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.
222 Comments
David B. · 22 May 2009
fnxtr · 22 May 2009
RDK · 22 May 2009
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.
Gingerbaker · 22 May 2009
Everybody loves to complain about the origin of adaptive immunity, but at least Behe wrote a letter.
jfx · 22 May 2009
jasonmitchell · 22 May 2009
DS · 22 May 2009
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.
Gunnar · 22 May 2009
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.
Richard Simons · 22 May 2009
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?
RDK · 22 May 2009
stevaroni · 22 May 2009
386sx · 22 May 2009
Richard Simons · 22 May 2009
RDK · 22 May 2009
386sx · 22 May 2009
RBH · 22 May 2009
Gunnar · 22 May 2009
Mike · 22 May 2009
RDK · 22 May 2009
jfx · 22 May 2009
386sx · 22 May 2009
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."
fnxtr · 22 May 2009
Oh, no, not the "DNA is like computer code" bullshit again.... didn't bobby get pummeled on this nonsense not too long ago?
stevaroni · 22 May 2009
RDK · 22 May 2009
wad of id · 22 May 2009
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.
slang · 22 May 2009
Bleh.. Behe + Immune System = "what good is half an eye?". Pathetic.
fnxtr · 22 May 2009
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'.
fnxtr · 22 May 2009
r
Gunnar · 22 May 2009
stevaroni · 22 May 2009
Dave C · 22 May 2009
386sx · 22 May 2009
Dave C · 22 May 2009
jfx · 22 May 2009
Gunnar · 22 May 2009
It didn't take you folks long to resort to name calling. And for the record, I have no religious reason to discount evolution. I am Roman Catholic. The church's official position is that evolution is indeed acceptable.
I just don't believe in non experimentally supported ideas for how life originated based on blind faith, or blind anti-relgious aethiesm.
RDK · 22 May 2009
Gunnar · 22 May 2009
"Sounds to me like the default is “teleological”.
You should look up the word.
Gunnar · 22 May 2009
"Evolution has nothing to do with the origin of life; that’s called abiogenesis"
Oh really? It's all about the origin of life, and this seems like you backpedaling. What's Darwin's book called? What's Behe's book about?
I'll take this admission by you as a big white flag waving. That was a lot easier than I expected.
jfx · 22 May 2009
386sx · 22 May 2009
On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life!!
Dave C · 22 May 2009
RDK · 22 May 2009
John Kwok · 22 May 2009
Dave C · 22 May 2009
DS · 22 May 2009
Gunnar wrote:
"Oh really? Then please, show me the experimental evidence that shows evolution of an ICS from nothing."
Well, you might want to read the Science article linked at the beginning of this post. It has lots of references to the experimental evidence found in the scientific literature. Now of course this research does not show that the immune system came "from nothing", quite the opposite. It shows how this supposedly "irreducibly complex" system evolved. It documents many of the simpler immune systems that have evolved and some of the steps that have occured as the system increased in complexity in certain lineages.
Perhaps you have some evidence that something poofed out of nothing? Thought not.
For someone who is supposedly "neutral" you sure use a lot of loaded creationist terminology.
RDK · 22 May 2009
RBH · 22 May 2009
RBH · 22 May 2009
Actually, the very first genetic algorithm I ever wrote, back in the mid-1980s, did nothing but randomly change bits in the 'genetic' code for a maze-learning critter.
John Kwok · 22 May 2009
I thought I'd share with you this e-mail I received from Behe back in late July of 2007:
It began with this friendly greeting from Behe:
"Hi, Mr. Kwok, nice to meet you. Here are some brief answers to your
questions."
I wrote:
Dear Professor Behe:
A journalist named David Marshall has posted at Amazon.com that he
will be interviewing you next week. I replied requesting that he ask
several questions of you, but he has declined. When you do meet with
him, I would appreciate it if you can provide some thoughtful,
eloquent, and extensive replies to these questions (In addition to my
original list to Mr. Marshall, I have included a few others.):
1) Why did you reject attorney Eric Rothschild's suggestion that you
try testing your concept of "Irreducible Complexity" via a test that you, yourself,
had proposed, and submit the results for publication in a peer-reviewed scientific
journal such as Science or Nature (You are undoubtedly aware that there have been
many experiments conducted in the biological sciences which have lasted for years.
For example, I am most familiar with Princeton University ecologist Peter R. Grant's
ongoing observations of microevolution in Darwin's Finches; this "experiment" has l
lasted for several decades.).
Behe replied:
"There are lots of tests and examples of IC already in the literature,
where a component of a system is removed and the system doesn't
function. Darwin's Black Box simply pointed out some of them, put a name
on the concept, and showed that it would be a problem for Darwinian
evolution."
I wrote:
2) Your definition of science is the same as the Discovery Institute's. Would
you still admit - as you did under oath when cross-examined by Attorney
Eric Rothschild during the Kitzmiller vs. Dover Area School District Trial - that
your definition would include astrology as a science that is just as valid as
chemistry and physics?
Behe replied:
"Was 17th century phlogiston theory a scientific theory? Scientists of
the time thought so. Was the 19th century theory that space is filled
with ether scientific? Again. folks who were living at the time thought
so. Can the stars affect events? Can the moon affect the tides? People
puzzling that out in the middle ages really didn't know the answers that
are obvious to us now. These days astrology is a carnival diversion, but
centuries ago some intelligent people thought it worth investigating,
which was my point. I was making a history-and-philosophy-of-science
point, that if you look through the years, defining 'science' is very
difficult, as philosophers of science readily agree (Rothschild, as
trial attorneys will do, tried to get as much ridicule-mileage out of it
as possible.) It's rather shortsighted to think that only the
explanations we accept today are scientific. If that were the case, then
the majority of scientist throughout history, who worked on ideas that
turned out to not be correct, weren't doing science at all! That would
be a surprise to them."
I wrote:
3) In "The Edge of Evolution" you have referred to the "Red Queen" as a
"silly statement". Why do you believe this to be true when it was
discovered, almost simultaneously, by eminent evolutionary biologists
Michael Rosenzweig and Leigh Van Valen (who coined the term "Red Queen")
more than thirty - almost thirty five - years ago, and has resulted in an ample
body of scientific literature in evolutionary biology (And it was an important aspect
of the PBS "Evolution" miniseries episode on coevolution.)?
Behe replied:
"You misread my book. I said that the statement of the Red Queen in the
book Alice in Wonderland (that there one has to run as fast as you can
just to stay in place,) was silly. Lewis Carroll's book is a satire and
contains many silly statements."
I wrote:
4) Why do you refer to covevolution as "trench warfare" when it is viewed by
evolutionary biologists as a "coevolutionary arms race" (One notable example
is the research of eminent marine ecologist Geerat Vermeij, which has been summarized
in his book "Evolution and Escalation".).
Behe replied:
"I explain in Chapter 2."
(EDITORIAL NOTE FROM ME: Anyone who has read my Amazon.com review of "The Edge of
Evolution" should recognize that it is one long argument from me slamming Behe for his woeful
understanding of evolutionary ecology, especially coevolution. Others, most notably, David
Wisker, have also recognized this.)
I wrote:
5) Since you accept the reality of "Common Descent" in "The Edge of Evolution", can you explain
why you believe Intelligent Design is a better scientific theory than contemporary evolutionary theory
("The Modern Synthesis") in explaining the past patterns of Planet Earth's biological diversity as seen
through its fossil record?
Behe replied:
"As I explain throughout the book, one has to look at the molecular level
of life, not at fossils, to judge the efficacy of random mutation."
I wrote:
6) How would you use probability theory to account for the "mathematical limits to Darwinism"?
Which probability distribution would you use, and why would you use it?
Behe replied:
"That was explained in Chapter 7 of the book, as well as in my replies to
critical reviews of the book by Sean Carroll, Kenneth Miller, and Jerry
Coyne. Those are posted on my Amazon.com author blog."
I wrote:
7) Why didn't you refer to cell biologist Kenneth R. Miller's elegant refutation
of your mousetrap model of "Irreducible Complexity" in your book "The Edge of Evolution"?
Behe replied:
"I disagree Miller showed anything relevant. Years ago I posted a long
discussion of spurious 'mousetrap evolution' examples by University of
Delaware biologist John McDonald (whose work Miller borrowed) on the
Discovery Institute website."
I wrote:
8) Why didn't you mention your testimony as the key witness for the
defense in the 2005 Kitzmiller vs. Dover Area School District Trial in
your book "The Edge of Evolution"?
Behe replied:
"Because it wasn't relevant to the issue at hand. I posted my response to
the court decision on the web a while ago."
(EDITORIAL NOTE FROM ME: Behe was still recuperating from his drubbing
at the Kitzmiller vs. Dover Area School District trial, which is why he
ignored it in "The Edge of Evolution".)
I wrote:
9) What do you think of Richard Dawkins's implied suggestion in his recently published
New York Times review - which was also formally requested by John Kwok of your publisher
(though this would be of any future book submitted by you or others which is critical of current
evolutionary biology) - to have your book "The Edge of Evolution" subjected to a peer review by
professional evolutionary biologists prior to its publication?
Behe replied:
"The book was read by professionals in various fields before publication.
We also approached several prominent evolutionary biologists who we
expected to be unsympathetic to the argument, for critical feedback.
They all refused to read the book. This reflects, I think, the very
strong feelings that surround this topic. Since the book was published
it has been reviewed by several experts, including Dawkins. Although
they all blustered and bellowed, none touched the substance of the book.
I have posted my replies to those reviews on my Amazon blog."
I wrote:
10) Why do you think you were subjected to ample ridicule, including howls of derision,
from the audience at the American Museum of Natural History's Intelligent Design debate?
Behe replied:
"You seem to be referring to an event that happened in some parallel
universe. I heard no such thing at the AMNH, nor would it even have been
tolerated by the hosts. (If you were there, perhaps you are thinking of
what passed through your own mind.) From my perspective, I thought the
debate there went quite well indeed, and I was approached afterwards by
many folks from the audience who agreed."
(EDITORIAL NOTE FROM ME: After Ken's Tuesday night talk here in NYC, I told him that Behe claimed
that no one was laughing at him and Dembski (who were arguing the PRO; Ken and Robert Pennock
the CON, with Genie Scott moderating) both during and after the Spring 2002 AMNH ID debate.
Ken still remembers that there was indeed ample mirth aimed at Behe and Dembski. Incidentally, it
was immediately after that debate that I asked Dembski twice, in person, how he could calculate the confidence limits
for his Explanatory Filter. He ignored me.)
Behe concluded his e-mail on this note:
"I enjoyed our exchange Mr. Kwok. Thanks for your interest in my book.
Best wishes.
Mike Behe"
(EDITORIAL COMMENT FROM ME: This was the only time that Behe has ever written back to me.)
Anyway, I have tried to convince Behe to write with Dembski the definitive textbook on Klingon Cosmology (which would make much sense since all Behe and Dembski are doing is merely writing dreadful science fiction. Behe's American publisher also publishes the "Star Trek" series of science fiction novels.). And Ken told me that it would be a good idea for Behe to write a textbook on Klingon Biochemistry.
Regards,
John
fnxtr · 22 May 2009
DS · 22 May 2009
RDK wrote:
"Anyone else have the feeling that perhaps this is Troy, iteration 2?"
Well if it is then for sure he will never read the Science article. He probably will not even know that Science is a journal. Now if he starts claiming that there are no transitional forms of the immune system, or that the immune system is the basis for racism, then we will know it is the same guy.
fnxtr · 22 May 2009
"They are both binary systems."
Binary? Really? Each codon is a set of three out of four possible amino acids. How is that "binary", i.e. base 2?
Do you mean digital -- discrete values -- as opposed to a continuous (analog) spectrum of values?
You would think someone in the programming profession would know the difference between "binary" (base 2) and "digital" (discrete units).
Flint · 22 May 2009
What I don't understand is why so many creationists seem to feel the need to lie about being creationists, lie about being neutral, lie about looking for information, and then lie about everything they discuss. Do they think anyone is fooled? When they're already convinced that the origin of life and the origin of the immune system are the same event!
My hypothesis is that this is a religious technique. You get up in church and you say: "I was lost, I didn't know where to turn, I couldn't find any answers, and THEN I found Jesus and saw the light!" And everyone nods and marvels and pretends you weren't indoctrinated into your faith by the age of two.
So they come here to put on the same show, as though they "discovered" their foregone conclusions by carefully cribbing misinformation from AiG. And we're all supposed to shout "Amen!" (or whatever they think knowledgeable people shout). Generally when we don't behave as a proper congregation, they declare victory and leave, as ignorant as when they came and even less aware of it.
stevaroni · 22 May 2009
DS · 22 May 2009
Gunnar wrote:
"They are both binary systems.”
Actually, there are four nucleotides that can form sixty four codons that code for twenty amino acids. Many of the codons are synonomous and many of the amino acid sequences are functionally similar. So no, not "binary" in any sense of the word. So what? How would that possibly set a limit to what sequences mutation can produce or what the effects of cumulative selection are?
Flint · 22 May 2009
Dave C · 22 May 2009
stevaroni · 22 May 2009
John Kwok · 22 May 2009
DS · 22 May 2009
Actually, protein coding regions are highly variable in length. However, a typical protein might be about 500 amino acids in length and therefore coded for by about 1500 bases. Of course, that doesn't include introns, promoters, enhancers, etc.
And before our troll de jour starts pumping out useless probability calculations, new genes don't come from "nothing" either.
jfx · 22 May 2009
John Kwok · 22 May 2009
James Stanhope · 22 May 2009
RDK · 22 May 2009
John Kwok · 22 May 2009
John Kwok · 22 May 2009
John Kwok · 22 May 2009
Stanton · 22 May 2009
Dave Thomas · 22 May 2009
Dave Luckett · 22 May 2009
I try to follow the discussion on mutation and the arising of the immune system, and know I can't fathom the detailed demonstrations of why the analogy with computer software is faulty. I simply haven't got the detailed knowledge of either biochemistry or computer software. But I know this, and I'm only a historian: an analogy is an illustration, not an argument.
Some things in history look like other things. Hell, they even work the same way with the same results, in some ways. But the kicker is that last phrase: in some ways. Some, not all. So you cannot use that apparent likeness for extrapolation or interpolation about the events themselves. It's faulty logic. It doesn't work. That dog won't hunt.
The parrot is dead.
RDK · 22 May 2009
tiredofthis · 23 May 2009
raven · 23 May 2009
raven · 23 May 2009
raven · 23 May 2009
Richard Simons · 23 May 2009
Gunnar,
Forget the comparison of DNA to computer code. It is misleading you into thinking that it is computer code. Remember, DNA can also be compared with a ladder or with a piece of string with about as much justification.
A more useful analogy would be with a recipe that gives the directions for making an organism. A recipe for a fruit cake could have random changes made to it and still produce a cake. Some changes, for example replacing currants by sardines, are likely to make it worse. Replacing the flour by salt would be a lethal mutation. Other changes, e.g. substituting raisins for currants, will probably have little effect on the outcome. Yet other changes may make it better, but the chance of this happening is low because the recipe has evolved over many generations to be good at making a cake and not a fish pie.
Stanton · 23 May 2009
Kenneth Baggaley · 23 May 2009
raven · 23 May 2009
Kenneth Baggaley · 23 May 2009
John Kwok · 23 May 2009
John Kwok · 23 May 2009
Keelyn · 23 May 2009
Paul Burnett · 23 May 2009
eric · 23 May 2009
All of this discussion of how much (or little) DNA is analogous to computer code misses the forest for the trees. That all life on earth shares the same hereditary mechanism is strong evidence for common descent, discovered almost 100 years after Darwin proposed it.
There's simply no good reason why separately created animals would have the same hereditary mechanism, and all sorts of good reasons why they shouldn't.
phantomreader42 · 23 May 2009
phantomreader42 · 23 May 2009
waynef · 23 May 2009
I see a recurring theme being played out here over and over. Let me start out this way:
Let's take for example, The Theory of Relativity and the Special Theory. Professor Einstein presented a number of Earth shattering and completely unintuitive theories based on years of careful study coupled with his unbelievable ability to wrap his mind around concepts that even today leaves people dumbfounded and drooling all over themselves trying to understand them. The speed of light is always constant? Curved space? There were obviously MANY critics.
Not until technology caught up with his concepts were his theories adequately tested. And to this day EVERY observation and EVERY experiment performed has done nothing but add more and more support to the gift he gave us so many years ago. Are there those on the fringe that reject Einstein's theories? I'm sure there are but then they are overwhelmed by the evidence and the huge majority of academia (You'll notice I didn't say the majority of the public).
Do you see how this is analogous to the Theory of Evolution? It also involved Earth shattering and completely unintuitive theories based on years of careful study. It also needed a fantastic mind to put the pieces together. It also required a great deal of experimentation and discovery to establish its validity. It's also been proven true by every discovery in every area of science, to this day.
Are there still discoveries to be made? Of course there are. I find that a constant theme expounded here by opposing views, such as in this thread, is to call out minor issues and claim that the lack of data invalidates the entire theory. Sure, maybe nobody knows (yet) exactly where the immune system began but do we know how the universe formed in such a way that the speed of light is always a constant? No. Does it matter and does it impact the validity of these theories? No it doesn't.
It would really be thrilling to see an opponent present a valid set of opposing data instead of simply bellowing, "I don't understand it so it can't be true!"
Paul Burnett · 23 May 2009
Paul Burnett · 23 May 2009
John Kwok · 23 May 2009
DS · 23 May 2009
Gunner wrote (again):
"Oh really? Then please, show me the experimental evidence that shows evolution of an ICS from nothing."
First, as has already been pointed out to you, something from nothing is a creationist hypothesis, that YOU have failed to provide any evidence for.
Second, have you read the Science article yet? Have you read the stack of research that Behe igonored at Dover yet? If not then quit whining about experimental evidenece already.
Your think is the only thing around here that is binary.
Keelyn · 23 May 2009
Mike Elzinga · 23 May 2009
Mike Elzinga · 23 May 2009
That’s weird!
I posted once, saw a single post, checked back later and saw two.
Henry J · 23 May 2009
RDK · 23 May 2009
Keelyn · 23 May 2009
Flint · 23 May 2009
fnxtr · 24 May 2009
polloi · 24 May 2009
Raven, please state the sources for your flat-earthers claims.
TFE society site is an obvious joke.
Paul Burnett · 24 May 2009
Stanton · 24 May 2009
Paul Burnett · 24 May 2009
raven · 24 May 2009
raven · 24 May 2009
John Kwok · 24 May 2009
John Kwok · 24 May 2009
Paul Burnett · 24 May 2009
eric · 24 May 2009
raven · 24 May 2009
Matt Young · 24 May 2009
waynef · 24 May 2009
Flint · 24 May 2009
Stanton · 24 May 2009
Stanton · 24 May 2009
Ichthyic · 24 May 2009
Sura 18:47: "…and you will see the earth as a levelled plain…"
obviously taken out of context, and I would guess more like looking at a local area.
Suras 20:53 and 43:10: "Who has made earth for you like a bed…"
meaning a comfortable place to lie?
Sura 79:30: "And after that He spread the earth"
I can do that too, with a hoe or a shovel. Don't see how this implies flatnes.
Sura 18:85-90: "So he followed a course. Until when he reached the place where the sun set, he found it going down into a black sea… Then he followed (another) course. Until when he reached the land of the rising of the sun…"
so, two different courses lead to areas where the sun rises and sets.
sounds like east and west to me. Again, how does this imply flatness?
I'm not saying that at the time the Qur'an was written, that there weren't flat earthers around, but I AM saying that none of these particular verses demonstrate your point.
eric · 24 May 2009
WKM · 24 May 2009
Dan · 24 May 2009
Dean Wentworth · 24 May 2009
Anthony · 25 May 2009
Rolf · 25 May 2009
Stanton · 25 May 2009
Frank J · 25 May 2009
John Kwok · 25 May 2009
John Kwok · 25 May 2009
jfx · 25 May 2009
John Kwok · 25 May 2009
John Kwok · 25 May 2009
Or rather, to put it most simply, and most bluntly, Behe ought to know better than to peddle any further his favorite mendacious intellectual pornography, ID cretinism (About a year ago, I heard eminent evolutionary geneticist Francisco J. Ayala say, during a public lecture, that, as a biochemist, Behe ought to know better than to stick with ID.).
RDK · 25 May 2009
John Kwok · 25 May 2009
It's not Dopey Dumbski, but apparently, yet another of his DI IDiot Borg drones trying to make an inane comparison for "excellent" design in biology from the perspective of architecture:
I especially liked this recent observations of yours in that risible comment thread over at Uncommon Dissent:
"Also, there’s the little problem of why the Creator didn’t design his creation for optimum efficiency. If you agree that it’s not about what’s “best”, but rather what works, or what’s “good enough”, then you’ve conceded that there’s nothing special about nature–nothing that couldn’t have proceeded from countless evolutionary changes. Because that’s exactly what evolution does."
Well, in other words, if Intelligent Design is so good, then why is Earth's biota replete with so many "jury-rigged" solutions for dealing with the "economy of nature", of which, of course, the best known example is the Panda's Thumb.
jfx · 25 May 2009
fnxtr · 25 May 2009
DS · 25 May 2009
I really like this little gem:
"...maximally unlikely..."
Do these people even read what they write. It seems maximally unlikely.
jfx · 25 May 2009
Paul Burnett · 25 May 2009
slang · 25 May 2009
RDK · 25 May 2009
fnxtr · 25 May 2009
CJYman, please use a hanky next time, or at least wipe up after yourself. Thank you.
Henry J · 25 May 2009
What the heck is a "physically inert meaning"? Or "physically inert “meaning/function"?
The substances of which a life form is made can't all be inert or it wouldn't be a life form.
Re "“Any system composed of chance and law absent previous intelligence will not produce physically inert meaning/function.”
"
I wonder if there's any way to translate that word salad into English?
-------------
Backtracking a moment to the loose analogy between DNA and human computer programming:
Computer programs are essentially sequential. DNA isn't; its processing is massively parallel.
Even in those programs that do run multiple threads concurrently, each thread is sequential.
Computers have a program counter to tell the CPU where to get the next instruction. DNA doesn't.
In computer programs, each step is likely to depend on results from previous steps. If a gene is active, the protein gets made; a miscalculation in previous steps won't change that.
In a machine language program, data is typically separated from code. A coding gene would be analogous to a constant (though longer than most program constants), and is therefore data, not program code. A change in a gene will change only the protein for which it is the recipe; it won't cause other genes to produce incorrect results.
Regulatory DNA might be a closer analogy to program code than coding genes are, as it can turn coding genes on or off depending on conditions, but even there the operations are still being done in parallel rather than in a predetermined order.
It puzzles me how a software engineer would be unable to figure out most of that with even a minimal introduction to how DNA works.
Henry
Dan · 25 May 2009
fnxtr · 25 May 2009
Henry, I think you're on to something. There are people with a sort of idealized concept of cellular activity (like an assembly line) not aware that's it's all a big, sloppy, wonderful mess, all the time.
Tom Coward · 25 May 2009
Possibly somewhat OT, but check out this statement from the webpage of Michael Behe's employer, the Biological Scients Dept. at Lehigh University:
"The faculty in the Department of Biological Sciences is committed to the highest standards of scientific integrity and academic function. This commitment carries with it unwavering support for academic freedom and the free exchange of ideas. It also demands the utmost respect for the scientific method, integrity in the conduct of research, and recognition that the validity of any scientific model comes only as a result of rational hypothesis testing, sound experimentation, and findings that can be replicated by others.
"The department faculty, then, are unequivocal in their support of evolutionary theory, which has its roots in the seminal work of Charles Darwin and has been supported by findings accumulated over 140 years. The sole dissenter from this position, Prof. Michael Behe, is a well-known proponent of "intelligent design." While we respect Prof. Behe's right to express his views, they are his alone and are in no way endorsed by the department. It is our collective position that intelligent design has no basis in science, has not been tested experimentally, and should not be regarded as scientific."
Dr. P · 25 May 2009
RDK · 26 May 2009
Frank · 26 May 2009
As a physicist (under education, tho it is my 4th profession :)) I am mostly surprised to observer how desperately Behe is grasping at straws. I mean, he is one of the few ID/Creationists (there is no significant distinction) that actually has a proper education. He clearly must know that what he's doing is just not science! I simply don't get it. I pointed out in my blog (the trackback) what I mean by that. I mean, I saw the reconstruction of the DOver trial, and his backpaddling was humorous at best.
As for the software/DNA analogy, it is just that, an analogy. It only works on a superficial level. This was debated at length a while ago on the freeratio.org message board with a IDist called "Pastor Winthrop". He apparently was some sort of software engineer too. He just wouldn't let the analogy go. Interesting discussion tho.
Frank J · 26 May 2009
Frank J · 26 May 2009
DS · 26 May 2009
CJYman wrote:
"...that is, Aristotle’s observation can be summed up as a prediction for future cases: “an intelligently designed system will contain a physically inert aspect.” I believe he referred, as an example, to how a ship’s configuration is not in the physical properties of the wood used to create it."
Yea, right. And the properties of water are not to be found anywhere in either hydrogen or oxygen atoms, therefore - wait for it - intelligently designed water! Fits right in with intelligent falling.
If these yahoos have not even heard of emergent properties they really should not be displaying their ignorance for all to see. Only the willfully ignorant would be fooled by such nonsense.
Is the "configuration" for a human being in the "physical properties" of the fertilized egg? If no, then God needs to intervene every time a child is born, that's not a very intelligent design. If yes, then no intervention is required and therefore humans are not intelligently designed. Why do these people always insist on inappropriate analogies that disproive their own point?
Stanton · 26 May 2009
Raging Bee · 26 May 2009
And, we have already discovered physically inert symbolic representation at the foundation of life. And no this is not merely a post-diction as I do believe that it was Aristotle (long before life was understood) who described how the effects of “telic processes” are not defined by the properties of the material utilized within the system in question — that is, Aristotle’s observation can be summed up as a prediction for future cases: “an intelligently designed system will contain a physically inert aspect.” I believe he referred, as an example, to how a ship’s configuration is not in the physical properties of the wood used to create it.
Minor question: what sort of dressing is best on word-salad?
eric · 26 May 2009
TomS · 26 May 2009
I'd like to note something else about "irreducible complexity", which is that something very much like it has been around for hundreds of years, and has been used to argue for the impossibility of other things about life. Such as that it is impossible for a body to develop complex, interdependent organs; but that rather they must have been preformed. See the Wikipedia article "Irreducible complexity" under the heading "Forerunners" for a quick survey of the history of irreducible complexity.
John Kwok · 26 May 2009
John Kwok · 26 May 2009
Martin · 26 May 2009
Not sure what is wrong with the DNA/program analogy. Other than that anything from creationists must a priori be wrong. Surely it would be possible, if inefficient, to add new features to a program by random modifications and selection.
John Kwok · 26 May 2009
John Kwok · 26 May 2009
John Kwok · 26 May 2009
@ Frank J (continued),
One of the prevailing problems that evolution denialists have is their inability to understand that while evolution may occur via natural selection (or a slightly related process), random mutation is important as the "source material" for natural selection. They make the mistake that "random mutations", while they are "random", have to act in accordance to the evolutionary history of the population(s) in question. That's why, for example, a "random" mutation in a population of chickens would never yield a human (or vice versa). Instead, one would expect such mutations to produce offspring that would conform to that population's evolutionary history. So whenever you read the term "random mutation", then that phrase doesn't mean a completely random event, but instead, one that is quite constrained by evolutionary history.
AgonisThorn · 26 May 2009
Frank J · 26 May 2009
DavidK · 26 May 2009
eric · 26 May 2009
Richard Simons · 26 May 2009
Charlie Wagner · 26 May 2009
"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].”
So where did the transposons come from? Clearly they came from outside the genome.
Frank J · 26 May 2009
Stanton · 26 May 2009
DavidK · 26 May 2009
Kevin B · 26 May 2009
DavidK · 26 May 2009
Hey, Horigan was an attorney like Phillip Johnson. I was thinking as I looked over this book whether or not Johnson plagerized information, you know, confidential attorney/attorney privileges, because Horigan was using the intelligent design terminology.
KP · 26 May 2009
I am late to the party on this one, having been gone all weekend. However, if Behe wants to nitpick the details of HOW the immune system evolved, then he is only managing to create a thin smokescreen over the fact THAT it evolved and that detailed tested explanations have been worked out for it.
And until he comes up with a detailed, testable ID-based explanation for the immune system, he can STFU. He adds nothing productive to science.
Raging Bee · 26 May 2009
eric · 26 May 2009
Mike Elzinga · 26 May 2009
RBH · 26 May 2009
fnxtr · 26 May 2009
Henry J · 26 May 2009
Henry J · 26 May 2009
Henry J · 26 May 2009
DNAJock · 27 May 2009
I am fairly sure that a 'feature' is a bug that has been documented.
John Kwok · 27 May 2009
Hi Raging Bee,
I managed to get myself involved in a rather silly - and somewhat crazy - exchange of e-mails with Pournelle last year. He thinks that banning the teaching of ID is an important aspect of "totalitarian science".
You may find this posting of his from last July rather interesting:
"I have another reason not to have an open Forum. Some people are fanatics. I thought those opposed to "teaching evolution" were fanatics when I was in high school in Tennessee where the Scopes Law was still on the books and there was periodic agitation to enforce it again. I encountered anti-evolutionists from time to time during my academic career, including offers of grants if I would oppose the teaching of evolution."
"I didn't pay a lot of attention to those: but now I find that the desire to censor any teaching of Intelligent Design or any other alternative to orthodox Darwinism comes with about the same arguments I used to hear about teaching evolution. The horror! Someone questions the consensus! And of course censorship means some national means of controlling local schools."
"I say that having national censorship of topics to be taught in local schools is a cure far worse than the supposed disease of having 'Intelligent Design nonsense' taught in at most a few score school districts across the country -- and usually taught by its opponents at that. I have more faith in rational discussion than I do in censorship as a means of enforcing correct opinions. Suppose Darwinism is as right as rain and Intelligent Design is worthless and indefensible: then why must Darwinism use censorship rather than rational discussion?"
"I do not find that there is much interest among American students in the whole question of scientific method and rational argument. I do not see that many teachers are given much instruction in the subject, and I do not see much of it taught."
"In any event, having an open Forum in which the ID people and Darwinists scream that the world will end if the other side is not censored is of no interest to me."
"If in fact the arguments for ID are ludicrous, I do not see why there is so much pressure for censorship and suppression. Either one believes in rational discussion or one does not. If ID is easy to refute, then refute it. Who knows, the ID people may give up, or refine their arguments; and the refutation should be instructive."
"If 100 mostly mid-western school districts required that alternatives to Darwinism be taught in school, would the Republic come to an end? Would that be worse than centralized control of subject matter? And where does the central control end? With jail for Global Warming Denial? I know that has been proposed."
You can find the rest of the comments from that post here:
http://www.jerrypournelle.com/view/2008/Q2/view525.html
Sadly it's not the only time he's weighed in favorably on behalf of ID, as a search of his website will demonstrate.
Regards,
John
P. S. I met him once back in the mid 1990s at some kind of science and technology conference in NYC. One of those also present was Arthur C. Clarke, and I found Pournelle far more courteous than Clarke.
fnxtr · 27 May 2009
fnxtr · 27 May 2009
...history of ID.
John Kwok · 27 May 2009
Frank J · 27 May 2009
John Kwok · 27 May 2009
Ravilyn Sanders · 27 May 2009
eric · 27 May 2009
Dean Wentworth · 27 May 2009
Frank J · 27 May 2009
John Kwok · 27 May 2009
John Kwok · 27 May 2009
John Kwok · 27 May 2009
John Kwok · 27 May 2009
Frank J,
If you read Pournelle's online blog, there's a strong dosage of libertarian thought. Sadly, however, in his case, Pournelle has conflated freedom of speech with what is recognized widely as scientific veracity, with respect, of course, to evolution and evolutionary biology.
Regards,
John
Ravilyn Sanders · 27 May 2009
Ravilyn Sanders · 27 May 2009
John Kwok · 27 May 2009
Stanton · 27 May 2009
Frank J · 28 May 2009
Frank J · 28 May 2009
eric · 28 May 2009
jasonmitchell · 28 May 2009
I disagree on your characterization of their motives but agree with you on what they're doing. I think they see all compulsory attendance events as opportunities to proselytize people who would not normally listen to their message. They're not worried about people suddenly wanting evolution when its not forced on them, they just want to use the compulsive power of the state to spread their religion.
Amen! brother....ahh, err, I mean I agree with you here. The ENTIRE creationism movement (and the ID scam) is 100% about evangelizing, 0% about science. It seems that no other religious group is so intent on using taxpayer resources for their ministries (the whole pathological inability to recognise what is and is not secular?)
John Kwok · 28 May 2009
Frank J · 28 May 2009
jasonmitchell · 28 May 2009
jasonmitchell · 28 May 2009
oops ---should be
"that person's dickishness" above
Martin · 30 May 2009
Martin · 30 May 2009
Martin · 30 May 2009
Dave Thomas · 30 May 2009
Henry J · 1 June 2009
Target? Weasel? Somebody might have to ferret out the pathetic level of detail...
Martin · 2 June 2009
Martin · 2 June 2009
Kevin B · 2 June 2009
Dave Thomas · 2 June 2009
Kevin B · 2 June 2009
Mike Elzinga · 2 June 2009
Dave Thomas · 3 June 2009
Binkyboy · 3 June 2009
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.
John · 1 December 2009
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?
phantomreader42 · 1 December 2009