“Intro to ID” by Gonzalez at U of Northern Iowa

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Things were hoppin’ last night in Cedar Falls for DI fellow Guillermo Gonzalez’s talk. I have about 6 pages of notes from the lecture and subsequent Q&A period here, so if yu’re interested in the nitty-gritty, read below. For anyone who just wants the newspaper version, I’ll try to provide a link to the story when it’s published. My thoughts are in italics below.

Edited to add: Not chance, but design, ISU professor says from the Des Moines Register (thanks, Jason Spaceman); ISU professor argues for intelligent design, from the Ames Tribune.

Additionally, wanted to add that the next Sigma Xi lecture, Thursday, Oct. 27, will present the other side of the ID argument, when John Staver, professor of science education and director of the Center for Science Education at Kansas State University, will speak on “Evolution vs. Intelligent Design: It’s Time to Saddle Up and Draw a Hard Line.”

The lecture took place in a pretty big lecture hall. I heard the seating capacity was 265, and all seats were full by 6:55 or so for the 7PM lecture. Others stood at the back or sat in the aisles, so there must have been at least 300 people there.

The title of his talk was, “What is ID?” He opened by saying what ID is not:

    creationism (doesn’t start with religious premises–rather, uses evidence of nature)(uh-huh. What about the Panda’s and People text? More on that in the questions.)

    natural theology

    a theory of mechanism

    cannot ID a designer uniquely

    not “Christian plot” or conspiracy theory

Then he went on to say what ID is:

    research program to answer scientific questions (such as “does nature display evidence of design?” (I thought that was already an assumption? A bit of circular reasoning here?)

    Design detection

    Testable and falsifiable

He went on to discuss “modern ID,” and mentioned two texts: Denton (1986), Evolution: A Theory in Crisis, and Thaxton, Bradley, and Olsen, Mystery of Life’s Origins (I might not have those names or title right–I don’t see that one in Amazon). He claimed ID is about specified complexity, then went on to talk about IC, giving the mousetrap example. (man, it was painful to listen to him talk about evolution.) He explained that IC items cannot be explained by direct Darwinian pathways, and that there is no direct evidence for indirect pathways that they may have evolved along. He noted that the flagella is an “icon” for ID, and said that the way to test for IC is just to do knockout experiments and see if it eliminates function.

He next talked about areas of ID focus in biology, which include the origin of life; origin of biological information (DNA); the Cambrian explosion; the origin of IC systems and machines; protein folding and assembly specificity (he kept mentioning Axe over and over throughout the talk–I really wish I’d boned up on the criticisms to Axe’s work beforehand); and convergence. Here he mentioned that Simon Conway Morris endorsed Gonzalez’s book. I’m only passingly familiar with him, so I wasn’t exactly sure what point this made here–is it related to convergence, or just the fact that another scientist supported him?

At this point, he went into Dembski’s Design Inference, and he made a big deal out of this being a “peer-reviewed” book. He then talked about specified complexity. He said that IC is a special case of SC–an indicator of activity of an intelligent agent, and used SETI (man, does he love that SETI example), archaeology, and forensics as examples. He then trotted out the Mt. Rushmore example, and said that complexity plus specificity always are a sign of intelligence.

Next he touched on the explanatory filter. Again, used the example of Contact and SETI (poor Sagan must be rolling in his grave). He asks first, do we have contingency? If yes, do we have complexity? If no, it’s chance. If yes, go on to ask–do we have specificity? If no, it’s again chance; if yes, then we can infer design. (I was looking around at this point; the crowd reaction was hilarious. Some literal jaw-drops, lots of laughing, and generally a group of people that weren’t swayed by the BS). The reaction was even better when he half-described Dembski’s calculations, and threw out his 10 to the 150th-power figure. I swear I heard guffaws.

After this, he went on to talk about modern ID and cosmology, beginning again with the timeline of this movement. He listed Henderson’s Fitness of Environment (1913) as a seminal text (Huh? I thought ID was “new”). Brown and Tipler, The Anthropic Cosmological Principle (1986) was another one. He then described the areas of focus of modern ID in physics:

    Fine-tuning for life: constants in physics, forms of laws of physics, etc.

    Properties of carbon and water

    Fine-tuning of local parameters; requirements for habitability. These are often discussed in the context of the anthropic principle.

Fine-tuning implies our universe is highly improbably. Ergo, design.

He talked about “rare earth” theories a bit then–the idea that complex life is rare. This alone isn’t enough to implicate design, though–it could be due to chance. Here’s where his Privileged Planet theory comes in. (And of course, he had plenty of DVDs there for everyone to buy as well).

So, TPP. In a nutshell, the same rare conditions that make the planet habitable also make it a great place for scientific measurement and discovery. He then mentioned that his book was funded by the Templeton foundation on a cosmology and fine-tuning grant, and claims he used methodological naturalism to collect evidence and examples of his “correlation”. (Whoopie!!) Examples include eclipses, planet neighbors, stars, galactic location, plate tectonics, transparency of atmosphere, cosmic time (?), and a fine-tuned cosmos. For example, there is a circumstellar habitable zone in which it is possible to have life. This determines the apparent size of the sun from earth. Having a large moon is also necessary for life, and this makes it more likely to have an eclipse. The earth is the most habitable place in the solar system, and also the most likely to see solar eclipses. Therefore, our existence on earth is linked to our ability to see solar eclipses. This link is established at the level of the laws of physics. (At least he sounded better talking about this stuff than he did about evolution). So, the pattern (from his n of 1) is that observers plus good conditions for observing go together. And, he’s “not a crackpot” (oh yeah, he said that) for saying that, because Kepler and Blumenberg observed the same thing.

He thinks that ID will be a paradigm shift–that it will shake metaphysical assumptions. He ended with that, then we went on to questions.

Some notable ones:

Q: why did you choose your 2 features (habitability + observability?) How does the “intrinsic value” (he mentions this in his book) get defined? A: for the “how did you choose” portion, he basically repeated what he’d already said in his lecture. For the “value” one, he said that everyone thinks astrobiology is a valid question. Answering a qustion about life elsewhere has intrinsic value. (Again, begging the question a bit here?)

Q: How to know when something is specific? A: he discussed pattern matching, and the necessity to bring in “background knowledge” of the item you’re trying to match it to.

Q: Link between design and intelligence. Is it intelligence? How do you study the designer? A: we have lots of experience with designed things. Even when we don’t see a designer, we infer design. We do this with ID but can’t ID the designer.

Q: You mentioned in the first slight that anti-ID people “mischaracterize” ID as religion or creationism. In light of the Wedge document and the use of “creationism” as a placeholder in the ID text “Pandas and Peoples” by ID-supportive authors, why do you still consider this a mischaracterization? A: ID stands alone, with or without its cultural implications. Brought up Dawkin’s quote about being an “intellectually fulfilled atheist,” asked if that makes Darwinism wrong. Religious views are irrelevant. (And yet his biggest criticism about Hector Avalos is that he’s an atheist!! My, the hypocrisy…) It’s not re-packaged creationism, because there was a 1987 court case (anyone know which one he’s talking about? I didn’t catch the names) and ID was already beginning before then.

He didn’t really address the “Pandas and People” item, but suggested that anyone who said ID was creationism was just a conspiracy theorist.

Q: What discoveries would falsify ID? A: for him–finding another planet with life but not good observability; finding life not based on carbon and water. Falsifying the bacterial flagella as IC for Behe, he claims.

Q: Some stuff I missed here on the philosophy of science, but then asked if one could make inductive arguments from ID. A: “Is SETI scientific?” (Told you he loved the SETI example) He kept asking that question over and over, not answering the question. It was pretty great–allowed everyone to see him evade. The guy beside the one who’d asked the question started clapping when they finally made Gonzalez stop asking about SETI, with a shout of “way to not answer the question!”

Q: “So now we have a theory that can explain everything?” (Audience laughs) A: TPP makes a specific prediction about finding supernovae. Predicted gamma ray bursts are standard candles (? There was still audience chatter and I couldn’t hear all of this answer).

Q: I’m an ecologist. A problem we run into is that it’s often easy to find what you’re looking for, even if it doesn’t exist. For instance, bats see Mt Rushmore as designed to provide roosting space. How do you deal with this? A: There’s a chapter in the book dealing with it. (There was some more back-n-forth here, where Gonzalez tried to mischaracterize her stance, then went back to the SETI thing. The questioner stuck to topic, saying “design is in the eye of the beholder,” with another person chiming in asking if the earth was designed for cockroaches. Almost as good as the philosophy exchange.)

Q: haven’t Behe’s IC systems already been refuted? A: Behe has a website dealing with that. I’m not a biologist.

There was also a question asking him when he came to believe ID, but that didn’t catch him on anything. Not as good as Jon Stewart’s question to Dembski.

Q: hy invoke ID–bad science, god of the gaps, made-up patterns. Is it only to feel comfortable? A: (Gonzalez was obviously testy here) That’s not specific enough. (He didn’t elaborate further)

Q: Lynn Margulis and symbiotic evolution–she suggests the flagella may have been a free-living spirochete that got co-opted. Might IC be explained by other examples like that? A: I’m not a biologist, but biologists need to be more open-minded.

Q: what are the practical applications of ID? A: (this one was great): if the universe is designed, that’s a truth of the universe we can know. This may lead us to ask other questions and look at the evidence more carefully.

(Yes, that’s really what he said).

There were a few other minor Q&As which I might put up later…have to run and wanted to get this out there. Overall, a rather entertaining night, but having seen him in person, I have even less respect and more incredulity for Gonzalez’s ideas.

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Bruce Chapman of the DI has a letter in the New York Times: At home, recent articles in The Wall Street Journal and Knight Ridder papers have described intelligent-design scientists at major universities (including Iowa State, the University of Min... Read More

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Anytime someone mentions Mt Rushmore in this context, there should be a question in the Q&A: What about the ‘Old Man in the Mountain’? Was it designed or not?

Good work- These guys sound like politicians. The DI must have party whips to send out talking point memos to all their fellows, because they seem to read the same answers from the same scripts.

In fact, all of their minions on the Internet seem to read the same memos. It is disappointing to see that even everyday people talk like politicians now, and nobody seems to have qualms about making an argument they don’t understand, if it supports their side.

It is notable that most scientists in this debate attempt de novo synthesis of their understanding of the issues. Of course we learn from others, but mostly we don’t go around making claims we don’t understand. I think this is what many of us find so aggravating about ID people. We go through the intellectually honest and laborious process of studying, learning and thinking, and IDists just skip ahead, starting with a conclusion and then read a book that purports to justify it. Then, despite circumventing the whole learning process, while making some egregious errors that are clear to anyone who has given serious thought to these matters, they have the gall to tell us we don’t understand our field of expertise and aren’t open minded enough. *big sigh*

Great example of intellectual charlatanry. If I were going to intelligently design a con-man, he’d come out just like Gonzalez. And like any really good con-man, he’s convinced of the “truth” in his circular reasoning and disproven assertions. One has to particularly appreciate the part where he repeatedly affirms that he’s not a biologist, yet feels qualified to criticize the fundamental unifying ideas of modern biology as if he understood what they were in the first place.

You have to give him this much… he certainly has balls to stand up on a stage and prevaricate this way in public.

The irony just made me choke on my lunch. I gave a talk in ID for Sigma Xi at the U of Arkansas last week, am giving one tomorrow at Fort Smith, and then to the Physics Department at U of A after that. The main points? What ID is… the newest Creationism… natural Theology… a theory with no mechanism… the Biblical God is clearly the designer… an evangelical fundamentalist Christian right wing plot. What ID is not… a scientific research program… able to detect design. I use their own words and published statements as much as possible to demonstrate the points. The only thing I agree on is that some of the premises and claims are falsifiable. Sadly, they have been falsified.

Q: What discoveries would falsify ID? A: for him—finding another planet with life but not good observability; finding life not based on carbon and water. Falsifying the bacterial flagella as IC for Behe, he claims.

How exactly does finding non-carbon based life demonstrate that carbon based life was not designed? It just doesn’t logically follow.

As usual, Gonzales confuses falsifying an argument with falsifying ID. The argument could be wrong yet ID still be correct. The fact that its own proponents keep coming up with obviously nonsensical explanations of how ID could be falsified is a good reason to think that it can’t be falsified.

Good job on the notes. Don’t have much time to comment now, but need to mention a couple of things, maybe more later.

The authors of the book The Anthropic Cosmological Principle are Barrow and Tipler (not Brown). Both authors are cosmologists who show an inclination to use cosmology for theistic purposes. The “anthropic principle” is a hot button issue in physics & cosmology, since in some forms it is used to draw theistic conclusions.

The idea of a “big bang” appeals to theistic people. It would be worthwhile for biologists arguing against ID to learn more about this, because the theistic interpretation of the “big bang” is part of the ID worldview. (Though most cosmologists reject this worldview.)

As for SETI, it seems quite germane. IDers would love to discover intelligent human-like species elsewhere, since if they show the same “design” that would be big time “proof” of ID.

As for SETI, it seems quite germane. IDers would love to discover intelligent human-like species elsewhere, since if they show the same “design” that would be big time “proof” of ID.

Yeah, but I don’t think that was the point of the continual SETI references–it was to hammer home the point that SETI is something that’s supported by many scientists, and it looks for “design.”

Also, thanks for the note on the book–I have to run now but I’ll correct it later.

What about the ‘Old Man in the Mountain’? Was it designed or not?

I’ve asked that before, but AFAIK, that’s a bit sketchy since parts of it have indeed been re-made over the years as it eroded. Never did look further into that, though.

It would seem that the 1987 court case he was talking about was the U.S. Supreme Court decision in Edwards v. Aguillard 482 U.S. 578, but it’s difficult to see how that case helps his argument at all, since the Supreme Court ruled against the Creationist side. Seventy-two American Nobel laureates in natural science signed an amicus curiae brief in that case. The brief is available on talkorigins.

“Q: Lynn Margulis and symbiotic evolution—she suggests the flagella may have been a free-living spirochete that got co-opted. Might IC be explained by other examples like that? A: I’m not a biologist, but biologists need to be more open-minded.”

Crap. There goes my Mark VIII Irony meter.

I don’t get why having eclipses is so important.

tara Wrote:

protein folding and assembly specificity (he kept mentioning Axe over and over throughout the talk—I really wish I’d boned up on the criticisms to Axe’s work beforehand); and convergence.

Presumably, the reference was to Axe et al. PNAS Vol. 93, Issue 11, 5590-5594, May 28, 1996 “Active barnase variants with completely random hydrophobic cores.” I fail to see how Gonzalez missed the following point, which demonstrates redundancy in the evolution of de novo protein function. In other words, Specified Complexity ain’t all that Specified.

Axe et al., 1996 Wrote:

Since attainment of crude function is the critical initial step in evolutionary innovation, the relatively scant requirements contributed by the hydrophobic core would greatly reduce the initial hurdle on the evolutionary pathway to novel enzymes.

If this silliness is typical of Gonzalez’ “scholarship” I can predict that the DI will have another academic “martyr” to join Dembski on the milk carton as “ID[C] scholars [sic] who can’t have an academic career.”

Piltdown Man Wrote:

It would seem that the 1987 court case he was talking about was the U.S. Supreme Court decision in Edwards v. Aguillard 482 U.S. 578, but it’s difficult to see how that case helps his argument at all, since the Supreme Court ruled against the Creationist side.

I think his point was that since ID apparently existed before the 1987 case, then ID can’t be creationism. Of course that doesn’t follow – creationists may have decided on a “creationism lite” strategy well before they lost in court, knowing full well the problems they faced.

But even if we accept the flawed reasoning, he’s still wrong. ID advocates almost universally date their movement’s origins to the early 90s, not the late 80s. One can find vague references to ID as early as ‘87, but this does not constitute a movement, and moreover, it would seem to support the notion that ID was a reaction to the impending Edwards decision. Indeed, in the Of Pandas and People book, the term “creation” was used in the 1989 edition, and was replaced by “intelligent design” only in the 1993 edition. This not only demonstrates that creationism and intelligent design are interchangeable (for at least a large and active subset of its proponents), but that the change in terminology took place after creationism was defeated in court.

frank schmidt Wrote:

Presumably, the reference was to Axe et al. PNAS Vol. 93, Issue 11, 5590-5594, May 28, 1996 “Active barnase variants with completely random hydrophobic cores.”

The reference was probably to Axe’s 2000 or 2004 papers in JMB.

“Yeah, but I don’t think that was the point of the continual SETI references—it was to hammer home the point that SETI is something that’s supported by many scientists, and it looks for “design.””

SETI doesn’t look for “design”. It looks for radio messages something like the ones we humans send. There’s absolutely no analogy to biological “design”, since we don’t have any organisms that we know we (or anyone else) designed. Even if we had designed organisms, and based design research on that knowledge, we would still be looking for “human-like design”, not “intelligent design”. How the hell do we know what the evidence of an omnipotent being’s design process is? As ever ID begs the question.

I don’t get why having eclipses is so important.

Because they happen. If they did NOT happen, then NOT having eclipses would be proof of design.

How exactly does finding non-carbon based life demonstrate that carbon based life was not designed? It just doesn’t logically follow.

No, it does not. But I think, the (il)logic goes something like this: Water and carbon are the official designing materials of the Intelligent Designer. The Intelligent Designer is the Only Designer. Life found using other than the official design materials could not have been designed.

The ultimate conclusion to be drawn here, it would seem, is, if it can be shown that any living system was not designed, then no living system was designed. Not sure that’s on the DI’s list of approved talking points.

Even if we had designed organisms, and based design research on that knowledge, we would still be looking for “human-like design”, not “intelligent design”. How the hell do we know what the evidence of an omnipotent being’s design process is?

As I understand it, the way we tell if some crop has been genetically modified is by looking up gene patterns in a database of all known human-engineered patterns. If we find a match, we conclude we’re looking at a modified crop. If we do NOT find a match, we conclude that we have no way of knowing. In other words, we have no reliable way of even reading *human* design from the raw data themselves.

As far as this observability aspect of Gonzalez’ argument goes, it seems inherently circular. Eclipses are important because we can see them, which proves we must be designed to see them, because they’re important.

Who knows what marvelous events happen which are only detectable in the stream of neutrinos that bathes us every second, but since we weren’t designed to detect neutrinos these events must not be important.

If “The Old Man in the Mountain” is problematic, you could always fall back on the canals of Mars, or George Bernard Shaw point, or, you know, lots of the false positives that Dembski says don’t exist.

Ginger Yellow Wrote:

SETI doesn’t look for “design”. It looks for radio messages something like the ones we humans send. There’s absolutely no analogy to biological “design”, since we don’t have any organisms that we know we (or anyone else) designed.

There’s a logical flaw here. If it is wrong to draw an analogy between “human” design and “biological” design because humans haven’t “designed” biological organisms, then it is equally wrong to draw an analogy between “radio messages” “designed” by humans and “radio messages” “designed” by aliens since we don’t know what “alien-designed” radio messages look like either. Just thought this might help.

Flint Wrote:

Because they happen. If they did NOT happen, then NOT having eclipses would be proof of design.

If I’m not mistaken, Gonzalez uses the example of “eclipses” in order to say that without these “eclipses”, Einstein’s Theory of General Relativity might not have been proved correct. His argument for design, it would seem, would be weakened if there were, in fact, no “eclipses.” So, I don’t think Gonzalez would argue as you speculate.

“As I understand it, the way we tell if some crop has been genetically modified is by looking up gene patterns in a database of all known human-engineered patterns. “

I’m certainly not an expert, but doesn’t the use of mosaic viruses in genetic engineering leave a tell-tale trace, regardless of the specific genes inserted? Of course, this is an inference based on the design mechanism, which is a big no-no in ID.

“There’s a logical flaw here. If it is wrong to draw an analogy between “human” design and “biological” design because humans haven’t “designed” biological organisms, then it is equally wrong to draw an analogy between “radio messages” “designed” by humans and “radio messages” “designed” by aliens since we don’t know what “alien-designed” radio messages look like either. Just thought this might help.”

Three points:

1) We have no point of comparison at all in the biological instance. We don’t know for certain any designed organisms, so we can’t even guess what they’d look like, let alone how they would be different from undesigned organisms.

2) SETI researchers, out of necessity, make a lot of assumptions, mainly along the lines that intelligent aliens are “human-like”. They assume they would use radio waves to send long distance messages, and that those messages would have a recognisable structure that would distinguish them from natural sources. Those assumptions could turn out to be completely wrong, as most SETI researchers would admit, but without them they couldn’t even begin to look with our current technology. ID’s assumptions (eg IC systems are unevolvable, SC means intelligence) are the theory, and no IDer will admit they could be wrong.

3) SETI researchers don’t claim to have constructed a theory of communication.

Steve Case,

At least if you are going to attack Gonzalez’s argument, try to argue against something that actually resembles it.

The argument about eclipses goes this way:

A large moon (which is already unexpected for a small inner planet) stabilizes the earth’s axis providing both rotational stability (no excessive wobbling) and seasons. Both are considered important for life. Furthermore, the moon is big enough that its tidal effect helps cleanse the oceans and resupply them with nutrients, clearly important. (But not too big, which would cause excessive erosion) Also, it slowed the earth’s rotation, also considered to be important. Even the creation of the moon from an impact is probably responsible for our thin, transparent atmosphere. And a new result, newer than the Privileged Planet, argues that if the moon were a little bigger the earth’s orbit would actually be unstable. (Dave Waltham, Astrobiology 4, No. 4: 460-468 (2004)) So the moon is big enough to have all these wonderful effects, but not too big.

So the PP hypothesis is that a moon of just the right size is also one that produces good solar eclipses. They in turn are extremely valuable for studying how stars work and, in one famous case, General Relativity.

There’s a logical flaw here. If it is wrong to draw an analogy between “human” design and “biological” design because humans haven’t “designed” biological organisms, then it is equally wrong to draw an analogy between “radio messages” “designed” by humans and “radio messages” “designed” by aliens since we don’t know what “alien-designed” radio messages look like either. Just thought this might help.

Yeah, we really needed a creationist to clear that up. The difference is “skill sets” (Thank you, Jon Stewart!) and intent. The necessary skill set to design, from the ground up, a functioning biological system, which creationists never tire of pointing out, really are fiendishly complex, is so far beyond the capacity of human beings at this time that it’s just a version of the argument from ignorance to claim that we could detect the hidden signs of this unknowable in principle process, of which design theorists (snicker) have been spectacularly unhelpful in elucidating even the rudiments. On the other hand, radio messages are old-hat. We share the skill of creating and using them with putative alien communicators. As for intent, one of the operating assumptions of (some, most?) SETI research is that an alien race wants to communicate with us. So, while we may not “know” exactly what we’re looking for, we can reasonably expect that some effort will be made on the other end to throw in some high primes, or the fibonacci sequence, or their version of Bach or what have you. With biological systems, what reason do we have for even supposing that there might be a “message” or an intent to make design obvious?

Does Jupiter have more eclipses? (smaller sun, many more moons).

Regarding water and carbon–Hydrogen, oxygen, and carbon have the chemical and physical properties they do because of the numbers and arrangements of subatomic units, which are consequences of the cosmological evolution of elements (adding protons and neutrons). Because of those properties, they happen to react in certain ways with other elements and are capable of building up into more complex “systems.” Isn’t this the sort of thing (like mineral crystals)that Dembski said was not specified complexity? The final product comes about, of thermodynamic necessity, because of the basic chemical and physical properties.

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Blast:

If I’m not mistaken, Gonzalez uses the example of “eclipses” in order to say that without these “eclipses”, Einstein’s Theory of General Relativity might not have been proved correct. His argument for design, it would seem, would be weakened if there were, in fact, no “eclipses.” So, I don’t think Gonzalez would argue as you speculate.

Sorry, but Gonzalez DOES argue this way; it’s not speculation. Perhaps you might reflect on all the accidents of coincidence that are NOT true of our situation, which have the effect of preventing or discouraging us from discovering all the stuff we WOULD have discovered, if only they had happened. Who could possibly say how many of which fortuituous circumstances we’ve been unfortunate enough NOT to enjoy, and what ideas this lack has stymied?

I have no problem with the assertion that given what we’ve got, we’ve made the best of it. I have no problem with the notion that if we’d been gifted with a bit less, we’d still have done our best but it would have been less. If we’d been gifted with more, we’d have done more with it.

Gonzalez notices, just as you and I do, that things are they way they are, and aren’t any different. I’m glad he’s satisfied that what little we’ve lucked into has him so delerious. But I point out that it’s easy to compare something we have, with not having it. It’s damn hard to compare something we do NOT have, with what it might be like to have it, because we don’t have what we don’t have.

In short: Gonzalez is bounded in a nut-shell and counts himself a king of infinite space, because he does NOT dream. Even Fred Hoyle had enough perspective for his Black Cloud to be astonished that life and intelligence (however paltry it was by comparison) could arise deep in a gravity well, where conditions were so uncongenial. But Gonzalez is unfortunately no Fred Hoyle.

David Heddle Wrote:

Steve Case,

At least if you are going to attack Gonzalez’s argument, try to argue against something that actually resembles it.

At least as regards the “observability” aspect, I think he did. Gonzalez apparently takes the fact that the moon allows us to observe certain things during an eclipse is something more than fortuitous. Of course, there are an infinite number of things which could have aided our observability that never happened. We don’t talk about them because they don’t exist.

A large moon (which is already unexpected for a small inner planet) stabilizes the earth’s axis providing both rotational stability (no excessive wobbling) and seasons. Both are considered important for life.

I don’t know anything about why wobbling would kill all life, but seasons are clearly not necessary, as life flourishes in the deep-sea, yet there are no seasons down there.

Unless of course you’re talking about human life with spring planting, fall harvests, and football games. In that case, yes, seasons are necessary. But this is just more of the tautological reasoning which holds that whatever exists must have been intended to exist, and therefore anything which caused it, if sufficently improbable, is evidence that a higher power must have intervened. If you start off with the premise that we humans, as we exist right now, are the intended consequence of the universe, then you can find all sorts amazing coincidences that allowed this to happen. I could go on for hours about all of the coincidences that had to have occurred to allow me to be sitting here right now writing this very paragraph, and reason backwards that an intelligent designer must have put those conditions in place, otherwise I wouldn’t be here doing this thing. Or I could consider the possibility that I’m not the intended consequence of the universe, in which case there’s nothing remarkable about it at all.

Intersting summary Tara!

The Axe papers are problematic from the standpoint of supporting ID per se. I’ve attached abstracts to the end of this post. The first seems really irrelevant from the standpoint of ID, since it was only when Axe combined multiple mutations. The second paper is potentially more relevant since it asserts that some enzymatic folds may be very difficult to find in protein sequence space. On the other hand, novel enzymes have clearly evolved very recently, like the nylon degrading enzyme at the end of this post.

J Mol Biol. 2000 Aug 18;301(3):585-95. Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors.

Axe DD.

MRC Centre, Centre for Protein Engineering, Hills Road, Cambridge, CB2 2QH, UK.

Mutagenesis studies and alignments of homologous sequences have demonstrated that protein function typically is compatible with a variety of amino-acid residues at most exterior non-active-site positions. These observations have led to the current view that functional constraints on sequence are minimal at these positions. Here, it is shown that this inference assumes that the set of acceptable residues at each position is independent of the overall sequence context. Two approaches are used to test this assumption. First, highly conservative replacements of exterior residues, none of which would cause significant functional disruption alone, are combined until roughly one in five have been changed. This is found to cause complete loss of function in vivo for two unrelated monomeric enzymes: barnase (a bacterial RNase) and TEM-1 beta-lactamase. Second, a set of hybrid sequences is constructed from the 50 %-identical TEM-1 and Proteus mirabilis beta-lactamases. These hybrids match the TEM-1 sequence except for a region at the C-terminal end, where they are random composites of the two parents. All of these hybrids are biologically inactive. In both experiments, complete loss of activity demonstrates the importance of sequence context in determining whether substitutions are functionally acceptable. Contrary to the prevalent view, then, enzyme function places severe constraints on residue identities at positions showing evolutionary variability, and at exterior non-active-site positions, in particular. Homologues sharing less than about two-thirds sequence identity should probably be viewed as distinct designs with their own sets of optimising features.

J Mol Biol. 2004 Aug 27;341(5):1295-315. Estimating the prevalence of protein sequences adopting functional enzyme folds.

Axe DD.

The Babraham Institute, Structural Biology Unit, Babraham Research Campus, Cambridge CB2 4AT, UK

Proteins employ a wide variety of folds to perform their biological functions. How are these folds first acquired? An important step toward answering this is to obtain an estimate of the overall prevalence of sequences adopting functional folds. Since tertiary structure is needed for a typical enzyme active site to form, one way to obtain this estimate is to measure the prevalence of sequences supporting a working active site. Although the immense number of sequence combinations makes wholly random sampling unfeasible, two key simplifications may provide a solution. First, given the importance of hydrophobic interactions to protein folding, it seems likely that the sample space can be restricted to sequences carrying the hydropathic signature of a known fold. Second, because folds are stabilized by the cooperative action of many local interactions distributed throughout the structure, the overall problem of fold stabilization may be viewed reasonably as a collection of coupled local problems. This enables the difficulty of the whole problem to be assessed by assessing the difficulty of several smaller problems. Using these simplifications, the difficulty of specifying a working beta-lactamase domain is assessed here. An alignment of homologous domain sequences is used to deduce the pattern of hydropathic constraints along chains that form the domain fold. Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10(64) signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77), adding to the body of evidence that functional folds require highly extraordinary sequences.

PNAS | April 15, 1984 | vol. 81 | no. 8 | 2421-2425 1984 Birth of a Unique Enzyme from an Alternative Reading Frame of the Preexisted, Internally Repetitious Coding Sequence

Susumu Ohno

The mechanism of gene duplication as the means to acquire new genes with previously nonexistent functions is inherently self limiting in that the function possessed by a new protein, in reality, is but a mere variation of the preexisted theme. As the source of a truly unique protein, I suggest an unused open reading frame of the existing coding sequence. Only those coding sequences that started from oligomeric repeats are likely to retain alternative long open reading frames. Analysis of the published base sequence residing in the pOAD2 plasmid of Flavobacterium Sp. K172 indicated that the 392-amino acid-residue-long bacterial enzyme 6-aminohexanoic acid linear oligomer hydrolase involved in degradation of nylon oligomers is specified by an alternative open reading frame of the preexisted coding sequence that originally specified a 472-residue-long arginine-rich protein.

I’m still reviewing the latter two, but as stated previously, the first Axe paper seems to strongly contradict ID, in the form of illustrating how Demski’s calculations are deeply flawed. WAD calculates the improbability of a protein or group of proteins by assuming a de novo synthesis of amino acid sequences and calculating whether the present structure could have randomly been assembled in this way, thus concluding it out of his universal probability bound when it cannot. However, among the many problems with his assumptions, is that proteins in real life mutate from previous ones, rather than come into being from a random string of peptides. By showing that a general core of hydrophobic peptides supports supports the general structure of many proteins, Axe seems to show that both the probability of deriving one protein from another is not as low as WAD assumes, and that the requirement for the exact sequences we see today is not as stringent to maintain function as WAD assumes. I don’t know why Gonzalez would bring up this example, but I can’t wait to read the two JMB papers.

You can try to disprove the conjecture of Darwin and evolutionary theory from over 100 years ago all you want, but it makes no difference. We have made numerous discoveries to expand and affirm the ToE since then.

Chuckle. Blast is referring to what he sees as your Bible. Doesn’t every faith have a Bible? Isn’t Darwinism your faith as much as Christianity is his? You are supposed to memorize and cite the Word of Your God, and worship it, and place your hand upon the Origin of Species when assuring people you’re being honest.

The notion of of a theory constantly being honed through the research of thousands of independent thinkers, and improving all the time, just does not fit. A living, changing doctrine is, sputter, hack, why, it’s heresy. You can’t even tell what you’re worshiping from day to do. It’s simply unthinkable.

This also explains why Blast continues to repeat the same old refuted chants, and claims they have never been answered. Doctrine can’t be “answered”, it can only be denied by the unfaithful. So Blast has a model of science very much like the earth-centered solar system model. Yes, it can be made to work, with some heavy lifting. But the more we learn, the heavier it gets, until the only reasonable options are to adopt a modern model or just lie. And when adopting a modern model is prohibited by doctrine…

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This page contains a single entry by Tara Smith published on September 29, 2005 9:25 AM.

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