Behe is still not impressed

| 222 Comments | 1 TrackBack

Apparently, Michael Behe just doesn’t know when to pack it in. In reply to Travis’s essay in Science, “On the Origin of The Immune System” (see previous PT posts: 1, 2), Behe has posted a letter he sent to Science. Instead of just sucking it up and admitting that his statements in Darwin’s Black Box that

“As scientists we yearn to understand how this magnificent mechanism came to be, but the complexity of the system dooms all Darwinian explanations to frustration.” (Darwin’s Black Box, p. 139)

and

We can look high or we can look low, in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system. (Darwin’s Black Box, p. 138)

…were wrong, or at the very least became wrong in the time between 1996 and 2005, Behe is still expressing proud, Kierkagaardian-esque defiance. In this (rejected) letter to the editor of Science, Behe reiterates his proud stand that the work of an entire field, the life’s achievements of hundreds of immunologists, complete with surprising experimental support for a surprising hypothesis (the transposon hypothesis), still has “no answers” to the question of how it evolved, and that Darwinian explanations are “doom[ed].”

Well, actually, he doesn’t quite say that, because somewhere along the line Behe retreated from his bold rhetoric, without ever admitting that he made an error (this is, I think, the key to understanding Behe: he will never, ever, admit a significant error). What Behe does now, as in his letter, is nitpick on subsidiary points, and conclude that because scientists don’t agree on everything, he is still justified in ignoring everything they have all come to agree on.

For example:

In the courtroom scenario Travis recounts, I was testifying that science has not shown that a Darwinian mechanism could account for the immune system. Travis’s article itself confirms that is still true. He cites some biologists who think the adaptive immune system arose in a “big bang”; he quotes other scientists who assert, “There was never a big bang of immunology.”

But just how significant is this debate in the grand scheme of things? The “big bang” idea essentially was based on the idea that the transposon insertion event kicked off a rapid diversification of the machinery of adaptive immunity. If you restrict your view of adaptive immunity to RAG (Recombination-Activating Genes) and VDJ recombination, it does appear that they appeared “suddenly” in jawed vertebrates (with “suddenly” meaning 50 million years). The “simple” transposon hypothesis provided an explanation – a rare mutational event in just the right place made things possible that were not possible before.

The questioning of the big bang model (which IDists/creationists would love to keep, actually, because they love anything “sudden” sounding, except that in this case they’d have to accept the transposon hypothesis) came when additional data showed that various “parts” of adaptive immunity, more broadly considered, are indeed distributed amongst the relatives of jawed vertebrates. Also, homologs of the RAG genes have been found in other deuterostomes, which makes it plausible that the transposon ancestral to RAG was already bouncing around in genomes before it took a key role in adaptive immunity. We won’t know which hypothesis is more likely correct until we get a bunch more genomes and biochemistry on the RAG homologs in them (I’m betting on the second hypothesis, based on my principle that Claimed Big Bangs in Biology Always Go Poof When You Look at Them Up Close; but we’ll see).

But in the grand scheme of things, this sort of thing is small potatoes. Both sides of this “argument” (I doubt anyone is very emotional about it) acknowledge that key remarkable features of the VDJ recombination system are ultimately derived from a transposon, and that the this very surprising, very evolutionary hypothesis received dramatic confirmation in recent decades. Both sides would agree that this is One Of The Friggin’ Answers about the origin of adaptive immunity that a guy like Behe should accept if he was actually fairly assessing the science and not just blindly trying to avoid admitting error.

To sum up, the “big bang” question is a subtle thing that depends on all kinds of subtle points – what does/should one mean by “big bang”, how are we going to delineate the borders of “adaptive immunity” such that it may or may not have banged, what does “sudden” mean anyway when “sudden” can mean 50 million years, etc. To pretend that splitting hairs over these points constitutes a serious challenge to widely-accepted discoveries in the field is silly.

Behe continues:

[Travis] discusses vertebrate immunologists who think they know what the selective advantage of the system is; he quotes invertebrate immunologists who feel otherwise. So are we to think that its history is uncertain and even its selective advantage is unknown, yet the mechanism by which the adaptive immune system arose is settled?

Let’s back up. Does Behe seriously think that it is possible there is no selective advantage for adaptive immunity? That’s not what he said at trial (1, 2). Neither he nor anyone thinks that. So actually, he’s just dissembling here [1]. The debate Travis mentions is, again, subtle. Organisms without adaptive immunity still have all other sorts of immune system defenses, and they seem to get by, so in that context what was the specific sub-category of extra advantage that adaptive immunity gave? This is a subtle and complex question. The basic answer is probably that diversity in immune receptors is good (there is massive evidence for this in almost every immune system, adaptive or not), and RAGs allowed for increased diversity, and that’s basically it. It may be that adaptive immune systems are more economical (the organism can get by with fewer immune cells in total; although, it is still the case that something like 1% of our cells are immune cells), or make it easier to be longer-lived and slower-reproducing (like many vertebrates, compared to invertebrates), or be social animals with lower costs in terms of the spread of disease, or (as Travis mentions) improve the ability to distinguish friendly from unfriendly bacteria (although, if Crohn’s disease is any guide, it appears that our sophisticated immune system has way too much of a propensity to misfire and attack helpful bugs and even our own cells). But again, these are all subtle sub-hypotheses of the basic idea that receptor diversity and memory are useful for fighting off invaders, which is something not in dispute – not even by Behe, if he were being forthright and paying attention to his own testimony and what he said in Darwin’s Black Box.

One can take any broad scientific question, ignore the basic conclusions a field has reached, and push out to the more detailed points where active debate occurs – indeed, this is made easy by the fact that scientists work and publish most actively at exactly those points, that’s what doing science is about. But citing such debates in a cheap attempt to discredit the basic points those experts agree on is an exceedingly weak argument. Behe is free to do it, but it is completely legitimate to keep bringing up embarrassing topics like evolutionary immunology as long as he does.

Notes

1. Behe also sometimes argues that the evolutionary immunology literature only relies on common ancestry, and doesn’t cover mutation or selection. But as I showed, Behe himself admitted selective advangtage for the immune system here and here, and furthermore he admitted transpositions are mutations here and here. So he’s sunk even on the narrow point, unless he retracts some of his testimony.

1 TrackBack

So, Michael Behe is still at it, 13 years after his book, Darwin’s Black Box, which has been a complete failure in proving Intelligent Design. Apparently a recent article in Science (or read the blog article) has caused Behe to write a letter in ... Read More

222 Comments

I was testifying that science has not shown that a Darwinian mechanism could account for the immune system. Travis’s article itself confirms that is still true. He cites some biologists who think the adaptive immune system arose in a “big bang”; he quotes other scientists who assert, “There was never a big bang of immunology.”

Surely if biologists are arguing over which mechanism does account for the immune system, then more than one mechanism could?

Intelligent design has no proper argument with the bare idea of common descent; rather, it disputes the sufficiency of ateleological mechanisms to explain all facets of biology.

Okay, Mike, all you have to do is show us some evidence of interference. Not number-juggling, actual evidence. Point to any stage/phase/frameshift/transposition and say “Here. Right here. Some Designer interfered here at some point, somehow.” Then you can move on to just what was done. Then, maybe, one day, how the designer did it. You don’t even have to name the designer, as we know most of your cronies don’t have the balls to do.

The Nobel awaits, Mikey.

(… and somewhere in the distance, a dog barked…)

I still don’t understand why Behe thinks simply being skeptical of non-teleological evolutionary mechanisms is sufficient to allow a decidedly evidenceless alternative (intelligent design) to replace it.

After getting spanked by mistakes in his own book, he turns around and accepts the reality of common descent, but still clings on to the ridiculous idea that a creator (oh, sorry; DESIGNER) interfered at some point in the evolutionary process.

Which ultimately creates more questions than answers. When exactly, and how many times, did the “designer” interfere with what would otherwise be considered a natural process? If he had to magically interfere with pre-immune system organisms so that the immune system could eventually come about, does that mean that the first iteration of organisms without immune systems were–dare I say it–imperfect? They needed revising? Why not create an evolutionary mechanism that could develop an early immune system on its own?

Oh wait, that would imply that there’s no need for a designer. My bad.

Everybody loves to complain about the origin of adaptive immunity, but at least Behe wrote a letter.

RDK said: I still don’t understand why Behe thinks simply being skeptical of non-teleological evolutionary mechanisms is sufficient to allow a decidedly evidenceless alternative (intelligent design) to replace it.

Because the root motive isn’t to offer a better empirical explanation, but to eventually toss empirical science altogether and replace it with a science consonant with Christian and theistic convictions?

Is that it? Do I win the toaster?

You’ve pointed out the logical fallacy, which Behe and the Clowns frame as a “logical inference”, which is basically the core nerve bundle of the stealth creationism marketing animal. If you can just fudge up the real science enough, maybe enough salt of the earth citizens will wander off into the tall weeds, get lost, throw up their hands, and decide GodDidIt is actually a “logical inference” that makes more sense than all this complicated pseudoevolutionary gobbledy-gook.

Behe is a rat.

RDK said:

I still don’t understand why Behe thinks simply being skeptical of non-teleological evolutionary mechanisms is sufficient to allow a decidedly evidenceless alternative (intelligent design) to replace it.

After getting spanked by mistakes in his own book, he turns around and accepts the reality of common descent, but still clings on to the ridiculous idea that a creator (oh, sorry; DESIGNER) interfered at some point in the evolutionary process.

Which ultimately creates more questions than answers. When exactly, and how many times, did the “designer” interfere with what would otherwise be considered a natural process? If he had to magically interfere with pre-immune system organisms so that the immune system could eventually come about, does that mean that the first iteration of organisms without immune systems were–dare I say it–imperfect? They needed revising? Why not create an evolutionary mechanism that could develop an early immune system on its own?

Oh wait, that would imply that there’s no need for a designer. My bad.

I don’t get Behe at all - look at this quote from his (rejected) letter (http://www.amazon.com/gp/blog/post/[…]MARVIW62Q7BE)

Although some news reporters, lawyers, and parents are confused on the topic, “intelligent design” is not the opposite of “evolution.” As some biologists before Darwin theorized, organisms might have descended with modification and be related by common descent, but the process might have been guided by some form of intelligence or teleological driving force in nature.

What driving force? how does/did it work? how to you test for it? why intelligence? (there are natural properties in systems that drive complexity beyond what would be expected due to ‘chance’ alone - crystal structure, fractals, etc.)why teleological? what evidence is there to support any of his suppositions? All of Behe’s actual ‘arguments’ in his books boil down to :

the odds of ‘x’ occurring by the pathway I describe are so astronomical as to be impossible (a fancy restatement of the tornado in a junkyard assembling a 747)

therefore some ‘teleological driving force /intelligence’ must have guided ‘x’

and I have yet to see one of Behe’s arguments that can’t be dismissed because: 1) the pathway for ‘x’ he describes is not reflected in reality 2) AND he calculates odds incorrectly

Well what else can he do? No matter how much evidence is collected, no matter how many reaonable hypotheses are proposed and tested, he can always shake his head and say NOT GOOD ENOUGH. Most telling is the fact that he isn’t trying to find the answer. He is apparently content to just sit back and say NOT GOOD ENOUGH forever. Of course eventually everyone else will get most of it figured out and he will be left sitting all alone still crying NOT GOOD ENOUGH. Oh well, what can you expect from a guy who has only two examples of things that could not possibly evolve and those things are being whittled away daily? At least he has come off the YOU GOT NOTHIN routine.

Seems to me that once you have admitted an ancient earth and common descent, any required interventions make the designer into an incompetent micromanager who just couldn’t get it right the first time. Too bad, unless of course it’s aliens.

Ok, I’m basically neutral on the big question here, but it seems to me that you folks have not explained how this could happen with only ateleological mechanisms.

As Behe explains, but you don’t seem to understand, ‘unknown’ is an acceptable answer. Given the choice between an apparently impossible natural selection speculative idea, and the assertion that little green men beamed complex systems into primordial gook, while passing by in a space ship, I will choose the 3rd option “it’s unknown”.

If adaptive change cannot explain how even a cell originated, it does not mean that ID is the alternative. You folks using ridicule and derogatory “creationist” insults only reflects on you, not the argument.

My understanding is that DNA is more like a software program, than anything else. I went from a believer in Evolution to being neutral when I learned that adaptation can also be explained by gene expression, rather than gene modification. For example, the ability to grow longer beaks is within the capability of the program.

As a software engineer, I can relate to the following common sense: Adaptive Evolution is like if one takes a very complex and sophisticated software program, and periodically changes bits in the binary code. In doing so, one can only introduce bugs, one can never introduce whole new features. I would consider anyone who claimed that we could develop new software features in this manner to be insane.

Therefore, the burden is on the evolution community to show exactly how extremely complex electromagnetic machinery could just happen. People like Behe need only show that it is extremely unlikely. You don’t make any significant argument by ridiculing the messenger or simply saying that researchers are writing papers on the subject.

I find it difficult to imagine what people like Behe actually do all day. AFAIK he is not carrying out experiments so does he just read papers trying to find loose ends that he can unpick, in the hope that the whole edifice comes unravelled? Given that he seemed to be unaware of all the research on the evolution of the immune system, I don’t think he can be doing this either, so how doth the little busy Behe improve each shining hour?

jasonmitchell said:

I don’t get Behe at all - look at this quote from his (rejected) letter (http://www.amazon.com/gp/blog/post/[…]MARVIW62Q7BE)

Although some news reporters, lawyers, and parents are confused on the topic, “intelligent design” is not the opposite of “evolution.” As some biologists before Darwin theorized, organisms might have descended with modification and be related by common descent, but the process might have been guided by some form of intelligence or teleological driving force in nature.

What driving force? how does/did it work? how to you test for it? why intelligence? (there are natural properties in systems that drive complexity beyond what would be expected due to ‘chance’ alone - crystal structure, fractals, etc.)why teleological? what evidence is there to support any of his suppositions? All of Behe’s actual ‘arguments’ in his books boil down to :

the odds of ‘x’ occurring by the pathway I describe are so astronomical as to be impossible (a fancy restatement of the tornado in a junkyard assembling a 747)

therefore some ‘teleological driving force /intelligence’ must have guided ‘x’

and I have yet to see one of Behe’s arguments that can’t be dismissed because: 1) the pathway for ‘x’ he describes is not reflected in reality 2) AND he calculates odds incorrectly

The part where his whole argument becomes immaterial is where he fails to define exactly what “intelligence” and “design” actually are. Intelligence is just a fancy way of saying that his deity did it, and design could encompass virtually anything given you zoom in or out far enough.

Also, the fact that he says:

the process might have been guided by some form of intelligence or teleological driving force in nature

automatically destroys his ridiculous argument from the get-go. Using standard creationist term-twisting, I could fit evolution via natural selection under the umbrella of “intelligence or teleological driving force”. Not to mention he says “in nature”, which automatically excludes the possibility of a supernatural entity.

Gingerbaker writes.…

Everybody loves to complain about the origin of adaptive immunity, but at least Behe wrote a letter.

Only creationists and members of their camp “complain” and “write letters”, since neither of these activities actually accomplishes anything as far as mining for the truth is concerned.

Anybody who’s really interested in the subject (as opposed to being interested in using it as a straw man) does “research” and “writes peer reviewed papers” instead.

A quick glance at PubMed shows somewhere north of 7685 people have done just that.

As opposed to Behe, who has actually done nothing to advance his argument.

DS said:

Seems to me that once you have admitted an ancient earth and common descent, any required interventions make the designer into an incompetent micromanager who just couldn’t get it right the first time. Too bad, unless of course it’s aliens.

Incompetent only in the context of the outrageously high standard of “infallibility”. I don’t know why anybody would think their god is “infallible” though. That’s an awful big claim when you think about it! Never getting anything wrong, ever? What a dumb claim for people to make.

Anyway, maybe the designer was infallible but likes to tinker around as a hobby or something. Ken Miller thinks that would be “cheating” or somehow dishonest for a god to do. Which seems to me like another dumb claim for somebody to make. Why would a creator tinkering around with stuff be cheating or dishonest? People sure do make a lot of dumb claims when they try to make sense out of dumb stuff.

Even if the designer god wasn’t infallible, creating a universe is an awful big project, and something is bound to go wrong somewhere. Calling a designer “incompetent” when it has the ability to create a universe that kinda works pretty good in the first place seems a bit harsh.

Gunnar says

As Behe explains, but you don’t seem to understand, ‘unknown’ is an acceptable answer.

No, what Behe is saying is ‘so far, unknown, therefore it was done by an external intelligence’. Moreover, he has said that biologists could not conceive of an evolutionary pathway for various things, even after such pathways had been proposed. With Behe, too, you need to be careful of what he is saying when, as he changes his stance without acknowledging it. For example, he has produced at least three definitions of irreducible complexity that I know of.

Therefore, the burden is on the evolution community to show exactly how extremely complex electromagnetic machinery could just happen. People like Behe need only show that it is extremely unlikely.

I am not sure what you have in mind when you refer to complex electromagnetic machinery. However, given that 1,000 million years in the life of an entire planet was available, in practice the extremely unlikely is going to happen. Behe needs to show that something is impossible. However, given his lack of information on current research in ‘his’ area (convincingly demonstrated in the Dover trial), I believe he will never succeed in demonstrating that anything is impossible.

Gunnar said:

Ok, I’m basically neutral on the big question here, but it seems to me that you folks have not explained how this could happen with only ateleological mechanisms.

As Behe explains, but you don’t seem to understand, ‘unknown’ is an acceptable answer. Given the choice between an apparently impossible natural selection speculative idea, and the assertion that little green men beamed complex systems into primordial gook, while passing by in a space ship, I will choose the 3rd option “it’s unknown”.

Behe doesn’t; understand this, or else he wouldn’t still be trying to push his ridiculous design theory onto the scientific community.

My understanding is that DNA is more like a software program, than anything else. I went from a believer in Evolution to being neutral when I learned that adaptation can also be explained by gene expression, rather than gene modification. For example, the ability to grow longer beaks is within the capability of the program.

This argument is inane. If it happens, obviously it’s within the capability of the program. That does not mean that “the information was always there”, or some such nonsense that William Dembski would like you to think. No information was smuggled in; a combination of previously existing information is new information.

Take the test recently done by scientists at NASA. They used algorithms based off of evolutionary mechanisms to create a better design of antennae:

http://biologicinstitute.org/2008/1[…]e-ingenious/

The point is that in designing the program, the scientists were searching for a better antennae design. They did not start out with the final design in mind. They needed the program to tell them what it would look like; there was no “smuggling of information” involved. New information was created using previously existing information.

As a software engineer, I can relate to the following common sense: Adaptive Evolution is like if one takes a very complex and sophisticated software program, and periodically changes bits in the binary code. In doing so, one can only introduce bugs, one can never introduce whole new features. I would consider anyone who claimed that we could develop new software features in this manner to be insane.

Once again, you’re putting too much emphasis on the computer program analogy. Evolution is not like a computer program. There are simliarites, kind of like the ones exploited in the article I just linked to above. But your understanding of evolution is apparently not on part with your understanding of computer programs.

Here’s what you’re not understanding: “bugs”, as you call them, can and do create new “functions” all the time. Completely new proteins are created, and even that doesn’t have to happen: already existing proteins can be co-opted for brand new functions.

Would you like me to go on about information theory and show you just how wrong you are?

RDK said:

This argument is inane. If it happens, obviously it’s within the capability of the program. That does not mean that “the information was always there”, or some such nonsense that William Dembski would like you to think. No information was smuggled in; a combination of previously existing information is new information.

Thanks I always wondered about that. Why the heck wouldn’t it be new information? I always thought the “no new information” argument was kind of stupid and simple-headed. (And lame.)

Gunnar wrote

As Behe explains, but you don’t seem to understand, ‘unknown’ is an acceptable answer. Given the choice between an apparently impossible natural selection speculative idea, and the assertion that little green men beamed complex systems into primordial gook, while passing by in a space ship, I will choose the 3rd option “it’s unknown”.

Except that the natural selection account is not a “speculative idea.” It employs known mechanisms working in known ways. Not knowing all the details is not equivalent to knowing nothing at all. Moreover, those “speculative ideas,” more commonly known as hypotheses, are testable and are being tested in labs around the world. Where are the ID scientists beavering away at the hypotheses generated by their “speculative ideas”?

Gunnar wrote

My understanding is that DNA is more like a software program, than anything else. I went from a believer in Evolution to being neutral when I learned that adaptation can also be explained by gene expression, rather than gene modification. For example, the ability to grow longer beaks is within the capability of the program.

Your understanding is faulty. While one can evolve computer code (google “genetic programming”), DNA is chemistry, not coding. Chemistry works a bit different from code.

Gunnar wrote

As a software engineer, I can relate to the following common sense: Adaptive Evolution is like if one takes a very complex and sophisticated software program, and periodically changes bits in the binary code. In doing so, one can only introduce bugs, one can never introduce whole new features. I would consider anyone who claimed that we could develop new software features in this manner to be insane.

Is there a subcategory of the Salem hypothesis for software engineers? Gunnar, read this summary and then get back to me on the “insane” claim.

They did not start out with the final design in mind.

A total straw man. No one is arguing that evolution doesn’t exist as a concept. Of course, we evolve our designs all the time.

Evolution is not like a computer program.

I said that DNA is like a computer program.

But your understanding of evolution is apparently not on part (sic) with your understanding of computer programs

Your understanding of critical thinking seems extremely limited, since you have not explained how a cell came into being. It is totally insufficient for you to merely poke holes in various statements by Behe and then rant about creationists. The default position is “unknown”. Reality, common sense and the existence of even one irreducibly complex system is enough to invalidate the evolution speculative idea. To counter that, you need to show that there are absolutely NO irreducibly complex systems in life.

Here’s what you’re not understanding: “bugs”, as you call them, can and do create new “functions” all the time

Then, you are a software idiot. A new feature requires millions of additional bits. You can change, add and subtract all the bits you want, but you will never get a new feature, because the natural selection takes place at the program/individual level.

The changed bit that would be beneficial to the individual would be so astronomically unlikely, that believing in it would take an act of blind faith. You are asserting that EVERY bit in a new system is beneficial to the individual. DNA makes any human created software program look like my son’s lego creation.

Would you like me to go on about information theory and show you just how wrong you are?

You aren’t capable of teaching me anything about software. This whole thing seems to be more about religion than about science. It’s your religion against theirs.

Gunnar said: I went from a believer in Evolution to being neutral when I learned that adaptation can also be explained by gene expression, rather than gene modification. For example, the ability to grow longer beaks is within the capability of the program.

As a software engineer,

And how do you imagine the differential gene expression is inherited? The mechanisms controlling gene expression are also coded for in the DNA. What do you imagine “gene expression” means? Perhaps a software engineer needs to consult with biologists, but I suspect there must be another reason for your being “neutral”, whatever that means.

Gunnar said:

A total straw man. No one is arguing that evolution doesn’t exist as a concept. Of course, we evolve our designs all the time.

Then where did the new design come from?

I said that DNA is like a computer program.

DNA is nothing like a computer program, or at least like the silly example you gave. Genetic mutations are in no way comparable to “changing bits in the binary code” in a way that doesn’t produce any new functionality.

Your understanding of critical thinking seems extremely limited, since you have not explained how a cell came into being.

When did the origin of cells ever enter into the discussion? We’re talking about the origin of the immune system.

Unless you’re talking about the origin of life, in which case you’re in a completely different field–that’s abiogenesis. And I’m the one with the critical thinking problem?

It is totally insufficient for you to merely poke holes in various statements by Behe and then rant about creationists. The default position is “unknown”. Reality, common sense and the existence of even one irreducibly complex system is enough to invalidate the evolution speculative idea. To counter that, you need to show that there are absolutely NO irreducibly complex systems in life.

Once again, your ignorance shines through. There are numerous examples of irreducibly complex systems in nature that arose naturally. If you take out one component of the final product, of course there are many simple systems that wouldn’t work anymore–but you’re completely ignoring the development process (I.E., how that organism came to be irreducibly complex) and instead looking at only the final product.

Examples in nature that might be considered irreducibly complex are not irreducibly complex in the way that creationists imagine them to be. For just one of numerous examples of evolution producing seemingly irreducibly complex results in the last century, look up information on how the S. chlorophenolica bacteria evolved to break down PCP, a highly toxic man-made chemical used in wood preservative.

Then, you are a software idiot. A new feature requires millions of additional bits. You can change, add and subtract all the bits you want, but you will never get a new feature, because the natural selection takes place at the program/individual level.

Notice how I put the terms “bugs” and “functions” in quotes, in order to mock your horrible analogy that compares evolution to bugs in a computer code. I wasn’t actually suggesting that bugs in a computer code create new functions, because they obviously don’t (as you just stated), and that’s why it is in no way comparable to mutations that occur in DNA during the evolutionary process. You just demonstrated how dumb your own argument was, but that’s no surprise coming from a closet creationist.

The changed bit that would be beneficial to the individual would be so astronomically unlikely, that believing in it would take an act of blind faith. You are asserting that EVERY bit in a new system is beneficial to the individual. DNA makes any human created software program look like my son’s lego creation.

Then why are you comparing mutations present in DNA transcription to bugs in a computer program? Yahweh only knows.

You aren’t capable of teaching me anything about software. This whole thing seems to be more about religion than about science. It’s your religion against theirs.

I wasn’t aware of any religion called science.

Gunnar said: Ok, I’m basically neutral on the big question here, but it seems to me that you folks have not explained how this could happen with only ateleological mechanisms.

I suspect that you are not “neutral”, because it seems a very odd thing to announce yourself as neutral, and then proceed to vomit out the “strengths and weaknesses” drivel as if you are reading from a Luskin pamphlet.

Science deals with empirical examinations of the physical mechanisms which drive natural phenomena. Which mechanisms in the panoply of gene-environment interaction would you like to discuss? Sorry, there are no teleological mechanisms that we can actually discuss here. Were you thinking of God/Designer? There are places on the internet to discuss that. But that’s not science.

Behe was asked on the stand in the Kitzmiller trial about the “mechanism” of Intelligent Design. Boy, that did not go well for him.

As Behe explains, but you don’t seem to understand, ‘unknown’ is an acceptable answer. Given the choice between an apparently impossible natural selection speculative idea, and the assertion that little green men beamed complex systems into primordial gook, while passing by in a space ship, I will choose the 3rd option “it’s unknown”.

Badly played. A moment ago, you were “neutral”. And now, natural selection is “apparently impossible,” and a “speculative idea”. Can you not hide your stripes any better? What is this, amateur hour? Are you a Discovery Institute intern fulfilling an initiation rite? Good grief.

If adaptive change cannot explain how even a cell originated, it does not mean that ID is the alternative. You folks using ridicule and derogatory “creationist” insults only reflects on you, not the argument

Ah, but that’s Behe’s “logical inference”. Problem is, you can’t run around overtly slinging the phrase Intelligent Design in school board meetings anymore, because the Kitzmiller judge slapped you down with the words stealth creationism. And what this argument reflects is how people (like you, Gunnar) who consider their cause righteous continually undermine their own Christian values by lying about their true motives. Christ does not think it’s cool for you to pretend to be neutral, nor does Christ think it’s cool for you to lie about Behe’s intent.

I am pretending to be a former believer in evolution even though I am a lying creationist troll who makes Jesus very unhappy.

There, fixed that for ya.

As a software engineer, I can relate to the following common sense: Adaptive Evolution is like if one takes a very complex and sophisticated software program, and periodically changes bits in the binary code. In doing so, one can only introduce bugs, one can never introduce whole new features. I would consider anyone who claimed that we could develop new software features in this manner to be insane.

Gee, if only software programs were living organisms that could reproduce for countless generations all by themselves over millions of years, your analogy would actually qualify as “common sense.” As it stands, this analogy qualifies you as “insane”.

Therefore, the burden is on real evolutionary biologists to show exactly how extremely complex organisms could evolve.

There. Fixed that for ya, also.

Yes, Gunnar, it is the responsibility of real scientists to do real science. It has been ever thus. Mike Behe sure isn’t doing any real science. And you really need to go back to the DI Blog Troll Woodshed and practice harder. Weaksauce.

Gunnar said: Ok, I’m basically neutral on the big question here, but it seems to me that you folks have not explained how this could happen with only ateleological mechanisms.

That seems like an odd way of stating something. It kind of gives away the whole plot doesn’t it?

“You folks have not explained how this could happen with only non pink-unicorn mechanisms.”

“You folks have not explained how this could happen with only non N-ray mechanisms.”

Oh, no, not the “DNA is like computer code” bullshit again.… didn’t bobby get pummeled on this nonsense not too long ago?

Gunnar said:

As a software engineer, I can relate to the following common sense: Adaptive Evolution is like if one takes a very complex and sophisticated software program, and periodically changes bits in the binary code. In doing so, one can only introduce bugs, one can never introduce whole new features. I would consider anyone who claimed that we could develop new software features in this manner to be insane.

Except that a billion-pair genome is not a billion line software program.

It’s more like a giant hard drive to which every organism that has ever run the program has write privileges.

It’s full of thousands copies of small files, multiple revisions of common programs, some programs in beta, some everyday workhorses, and some plenty of archival junk, broken code that hasn’t run in eons.

Although new copies and revisions are constantly created all the time, nobody ever stops to clean out all the junk or defrag the thing.

Furthermore, the operating system is kind a weird, in that all the little code fragments are allowed to constantly run in parallel.

Consequently, since there are multiple copies of most genes, if one does break, via mutation or whatever, it doesn’t doom entire organism, the other copies just sail on.

Don’t forget, most genes are small. The average protein is expressed by a gene with maybe 60 base pairs. It’s only the odd piece of code that ever gets close to “big” (meyelin synthesis, for example, is a couple of thousand base pairs).

While it’s inconceivable to imagine a billion-line syntax-dependent program to mutate itself into working, it is manifestly not inconceivable to image a 128 byte chunk of assembly language doing so.

In fact, it’s so not inconceivable, it’s actually been demonstrated. You can find it at Genetic Evolution of Machine Language Software Ronald L. Crepeau NCCOSC RDTE Division San Diego, CA 92152-5000 July 1999

fnxtr said:

Oh, no, not the “DNA is like computer code” bullshit again.… didn’t bobby get pummeled on this nonsense not too long ago?

The funny part is that our boy Gunnar here shot himself in the foot with his own argument. And it all happened within the course of two posts. He’s not even a competent troll.

John 11:35

Just as evolution of organisms does not operate on the level of individual atoms, evolution of software does not operate on the level of bits. The granularity of comparison is completely off. Software evolves all the time at the level of functions. I dare the IDiot to program without copying and pasting code from a pre-existing code. I dare the IDiot to name his variables so that they share no common parts with other variables. I dare the IDiot to program without object-oriented inheritance (note the keyword). Software definitely evolves by trial-and-error coupled with selection. I dare the IDiot to write bug-free code at the level of complexity that impresses him on the first try.

Bleh.. Behe + Immune System = “what good is half an eye?”. Pathetic.

It makes as much sense to say DNA is like computer code as to say it’s like a jacquard loom punch card or a player piano roll.

DNA is what it is, dependent on the topography and chemistry of its own molecules, and those of the substances with which it reacts.

Calling DNA a ‘progam’ is like calling the sun an ‘oven’.

Moreover, those “speculative ideas,” more commonly known as hypotheses, are testable and are being tested in labs around the world.

Oh really? Then please, show me the experimental evidence that shows evolution of an ICS from nothing.

Where are the ID scientists beavering away at the hypotheses generated by their “speculative ideas”?

Straw man. I don’t argue for ID. The default is “unknown”.

Your understanding is faulty. While one can evolve computer code (google “genetic programming”)

Your understanding of GP is faulty. It’s basically a search algorithm. It does NOT involve randomly changing binary code bits. That would be insane, and believing in that to improve anything is blind faith.

DNA is chemistry, not coding. Chemistry works a bit different from code.

Of course there are differences, but in essence, it’s like software. They are both binary systems. A single gene can be considered a program or subroutine. The average human gene is 1 kilabit. It’s a group of “bits” that seem to control a certain pheno type (aspect) of a organism. In theory each gene creates one functioning protein. Genes are like functions, alleles would be arguments, and the genome would be the entire program.

They could be compared to functions with a event driven architecture as well.

Straw man. I don’t argue for ID. The default is “unknown”.

Um, no, the default for biological processes is “not supernatural until some form of miracle is demonstrated.”.

Martin said:

Henry J said:

Certainly it would be possible in theory (but may well be uneconomical in practice). But of course anti-evolutionists would attack it with the same excuse as for their attacks on the “Weasel” program - it would involve a preselected target.

Henry

You could run the resulting programs against some sort of test suite that gave them a rating. There is no need to set an a priori answer like the ‘weasel’. … The initial program is another question, but then I understand that evolution is not about the origins of life, only its subsequent development.

What’s that? Did someone say Target? and Weasel?

Cheers, Dave

Target? Weasel? Somebody might have to ferret out the pathetic level of detail…

Henry J said:

Target? Weasel? Somebody might have to ferret out the pathetic level of detail…

Sorry please explain in English.

Sorry, I have now read Dave Thomas’ links. They are saying what i was trying to say.

Martin said:

Henry J said:

Target? Weasel? Somebody might have to ferret out the pathetic level of detail…

Sorry please explain in English.

Henry J said:

Target? Weasel? Somebody might have to ferret out the pathetic level of detail…

While we’re driving past that area of rugged landscape known as “The Weasels”, what actually was the outcome of the recent software project over at Dembski’s place (drat! what’s its name? Unpleasant Dissent? Undescended Testables? .…) They were muttering about implementing their own version of the Weasel, but the discussion threads got closed at about the point at which it was becoming clear that the whole “locking” argument was untenable.….

Kevin B said:

Henry J said:

Target? Weasel? Somebody might have to ferret out the pathetic level of detail…

While we’re driving past that area of rugged landscape known as “The Weasels”, what actually was the outcome of the recent software project over at Dembski’s place (drat! what’s its name? Unpleasant Dissent? Undescended Testables? .…) They were muttering about implementing their own version of the Weasel, but the discussion threads got closed at about the point at which it was becoming clear that the whole “locking” argument was untenable.….

The upshot is that the only changes over at EIL (Evolutionary Informatics Lab) are algorithms that supposedly look at latching versus no latching - but this is still implemented incorrectly! The pages that discuss the “math” have not been updated at all.

Trying the phrase “METHINKS IT IS LIKE A WEASEL” at Dembski’s crew’s EIL site, with a population of 30 and a mutation rate of 4%, gave me well over 5000 to 8000 “generations” for the “Proximity Reward Search” (which I’m taking as “Latching”), and no end in sight after tens of thousands of generations for the “Proximity Neutral Search” (which I’m taking as “No Latching”).

My own Python weasel, as was the case with many other versions from the rationalist side of the Divide, converged in just a few hundred generations, latching or no.

So, other than not adding any new explanations, and totally mucking up the “new” calculations, I guess you could say Dembski’s crew did “update the Weaselware program.”

Dave

Dave Thomas said:

Kevin B said:

Henry J said:

Target? Weasel? Somebody might have to ferret out the pathetic level of detail…

While we’re driving past that area of rugged landscape known as “The Weasels”, what actually was the outcome of the recent software project over at Dembski’s place (drat! what’s its name? Unpleasant Dissent? Undescended Testables? .…) They were muttering about implementing their own version of the Weasel, but the discussion threads got closed at about the point at which it was becoming clear that the whole “locking” argument was untenable.….

The upshot is that the only changes over at EIL (Evolutionary Informatics Lab) are algorithms that supposedly look at latching versus no latching - but this is still implemented incorrectly! The pages that discuss the “math” have not been updated at all.

Trying the phrase “METHINKS IT IS LIKE A WEASEL” at Dembski’s crew’s EIL site, with a population of 30 and a mutation rate of 4%, gave me well over 5000 to 8000 “generations” for the “Proximity Reward Search” (which I’m taking as “Latching”), and no end in sight after tens of thousands of generations for the “Proximity Neutral Search” (which I’m taking as “No Latching”).

My own Python weasel, as was the case with many other versions from the rationalist side of the Divide, converged in just a few hundred generations, latching or no.

So, other than not adding any new explanations, and totally mucking up the “new” calculations, I guess you could say Dembski’s crew did “update the Weaselware program.”

Dave

Yes, I thought that’s what happened.

If you take the last component off the EIL URL, you’ll get a directory which has a text file with some explanation of what they mean by “Proximity Neutral”, which rather looks as if they are just playing games.….

There are fitness functions that hardly reference the target string at all, other than using information about the target length (such as CRC32, Simple Sum and Wave Interference) and there are those that use some information about the target string to further narrow the search space. These functions (prefixed with “Partially Neutral: “) do narrow the relevant search space, but not to the extent of a Proximity Reward function.

It doesn’t look as if the WeaselWare suite includes the correct Dawkins version, where the fitness function yields a value which indicates which of the candidate strings in a particular generation is “best”, without giving any indication of why it is the best. The writer of the WeaselWare help text explains Dawkins’ version as being the “locking” one.

This is probably to do with this fixationthey have about the target information being “built into” the program. Just for the fun of it, I replaced the fitness function in a Perl weasel program with a function that scored the candidate strings as palindromes - it converged very nicely. It would be interesting to consider a fitness function that scored for English sentences, although I am a little dubious as to whether it would stretch the framework a little too far. (Perhaps a two-level scheme, with individual “genes” to create words, with a second scoring system for sentences made out of subsets of the words.…)

Kevin B Wrote:

The writer of the WeaselWare help text explains Dawkins’ version as being the “locking” one.

This is probably to do with this fixation they have about the target information being “built into” the program.

As near as I can tell from their incoherent gibberish, they seem to think the existence of the “target string” is some kind of flaw. If that is what they really believe, it is evidence that none of them understands how Nature really works.

In their world, electrostatic potentials, gravitational wells, and potential energy wells of any kind are “targets” or “teleological goals” and therefore they are either flaws or they are evidence of intelligent guidance.

The fact that one can change the target string at some point in the search and still have the results track and converge to the new string doesn’t seem to jar any recognition on their part of what happens in evolution when the environment changes making a different creature a better fit to the new environment.

By the way, Dave’s Python weasel was written during a car pool (take that, ID crowd!); and it also includes some semi-log plotting that reveals some additional interesting features of the convergence. Cute!

Mike Elzinga said:

By the way, Dave’s Python weasel was written during a car pool (take that, ID crowd!); and it also includes some semi-log plotting that reveals some additional interesting features of the convergence. Cute!

Yeah, last week in the carpool I banged out some interactive Sudoku pages. Give ‘em a try!

Dave

Gunnar makes me embarrassed to be a software engineer. Evidently he’s never heard of the concept of self-adapting software, or software that can create software. Genetic algorithms can create new executable code through iterative attempts.

Why are so many engineers oblivious to the fact that they don’t know everything? Why are they such arrogant bastards?

Questions to which I’ll never have the answers. But I have realized that not all engineers are scientists, and the ones that do have full grasps of science are rare gems. That probably explains my hiring practices.

In Dembski’s book “The Design of Life” he talks about Behe and irriducible complexity, and how it works, and as i read this book i was very drawn in by this thought of irreducible complexity. I know that Darwinians think that a bacterium with a flagellum just kind of evolved because of the Darwinian selection mechanism from the bacterium lacking flagellum and the genes coding for flagellar protiens. But as i read this exert from the book it uses something John Postgate says in describing the complexity of the bacterial flagellum. He says:

A typical bacterial flagellum, we now know is a long, tubular filament of protein. It is indeed loosely coiled, like a pulled-out, left handed spring, or perhaps a corkscrew, and it terminates, close to the cell wall, as a thickened, flexible zone, called a hook because it is usually bent.… One can imagine a bacterial cell as having a tough outer envelope within which is a softer more flexible one, and inside that the jelly-like protoplasm resides. The flagellum and its hook are attached to the cell just at, or just inside, these skins, and the remarkable feature is the way in which they are anchored. In a bacterium called Bacillus subtilis… the hook extends, as a rod, through the outer wall, and at the end of the rod, separated by its last few nanometers, are two discs. There is one at the very end which seems to be set in the inner membrane, the one which covers the cell’s protoplasm, and the near-terminal disc is set just inside the cell wall. In effect, the long flagellum seems to be held in place by its hook, with two discs acting as a double bolt, or perhaps a bolt and washer…

This little exert to me just shows how complex this is and how Behe is definately on to something with this. Any thoughts?

John said:

In Dembski’s book “The Design of Life” he talks about Behe and irriducible complexity, and how it works, and as i read this book i was very drawn in by this thought of irreducible complexity. I know that Darwinians think that a bacterium with a flagellum just kind of evolved because of the Darwinian selection mechanism from the bacterium lacking flagellum and the genes coding for flagellar protiens. But as i read this exert from the book it uses something John Postgate says in describing the complexity of the bacterial flagellum. He says:

A typical bacterial flagellum, we now know is a long, tubular filament of protein. It is indeed loosely coiled, like a pulled-out, left handed spring, or perhaps a corkscrew, and it terminates, close to the cell wall, as a thickened, flexible zone, called a hook because it is usually bent.… One can imagine a bacterial cell as having a tough outer envelope within which is a softer more flexible one, and inside that the jelly-like protoplasm resides. The flagellum and its hook are attached to the cell just at, or just inside, these skins, and the remarkable feature is the way in which they are anchored. In a bacterium called Bacillus subtilis… the hook extends, as a rod, through the outer wall, and at the end of the rod, separated by its last few nanometers, are two discs. There is one at the very end which seems to be set in the inner membrane, the one which covers the cell’s protoplasm, and the near-terminal disc is set just inside the cell wall. In effect, the long flagellum seems to be held in place by its hook, with two discs acting as a double bolt, or perhaps a bolt and washer…

This little exert to me just shows how complex this is and how Behe is definately on to something with this. Any thoughts?

It’s obvious from your poorly-written bit of thread necromancy that you have terrible reading comprehension, a tenuous grasp on the English language, and no reasoning ability to speak of, so I doubt I’ll get a useful answer to this question, but here goes:

Do you have the slightest speck of evidence that your god, or for that matter ANY god, actually exists? Any evidence at all? Anything?

About this Entry

This page contains a single entry by Nick Matzke published on May 22, 2009 1:28 PM.

AAAS Science Resource Prize was the previous entry in this blog.

Fregata magnificens is the next entry in this blog.

Find recent content on the main index or look in the archives to find all content.

Categories

Archives

Author Archives

Powered by Movable Type 4.361

Site Meter