. Egnor's attempt to impose "design inferences" on his historical example seems to rest on Watson and Crick's own words concerning the relation between the structure and function of DNA:
It is probably impossible to build this structure with a ribose sugar in place of the deoxyribose, as the extra oxygen atom would make too close a van der Waals contact.
It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.
As far as I can see, this is no more than to say that, because the molecule functions in a certain observed way, it must have a structure that allows for it to behave that way -- which says nothing about it having been designed (or not) by a concious agent.

But lets do a simple case study using Egnor's reasoning (insofar as I can decipher it):

Consider a rock -- a moderate-sized, hold-in-your-hand, ordinary rock. Doing an initial black-box analysis, I observe that it has a certain heft to it -- with some simple apparatus I could measure its volume and mass, and calculate its average density. What else? I tap it with a hammer, and observe that it doesn't shatter. From this I make an inference about the internal structure of my rock: it's not hollow (this cannot be taken for granted, as some rocks are). To confirm my hypothesis, I hit it really hard and smash it open. Sure enough, it's solid all the way through.

Now, does this internal part serve any function? Sure it does: it supports the outside, and contributes to the mass. In other words, it enables the "black box" behaviour, just as much as the specific constituents of DNA enable its observed behaviour. And if I'm entitled to make the "design inference" in the one case, I'm entitled to make it in the other. So I conclude: my rock is designed by an intelligent entity.

It should be noted, of course, that this is entirely consistent with traditional Christian theology, which holds that everything in heaven and earth is in some sense under the sovereign supervision of God. But for some reason, the IDists (despite almost all being Christians of some stripe) only think that some things are designed. Maybe they're heretics; I don't know :-).

1. See, for example: page 197 of Michael Behe Darwin's Black Box, Simon & Schuster 1996

Monday, April 2, 2007

Creationist Forum -- Eamon's View

On the evening of February 23, Citizens for Origins Research and Education (CORE) held the first of three "Evidence Forums" in a small auditorium at the Ottawa Citizen building. Four of us from HAO/Ottawa Brights Meetup were in attendance, along with maybe 20 other people of unknown affiliation (though mostly likely from local churches where creationism is taken seriously – which fortunately is probably not all that many). Theo and I are old hands from talk.origins, and have been getting the CORE newsletter for about 15 years, so we knew more or less what to expect, but I think it was a bit of a surprise to our friends. The speakers were Jonathan Cucan and Rev. George Desjardins (the third presenter, Paul Milne had to cancel).

Even before the official proceedings got started, things got interesting. Cucan and Desjardins got up a bit of one-line repartee about things seemingly irrelevant to the evening's stated topic. “Global warming?” said one of them (I forget which one). Dismissed with a snicker -- yes it's happening, but it's not our fault. Apparently the sun has increased its output in the last few decades (something like that). Ditto, Antarctic ozone depletion -- caused (snicker) by bromine. Church-state separation? -- it's (snicker, guffaw) a myth. There was no expansion on any of these points; they were just sort of throw-away comments to warm up the audience. To me the experience was sort of like watching a comedy duo act in which only the performers seem to be getting the punchlines (but think themselves devastatingly humorous).

After an opening prayer, Rev. Desjardins started the presentation with a list of factoids about “fulfilled prophecy” and so forth – basically, Josh McDowell-type stuff. There was, however, one jaw-dropping moment worth mentioning: someone (an acquaintance of Cucan's from the RASC) who asked something about aliens. Desjardins replied that yes, he thought they existed, there was some possible Biblical mention of them – and they are our ancestors. *boggle*. We didn't really get into this point, but I'm guessing that Desjardins subscribes to some form of the ancient-civilizations-developed-high-technology-including-space-travel schtick. On this view, UFOs would be some of those antediluvians coming back for a visit from their colony on wherever. Fascinating how pseudo-scientists often manage to go in for several kinds of crackpottery, simultaneously.

Anyways, none of this was really what we came for, so Theo asked where the creationism was – which got Jonathan Cucan rolling. And rolling. Basically, Cucan has two modes of argumentation: Argumentum ad Sneer (described above), and Argumentum ad Steamroller. In the latter mode, you get about six words into your objection, and he interrupts to tell you how wrong you are, and continues at length.

So what we got was the old Gish Gallop (which was more or less what I expected, of course). Since the format was informal, various audience members (including us four heathens) were interjecting questions and responses at quasi-random intervals, so I'll just summarize a few of the points I recall or took notes of (I mostly gave up trying to take notes):

  • There are 100,000 scientists who reject evolution (though he later revised this to 10,000). No cite, of course. And how many of them are actually engineers or doctors, or whose credentials are otherwise unrelated to the job of figuring out earth history?

  • The Urey-Miller experiment “failed”. Not sure in what way, but this was followed by further claims about the impossibility of abiogenesis, as proven by certain “scientists” (read: the Institute for Creation Research). We got a spirited back-and-forth going about this, between Cucan and us. I objected that any kind of probability calculation was conditional on the model under consideration, therefore universal assertions on the subject are impossible. I further objected that simply saying “....therefore God did it by a miracle” is a non-explanation – no different from saying “It happened by magic”. At this point, Cucan interrupted me to re-assert: No, no: these scientists have proven that abiogenesis is impossible – missing the point of my objection.

  • Cucan mentioned several claims made by the ICR's RATE project as knock-down (with the obligatory sneer and a chuckle) proofs that “evolutionary scientists” have it all wrong and the evidence points to a young earth:

    • Rock samples from modern lava flows at Mount St. Helens were potassium-argon dated to between 500 thousand and three million years old (the obvious implication being that K/Ar – and isotope dating in general -- doesn't work). This appears to be a reference to dacite rock from the MSH lava dome which they had analyzed by a commercial lab which provides such services. The short answer is that such dates are close to the lower limits of the K/Ar dating method (ie. where minor argon contamination can give a falsely old date), and it also appears that Steve Austin (the ICR geologist who did the work) did not prepare the samples correctly. See here for a detailed examination of this claim.

    • Next he said something a bit confusing: that they asked the same laboratories (he specifically mentioned Harvard and Yale) to check for the presence of retained helium in the samples – the idea being that a young rock may contain helium, but a truly ancient rock will have lost all its helium by diffusion. As near as I can tell, he's managed to conflate two claims coming from his own side – the MSH dacite K/Ar work (above) with a separate claim about He retention in zircons from a site in New Mexico. About the latter, the short story again appears to be that both the mineralogy and the lab work were incompetent: helium diffusion rates vary widely according to conditions, and the method used to measure retained He was wrong.

    • Next up we had “Diamonds are a creationist's best friend” ie. that measurable amounts of carbon-14 can be found in diamonds – which should not be the case if diamonds are millions of years old, as all the C-14 should have decayed away. This was discussed on talk.origins, and once again (no surprise!): the claimed C-14 “date” of 58000 years is close to the limits of the method, where contamination and background noise can skew the results.

  • The details of the above can get pretty technical (more than I understand, or have time to get up to speed on – though I doubt Cucan knows any more about it than I do), but the most charitable assessment I can give his claims is: they're simply not the knock-down killer of standard geology that Cucan likes to spout them as. (My non-charitable assessment is: they're complete crap from a bunch of ideologues whom Cucan considers infallible heroes).

  • Raymond Damadian, Martyr for Creationism: Damadian was one of the key developers of the MRI medical diagnostic technology, but was passed over for the 2003 Nobel Prize in medicine in favour of two other scientists who also worked in the field. Creationists like to claim that this was due to Damadian's young-earth beliefs – a clear example of persecution. In fact, there is to my knowledge no evidence that Damadian's beliefs influenced the Nobel committee (or that they were even aware of his beliefs); it is pure speculation. But creationists just love to play the persecution card. (There was extensive discussion of this on the talk.origins Usenet group at the time.)

The point of showing up for events like this, of course, is not that you'll convince the presenters, or any of the True Believers – that's pretty much an impossible task. But in the audience there are likely to be the novices and fence-sitters -- those who haven't yet drained the kool-aid right to the dregs. It's important to show these folks that, actually, the “evolutionists” have heard the creationist side, and have answers. The purveyors of nonsense shouldn't get a free ride with the public. After the meeting was over, but people were still hanging around, I got into a bit of a conversation with one gentleman from the audience about transitional fossils. I gave him the URL of the talk.origins FAQ, along with the names of several of the early whales for him to look up for himself.

Then I went to have a little chat with Cucan himself. A few snippets from this conversation,as I recall them:

  • Cucan claimed that scientists were coming round to creationism. When I stated that I didn't believe him, he replied with an anecdote about a personal acquaintance – a computer scientist – whom Cucan had given his creationist spiel, and the guy had converted and been baptized, hallelujah. I didn't get the chance to point out that computer science is not, strictly speaking, science, any more than engineering is: his friend's CS degree is not much different from my Master's degree in Systems and Computer Engineering, and neither credential is relevant to the age of the earth, or biological evolution. This claiming of peripheral professions as “scientists” in order to inflate the numbers is a standard part of creationist rhetoric.

  • Next he went off into some story about how trilobite eyes are just as complex as frog's eyes, which was supposed to prove...something – I would guess about how evolution is supposed to make things more complex over time. So I (a little tired of the torrent of verbiage) interrupted to tell him he didn't understand evolution – at which point he interrupted back to say that I didn't understand evolution! Oh boy. “Simple” seems to one the trigger words that will cause Cucan to immediately interrupt and steamroller you.

  • I pointed to the Bible lying on the table and said (more or less), Look, don't tell me that you lot are interested in evidence or truth, because your heroes at the ICR have made a commitment that any and all conclusions they come up with must be consistent with a literal interpretation of this book....(interruption) No, no Cucan replies, if you come up with something that contradicts the Bible then you re-examine your interpretation. Which is of course, rubbish: if these guys were actually listening to the evidence instead of bending it to fit their hermeneutics, they'd all be hanging out with Francis Collins in the Theistic Evolution camp. Consider for example, the case of Kurt Wise (one of the few YECs with legitimate credentials in earth science), who is on record as admitting that, even if all the evidence pointed to an old earth, he would remain a YEC for theological reasons. Or read any of the prominent YEC websites (or the most recent CORE newsletter) calling for uncompromising allegiance to a strict YECism, and criticizing the old-earth interpretations like “Day-Age” as compromising with the Great Satan of evolutionism (you have to understand that “compromise” is a very dirty word to fundamentalists). So I just flatly don't believe Cucan's claim – it is obvious to anyone who spends any time interacting with YECs (or indeed, any other variety of creationist) that with them, ideology trumps evidence.

  • One of the other organizers, a young minister whose name I don't recall, chimed in with the old canard about evolution being invented as an excuse to ignore human accountability to God. I came down hard and fast on him, to the effect that the statement is a calumny which I would not allow to stand. Cucan stepped in fairly quickly with some conciliatory words to the effect that you can't apply that to individuals – though it's clear he still believes the statement as an historical generality. This is one of my hot-buttons: there are certain common creationist ad hominems (Nazi comparisons and Darwin-was-a-racist being the other ones which come to mind) which are so false, vile and slanderous that they should never be allowed to go unchallenged. Never ever. Zero tolerance.

My impression of Jonathan Cucan is that he seems to think the ICR is a source of infallible truth, and he just doesn't take seriously anyone who disagrees with the general YEC line – he “knows” he is right. OK, we're even there: I don't take him and his heroes seriously either – the difference being that I've spent about 16 years listening at some length to the creationist side (as well as learning a whole lot about evolution) AND I used to be a fundamentalist (so the culture is familiar to me), whereas he seems oblivious to the fact that there are cogent, devastating refutations of YEC arguments – and has no idea how to handle people who know what they're talking about. Hence, the steamroller tactic.

There was another one of these things in March, which we missed, but we're planning to show up for the final one on April 20.

Creationist Forum - Theo's view

We have been on the mailing list for the Ottawa creationist group CORE for some years. Recently, having received an invitation to their "Scientific Creation Forum" we rounded up a few members of the Humanist Association of Ottawa and the Ottawa atheist meetup/bookclub and assembled us a "posse" (ok, maybe I have been watching too much Firefly).

The meeting was to be held at the headquarters of the Ottawa Citizen newspaper, and we speculated for a bit as to whether there was any connection between the paper and CORE, and if not, whether the room could be booked by the public, and might be a possible location for Ottawa Humanist meetings.

Our posse of 4 was among the first to arrive, but eventually there were about 20 people seated, and the meeting started, unfortunately minus the promised scientist (Organic Chem PhD). The MC, Jonathan Cucan, opened with a bible reading/prayer, then turned the floor over to George Desjardins. Dejardins spoke on the "reliability" of the bible: that it was directly handed to humans from God, that it was accurate, that modern archaeology was consistently confirming "facts" from the bible, that the bible's authenticity was confirmed by fulfillment of prophecy, etc. I had heard all this before (not to mention the fact that I had at one time been convinced that it was true), so I raised my hand and asked when we were going to get to the discussion of Scientific Creation, which was the advertised topic of the meeting.

So, on we went to Scientific Creation. Cucan gave an account of his first challenge to his faith by the theory of evolution ("it's not even a theory, it's just a hypothesis", he says with a sneer and a smarmy laugh). Apparently, when he was 10 he came home from school and told his father that he was very upset because his science teacher had told him that the earth was billions of years old, but he knew that the bible said that God had created the universe only a few thousand years ago. His father re-assured him that the teacher was wrong and the bible was the authority on the matter, at which point young Jonathan decided to devote the rest of his life to defending Young Earth Creationism (YEC).

Cucan's view, typical of many creationists, is that any threat or challenge to the theory of evolution (or even any threat or challenge to conventional science) is a point in favour of of young-earth creationism. His technique is to fire off a series of objections which appear logical and plausible to the audience, and demand an explanation. Of course, all of these claims could be easily debunked in 5-10 minutes, with the assistance of Our Friend Google and the talkorigins archive, but it only takes 20-30 seconds to assert the claim (and in Cucan's case, laugh derisively and move on to the next one before giving anyone in the audience a chance to get a word in edgewise).

In addition to those listed in Eamon's report, here are a few more:

  • Ocean Salinity: The oceans are not salty enough for a multibillion year old Earth
  • Bromine caused the Ozone Hole (not related to evolution, just a general attack on conventional science): According to Cucan, when scientists got to Antarctica, they were shocked to find that the ozone hole was caused by bromine. (I think he actually got this from "Reasons to Believe" , where it is cited as evidence that the earth's atmosphere is such a complex system that there must be a Supreme Being personally supervising all the chemical reactions.)
  • Human/Chimpanzee DNA comparison: The ~99% similarity of human and chimp DNA is often cited as evidence that the 2 species have a relatively recent common ancestor. Cucan was delighted to cite recent research that "revised" the conventional statistic to 95-96%. This, of course, casts doubt on the validity of the Theory of Evolution!? (The actual quote from the NIH: The DNA sequence that can be directly compared between the two genomes is almost 99 percent identical. When DNA insertions and deletions are taken into account, humans and chimps still share 96 percent of their sequence.)

One of his major thrusts was regarding the complexity of DNA, and how it is utterly impossible that the DNA required to assemble something as "basic" as a blade of grass could just come together "by chance". Interestingly, when I stated that grass was not a very good example of a "simple" organism, he responded with glee, saying that if even grass was not considered simple, how could we expect the DNA for anything "really complex" like humans to have arisen, "by chance". At that point, I tried to explain natural selection. Cucan evidently was not listening, but apparently some members of the audience were, and there was some good discussion with them afterwards - they asked about how "something as complex as the eye" could have evolved "by chance", and we were able to provide some insight as to how natural selection works for making eyes - no ID required here.

At the end, I had a one-on-one discussion with Cucan. He first said to me that evolutionists were losing the battle since so many atheists were becoming Christians, and then said that the secular education system was being threatened since so many Christian parents were pulling their kids out of public schools and colleges where evolution was being taught. He proceeded to explain that both evolution and creationism were "just theories", and ought to be taught side by side. I confirmed his previous statement that he rejected evolution in favour of YEC for religious reasons, and asked him why it should be taught in science class. He responded that evolution was also religious, so I asked him how that could be, given that many religious people accept evolution and conventional science. That appeared to give him pause to think - he eventually conceded that he believed that Christian evolutionists are wrong, but not in peril of their immortal souls!

We skipped the March meeting (but did pause to wonder what account Cucan might have given to the audience about the "challenges" he had presented, and whether he would have suggested that the anti-creationists were afraid to return). We're back to the battle for the April 20 meeting - if you are in the Ottawa area, come one out for the show.