Another Take on Behe & Class Discussion
First off, thanks to Elena for getting the ball rolling on class posts. I am another member of Allen’s class, and I too apologize for my ignorance of scientific theory. Nevertheless, I do have a few opinions to express on Behe’s “Black Box” and our class discussions.
Though I choose not to speculate on Behe’s possible motives (if there were any at all) for confusing the basic terminology of evolution/descent with modification/natural selection, I think it is important to note that after so much work was built on his own, which supposedly undermines evolution, he had a responsibility to define his views on the unanswered implications of his book, namely that his argument dispells “evolution”. Behe did not take the 10 year downtime between editions of Black Box to address what his book implied (that his theory overthrew evolution) whether he expressly stated it or not. Further, the fact that he wrote in the book that he believes the evidence supportes common descent is an even stronger reason for him to publically set the record straight on his views in the afterword of the new edition. Because he chose not to do so, it is difficult for me to believe he sincerely meant what he wrote on page 176.
In terms of the science behind Behe’s arguement (regarding which, as Darwin would put it, “my ignorance of the laws of biochemistry is profound”) the question to his underlying assumption is, I believe: are his examples really irreducibly complex? Well, it seems to me that depends on whether you consider any intermediate funtions of the proposed trait to be beneficial. Taking Behe’s popular example of the cilia: is it, with any aspect removed, still functional? As a whole cilia in the manner we know it now, no it is not. However, could these cilia have been functional in another way at an intermediate point in evolution? If so, then Behe’s concept of irreducible complexity doesn’t really challenge natural selection either. Though i recognize this logic is somewhat teleological, it is no more so than the concept of function/benefit in adaptations in general.
In a broader sense, I believe leaders of the ID movement (namely Behe and Dempski) are wrapped up in a similar problem to that which doomed some aspects of the modern synthesis: they focus to heavily on the micro-scale mathematical (and in Behe’s case biochemical) aspects of evolution, and in doing so tend to miss the forest for the trees. Often these minute changes do not even manifest at the level of phenotype upon which Darwin based his arguments for descent with modification and natural selection. In the same way that Fisher reduced natural selection to the level of alleles, Behe has reduced ID to the level of biochemical pathways. I believe these arguments tend to miss the significance of evolution on the level of phenotypes. Similarly, I believe Dawkin’s reductionist defense of evolution was equally as non-compelling. In my opinion, the most convincing argument for descent with modification and natural selection is still what I refer to as Darwin’s “look around you!” argument in the origin of species. Although this may not be based on hard math, I am not convinced that math and physics are the best means by which to judge biologoical processes. Though I realize this is a grossly over-generalized statement, please bare with me, as I am certainly not at the scientific level of those posting on this site. If someone with a greater degree of scientific understanding would like to explain why it is a good thing that biology be “more like physics/math” I would looking forward to reading it. Thank you.
Welcome, Josh, and thanks for entering the fray! When I’m not rushing to actually get to class, I will attempt to address your question vis-a-vis the relationship between mathematics and science. It’s a question I’ve thought about a lot since getting into this debate, and one that I believe gets at the heart of many of the misunderstandings between IDers and EBers. See you tonight!
Comment by Allen MacNeill — July 13, 2006 @ 4:42 pm
Welcome Josh,
I thought your reservations regarding Irreducibly Complex (IC) systems were quite reasonable, they’ve certainly been reservations I’ve pondered myself.
My view is Behe’s critique is a “challenge” (as the title of his book suggests), not an absolute refutation. That said, I do think the challenge is very formidable, almost enough to stand on its own, but not quite enough for my comfort level.
So how did I tie up what I saw were loose ends? What I did is say to myself, “let’s be generous, let’s assume IC systems can be evolved via natural selection, was there enough time, chance, and population resources to make this happen?” I concluded the answer was no. Cornell geneticist John Sanford in Genetic Entropy reflect my views quite well on this issue, and parallels how I came to my conclusions.
The most objective way one can actually measure natural selection’s involvement in evolution is through the science of population genetics. Population genetics can estimate if a population is producing enough offspring over time to fuel evolutionary change through natural selection. Sanford and other IDers have concluded that natural selection could not have possibly been the prime-mover of evolution. There simply were not enough population resrouce to mold the billions of nucleotides in something like a human being (this is somewhat intuitively obvious when one considers human populations would have been much much smaller, less than several million, for most of history).
Thus, for me, the issue of IC can become a moot point anyway. And that is personally how I came to terms with the possible loose ends. Still, I think Behe made a very powerful case on his own…
Finally, Behe’s arguments for ID in 1996 are not as in depth as the arguments for ID today, but I consider them a first step.
IMHO, Wigner, Barrow, Tipler, Belinfante, and Dembski provide a rigorous basis for ID from pure physics, math, and information science. (Barrow, by the way, is a world class physicist and received a 1.4 milliion prize for his work on physics and it’s connection to questions of religion. He wrote an ID-sympathetic work The Anthropic Cosmological Principal. Wigner was a Nobel laureate who made very important indirect contributions to ID, and had publicly expressed reservations over Darwinian evolution.)
There is a very strong trend within biology (completely independent of ID) toward math, physics, and engineering. It is called systems biology, and it could be very revolutionary. As you might suspect, this trend is driven partly by a profit oriented mentality for the booming bio-tech, medical, and pharmaceutical industry.
The engineering and teleological perspective permeates systems biology. Thus, there is a purely demographic consideration for biology becoming more ID friendly because engineers (relative to evolutionary biologists) tend to by that way by nature (after all, they are designers).
This doesn’t absolutely justify an engineering viewpoint of biology, but it seems to be a perspective good enough to be practical, and for most people, practical rather than ideological is good enough.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 13, 2006 @ 6:41 pm
Salvador,
Given your comments and views (expressed here and elsewhere) on biochemical complexity and probabilistic criticisms of evolution, I’d like to invite you to read some of the science that I’ve considered in the Molecular Evolution section of my own blog.
There, you should have no problem finding helpful scientific studies on:
…”Modelling Evolution of Protein-DNA interactions” (using computational biology to explain the divergence of regulatory pathways and increases in complexity)
…Kinome Evolution (comparative genomics of a single superfamily of proteins)
…”Molecular Evolution in a Bottle” (merging population and molecular genetics in the decent with modification of a key bacterial protein)
…and…
…”Reducing Complexity” (a variation on genetic algorithms that demonstrates the acquisition of complexity and robustness, with only self-replication and a random source of variation as drivers to population change)
Each of these, and many other studies out there, strongly make the case for “RM+NS” as not only sufficient for evolution to take place, but facilitating modification and complexity.
Please, I invite anyone who thinks that Behe, Dembski, or others might “be on to something here” to explain away such studies…
Comment by Dan — July 13, 2006 @ 7:03 pm
Salvador wrote
Um, Sal? That stuff that you mention about enough time? All else equal, both the probability of fixation of a beneficial mutation and the time to fix a mutation varies with population size, with shorter time to fixation in smaller populations. The “intuitively obvious” conclusion you reach is precisely the opposite of what popgen teaches us.RBH
Comment by Richard B. Hoppe — July 13, 2006 @ 8:08 pm
RBH,
The problem however with smaller population sizes is the lower likelihood of selectively advantaged mutations popping up in the population. Lot’s of critters, the better likelihood of a new mutation appearing. Fewer critters, better likelihood of fixation (as you note). Therefore, the situation regarding population sizes being large or small, when all factors considered is :”darned if you do, darned if you don’t.”
Haldane suggested some optimization parameters for an ideal population size (I think something on the order of 10,000????), but it still resulted in a fixation rate of about 1 trait every 300 generations. This was fatal to scenarios of human evolution, and this problem has been dubbed, “Haldane’s dilemma”.
The point in citing 1,000,000 in an off-the-cuff manner was just to give a feel for the difficulty of the task of comming up with new mutations. Since Lenski estimates a truly beneficial popping up 1 out of every 1 million times, even assuming monstorous selective sweeps and population replenishments, natural selection is too inefficient. A million people would have to be dying off and reproducing every generation just to keep pace with the nucleotides from the split with our last ape-like ancestor.
Ok, there are a buzillion caveats and qualifiers and counter-caveats and counter-qualifiesr to all of what I said, and I can’t possibly fit them in the space of this thread, let alone post. So Perhaps I should simply refer everyone to Sanford’s book. He goes into the numbers in more brutal detail.
Nevertheless, you still made an astute observation, and I credit you with catching me making a less-than-formal argument. I salute you, sir.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 13, 2006 @ 8:38 pm
Thanks Josh for frank comments.
As an engineer with “some” math, I expect that Darwin’s theory will rapidly founder on the explosion in genomic and biochemical data. Behe’s Ch 7 “Road Kill” (especially p 141 and 160) summarizes the argument. If you can, highly recommend Sanford’s Genomic Entropy that Sal referred to. If evolutionists actually applied population dynamics to each Darwinian “small step,” they would soon find all their “models” rapidly disappearing beyond Dembski’s Universal Probability Bound and all realm of even the remotest possibility over the entire age of the universe. Physicists, mathematicians and engineers who have looked into the implications of the models Sandford sumamrizes conclude that most evolutionary models are alot of inconsequential handwaving (or “Just-so stories without substance. E.g., Sir Fred Hoyle (Mathematics of Evolution, 1999, ISBN 0-9669934-0-3) estimates the probability at about 10^-4000, compared to the Universal Probability Bound of about 10^-120. i.e. “Zip”, “nada,” forget it.
Comment by David L. Hagen — July 13, 2006 @ 11:17 pm
As we will see in the intro evolution course, the argument from “random mutation and natural selection” alone is essentially a straw-man argument. For reasons that I will get into in the course (and have outlined in detail in several posts at The Evolution List, mutations at virtually all levels aren’t really “random”, if by that term one means “totally unconstrained”. On the contrary, changes in both gene sequence and gene expression are highly dependent on position within the genome (i.e. relative to each other and to regulatory sites), to intracellular environment (i.e. chemical factors altering gene expression), and to external environment (which are ultimately transduced to the genome level via chemistry-based gene regulatory processes).
And, as even a cursory read through Mary Jane West-Eberhard’s (2003) book, Developmental Plasticity and Evolution, would indicate, there are a multitude of mechanisms by which phenotypes can change that are not subsumed under the “modern synthesis” definition of “random mutation.”
As to natural selection, it is clearly not the only mechanism by which the foregoing changes can be “preserved” and/or promoted within and between populations. Darwin himself also proposed sexual selection, and as recent research into the diversification of many animal species (e.g. the cichlids of Lake Victoria) has indicated, this mechanism can have startling consequences (and happen at truly amazing speeds). In addition, Sewell Wright’s mechanism of genetic drift (along with Mayr’s “founder effect” and genetic “bottlenecks”) can interact with both types of selection to produce patterns of change different from those one would predict on the basis of natural selection alone (and without the “cost of selection” problems outlined by Haldane).
In a nutshell, attacking current evolutionary theory on the basis of how closely it hews to the “modern synthesis” is to attack a theoretical framework that many current historians of evolutionary biology (Will Provine chief among them) have shown was superceded almost half a century ago.
Comment by Allen MacNeill — July 13, 2006 @ 11:41 pm
In comment #5, Davud Hagen wrote:
On the contrary, recent discoveries in genomics and bioinformatics have had just the opposite effect: they have provided empirical support for the “new synthesis” of traditional evolutionary biology and the dynamic field of evolutionary develoment. Indeed, the newest national center for such discoveries is right here at Cornell, where new and extremely exciting work based on comparisons between chimp and human genomes have resulted in major advances in our understanding of the divergence of these two species from their common evolutionary ancestor in the Pliocene. In addition, the new center for genomes at Cornell, currently under construction, will provide a launching pad, not for more theoretical speculation into ID unsupported by empirical evidence, but rather an avalanche of new empirical support for the developing “21st century synthesis” of evolutionary biology, evolutionary development, and genomics.
How can I state this so confidently? Because Cornell’s departments of ecology & evolutionary biology, genetics & development, and molecular biology are the premier departments of their kind in the world. I know many of them personally, and many of the rest by reputation. They are first rate empirical scientists and profound thinkers, virtually all of whom are willing and able to “push the envelope” of the new synthesis. It’s an exciting time to be an evolutionary biologist, and this is an extraordinarily exciting place to be one!
Comment by Allen MacNeill — July 13, 2006 @ 11:50 pm
RBH —
Just to point out, if you have a smaller population size, you have a smaller generative population for producing a given mutation. There is no reason to expect from a non-telic evolution that a smaller population would produce more beneficial mutations per capita. I don’t know quantitatively how much this would impact a given scenario, but it is certainly something to keep in mind.
Comment by Jonathan Bartlett — July 14, 2006 @ 12:01 am
Josh,
If you’re still reading, it might be helpful to get a survey of primary opinions of IDers.
1. A good fraction believe in universal common ancestry, but many (like me) don’t. Some are agnostic to the issue.
2. Even those who reject universal common ancestry (like me) are still very favorable to pre-programmed design as an explanation for some evolution. Thus one could make a statement that most IDers are not averse to some kinds of evolution, especially if it pre-programed (designed).
3. Natural selection as a prime-mover is largely rejected by IDers (and often with enormous emotion to boot)
4. Non-intelligent origin of life is largely rejected by IDers
5. Surprisingly, evo-devo has some interest from IDers because it supports the idea of pre-programmed evolution.
6. neutral evolution has a lot of support from IDers (that’s a gross simplification on my part however, so please be aware of this caveat)
It is on point #5 that the various sides might actually find some common ground and support each other.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 14, 2006 @ 12:38 am
Salvador again makes many unsupported claims and given his unwillingness to support them (at least in the past), I am somewhat discouraged from asking him to follow the rules of engagement of this board.
Whatever Standford believes he has shown, reality quickly contradicts his claims. What good is an idea when it is at odds with the evidence.
Of course Stanford’s work seems to have little relevance to ID which relies on the absence of any pathways or explanations to infer something called ‘design’.
So back to Behe, his concept of IC was, contrary to what one would expect, an attempt to attack natural selection. Since Natural Selection however is hardly the sole mechanism of evolution and since plausible and credible pathways to IC have been proposed and identified, it seems that IC has to be rejected as a reliable indicator of ID. In fact, I’d argue that IC never could have been an argument in favor of ID since it is based on a false duality and an argument from analogy, which is, as Allen has shown, one of the weakest arguments.
What frustrates me is how ID proponents seem to be largely unfamiliar with scientific progress and evolutionary theory as it presently stands, and merely claim whenever science argues something new that this somehow is relevant to ID. But since ID cannot depend on science finding answers, since this would block the ID inference, it seems quite illogical for ID and ID proponents to make these claims.
While I understand that, lacking any scientific relevance, ID’s short term survival may depend on claiming scientific credibility via a few ‘peer reviewed’ papers of dubious quality and relevance, an embracing of new research as if it were ID relevant, and an overselling of the credentials of ID proponents, it seems clear to me that this may work for a short time, but that for a long term solution, this is likely to fail exactly because ID presents no hope of becoming scientifically relevant unless it abandons its eliminative approach and its appeal to analogy.
It’s time to do hard science, of course, the problem with ID is that hard science ends up blocking ID claims.
Ironic isn’t it?
Comment by PvM — July 14, 2006 @ 12:39 am
Salvador once again makes illogical claims when he states that ID places its hopes on science. If evo-devo and/or neutral evolution are relevant mechanisms then ID becomes superfluous as an ‘explanation’ since it adds nothing scientifically.
ID has a lot to fear from evo-devo or neutrality in evolution since these relatively new areas of evolutionary research show how evolution could have been quite succesful after all, and a significant role is given to variation and selection.
That ID is embracing science is a good first step but it should be clear that it cannot embrace science and claim science to be relevant to ID since ID is based on elimination of scientific pathways.
So far, IDers seem to have avoided dealing with this simple fact.
Perhaps Sal or Hannah can explain their thoughts as to why we should take Sal’s claims seriously? This would mean we have to reject the foundation of the intelligent design approaches.
Is that what Sal is proposing?
Comment by PvM — July 14, 2006 @ 12:43 am
Sal: I think it’s instructive that books in the popular press could be so persuasive to PhD’s accustomed to peer-reviewed literature.
I think Sal has hit the nail on the head. While there is plenty of peer reviewed research to show that ID is vacuous, ID proponents seem to limit themselves to popular science or more obscure books.
As an ex-yec’er I used to stick to obscure books as well, until I decided to look beyond the carefully selected books and ‘research’. What I found was earth shattering and even faith shattering. What I have considered to be solid science, after all was it not sold as such, was actually poor supported claims contradicted by countless scientific evidences.
I do understand that people like to limit their exposure to that with which they agree, however I have found that I learn more from those with whom I disagree. After all it forces me to look at and consider seriously, contradictory claims.
Remember Behe, who based on some obscure book, spent much time showing that IC can evolve after all, while really doing no research that had much of any relevance to intelligent design. Look at Meyer’s paper on the Cambrian which ignores much of the available research.
I also understand the distrust some Christians may have in peer reviewed literature which does not conform to theological principles and it took me personally some time to shake this distrust only to come to the conclusion that science should not be avoided but rather embraced. Presently I am an emotionally and intellectually fulfilled Christian who does not fear science and rather sees it as a way to understand God’s Creation.
Which is why, as a Christian, I have such problems with intelligent design which seems to propose a theologically risky philosophy while lacking as a science. In other words, it’s vacuous scientifically and risky theologically.
Now I understand Sal’s background in Young Earth Creationism, a background which I have found to require a rejection of much good science in favor of ones beliefs and I cannot fail my fellow ID Christians for wanting to see Christ in His Creation. As I have explained, I see such an effort to be counterproductive from both a scientific and theological perspective.
Point in case seems to have been our discussion on redundancy. As I showed, in nature, rather than see redundant systems we see ‘degenerate’ or ‘distributed redundant’ systems.
In other words, contrary to designed technology which is almost uniquely redundant via backup systems, biology is robust through a network of interactions which have been shown to arise trivially from evolutionary processes.
As such redundancy in nature is much better understood in terms of natural processes and thus any ID inference has been effectively blocked.
Yet, IDers still argue, without any evidence of logical analysis, that ID somehow still explains redundancy better even though it cannot even use analogy.
So what does ID have to support its claims? Nothing. Certainly, the foundation of ID, which is purely eliminative renders ID powerless to propose positive hypotheses which follow directly from the premises of ID. But in addition, the fact that natural processes can explain at least in principle the observations of degenerate systems or ‘distributed redundancy’ effectivel shows that science has much better explanations. The proof is purely in the pudding: Show us the ID hypothesis and explain to us why it is better than those provided by science?
Which of course does require one to be familiar with how science explains degeneracy in nature. Extensive literature exists on this topic and I intend to discuss this in more details. I hope that such an approach can help focus the discussions on a very relevant topic namely a direct comparison of an ID claim versus how science explains it.
So for starters: How does ID explain degeneracy in nature? Especially when degeneracy is seldomly found in technological (designed) systems.
Comment by PvM — July 14, 2006 @ 1:57 am
In comment #13, PvM wrote:
This was also Darwin’s technique. As he pointed out in the Origin and in his autobiography, he discounted comments, letters, and reviews that were favorable to his theories, and concentrated on those that were opposed to his theories, always updating his work to address such criticisms. This is why most of his published works grew larger with each edition, as he published more and more responses to his critics.
By contract, Michael Behe didn’t change as single word in Darwin’s Black Box from the first edition to the second, and in the afterword to the latter he basically reiterates his position. This, despite the fact that extensive critical reviews of his work have appeared around the world, providing him with ample opportunities to revise his conclusions (and to present new empirical research that supports his hypotheses).
What are we to conclude from these two examples? That EBers care a great deal about accuracy and count on their critics to improve it. By contrast, IDers can’t be bothered, since their positions aren’t really held for scientific reasons anyway.
P.S. This is also why I have always tried to maintain cordial and productive relationships with people who hold opinions in opposition to mine (like Hannah and the members of the Cornell IDEA Club, Salvador, MikeGene, and some other IDers). From the standpoint of sharpening my own arguments and responding to critics, they are my best friends, doing for me what I can’t do for myself: showing me the other side of the issue from the perspective of the other side, thereby allowing me to continue to learn and to refine my understanding. And so, to the “loyal opposition” I offer a heartfelt “thank you!”
Comment by Allen MacNeill — July 14, 2006 @ 10:25 am
Michael Behe has published– online and in print– many responses to his critics; and though he said he would not have changed much in his book if he wrote it again now, he also said he would add a great deal.
Moreover, you yourself agreed that the “extensive critical reviews” which appeared following his work brought up nothing new; it is all of the same caliber with the just-so stories he addresses in detail in the first edition of his book, and really not to the point at all.
I had read a great deal of his critics before I first read the book in full, and– as you usually do if you focus just on one side of the argument– had a rather warped idea of vigor of his arguments. It did seem to me he was onto something with irreducible complexity, but there were alot of critics, and I wished he would address them in detail. Then I actually read the book, and was surprised that he had addressed them all back in 1996. It seemed most of the critics hadn’t read more than a cliffnotes version of the book, and didn’t really understand that either. When they actually address his arguments there will be time enough to revise the book.
Are you making a categorical statement, and are you prepared to defend it?
Comment by Hannah — July 14, 2006 @ 11:04 am
In comment #14, I wrote:
and then I made the comments that I did. I believe, on the basis of the two examples cited (i.e. the six editions of Darwin’s Origin of Species and the two editions of Behe’s Darwin’s Black Box, widely touted as one of the founding documents of ID) that, indeed, EBers (as represented by Darwin) take a lot of time and trouble to address their critics and update their arguments, whereas IDers (as exemplified by Behe) do not.
It is illustrative of my point that the six editions of the Origin to which I refer were published between 1859 and 1872, a span of 13 years. Over that period of time, the book almost doubled in size, mostly as the result of inclusion of responses by Darwin to his critics.
By contrast, there have been 10 years between the first and second editions of Darwin’s Black box, and over that time Behe added or altered not one word of the main text, and in the Afterword to the second edition basically reiterated his original position without significant modification. This despite ten years of extraordinary productivity in the biological sciences in general, and evolutionary biology in particular. One searches in vain in DBB for any mention of evo-devo, new discoveries in the phylogeny of the mammalian blood clotting system, updates on our understanding of the phylogeny of the vertebrate immune system, etc. They aren’t in either the main text of the second edition of DBB nor in the Afterword.
Furthermore, in 1999 the Discovery Institute (in the “wedge” document) called for a vigorous program of empirical research into ID: at least 100 papers from field and laboratory researchers, presenting empirically testable hypotheses, followed by descriptions of such tests, results obtained, and analysis of the import of such results to the overall research program.
And how much of this has the ID movement accomplished? Nothing. Zilch. Nada. Not one single journal article in the peer-reviewed literature in which the results of an empirical test of an hypothesis derived from ID theory have been either validated or falsified.
Comment by Allen MacNeill — July 14, 2006 @ 12:13 pm
So, it’s a “limited” categorical statement, based on exemplary cases (rather than a numerical analysis). And, if I could edit my comment, I would insert the word “apparently” in front of the phrase “can’t be bothered” and phrase my explanation as to why as an hypothesis, rather than an assertion (it was late/early, I was tired, mea culpa).
Comment by Allen MacNeill — July 14, 2006 @ 12:15 pm
When they actually address his arguments there will be time enough to revise the book.
Of course that’s wishful thinking since critics have in fact addressed his arguments and shown then to be significantly wanting and Behe has done little to address the critics’ comments.
Perhaps Hannah can give us an example? Or perhaps she can address my observations that 1) IC is an argument against Darwinism and thus cannot be an argument for ID 2) natural pathways to IC systems exist and thus IC is not even a reliable indicator.
Is Behe’s book much ado about nothing?
Comment by PvM — July 14, 2006 @ 12:34 pm
And honestly, if it takes public shaming to get IDers to buckle down and get their hands dirty doing the difficult and generally unglamorous field and lab work (compared with doing high-profile debates and writing glitzy press releases) that is clearly necessary to test their hypotheses, then I’m ready to dish some of it out. Let’s see if they can take it…
Comment by Allen MacNeill — July 14, 2006 @ 12:34 pm
You are more than welcome, and I am sincerely grateful you have exerted every effort to remain cordial to “the opposition” under a flag of truce.
Although I can foresee that we probably will not come to agreement on many things, the one reason I have great respect for you, Allen, is you will at least have the students buy IDers books and read them. For what it’s worth, I would have no hesitation recommending IDers learn from you.
I want IDEA members schooled in evolutionary literature. I am proud of IDEA members who have as much a command evolutionary literature as any typical working scientist. As Allen Orr noted, even most scientists are not familiar with evolution:
Perhaps this is the one thing we can agree on, that it’s good for everyone to be exposed to ideas. That up and coming proponents of ID should get some schooling in evolutionary biology.
Well maybe there are perhaps other areas we can agree on, namely some forms of evolution which might be of interest to both sides. Darwin wrote in Chapter 14, “the progenitor of innumerable extinct and living descendants, was created.” Many IDers could live with that or some variant of thereof (such as the assumption that there were various kinds of “first creatures” rather than only one). Evolutionary theory defined in that way would actually be exciting to IDers.
Evolution defined as pre-programmed from the progenitor(s) is acceptable and even of immense interest to IDers. If Darwin could accept special creation of the progenitor, I see no reason it should be problematic for IDers participating in evolutionary biology to accept special creation of the progenitor(s). I would hope, that even though you may consider the idea of a intelligence superfluous to empirical research, that you might find something of scientific value in the quest for artifacts in the cells of creature which could recapitulate phylogeny in the lab! An IDer would be thrilled to be involved in such a glorious (and hopefully profitable) quest, and I would hope you as well.
Ok, so now here is where we disagree. IDers will not presume this regress to more pre-programming to continue forever. At some point it must terminate at a designed artifact or an intelligent designer. OOL and natural selection appear to IDers like the concept of perpetual motion. And what is frustrating to us is that demands to create a lab experiment to illustrate the impossibility of perpetual motion simply can’t be done. It would be like asking us to create an experiment proving square circles don’t exist! And then because we do no such experiments we are viewed as not being empiricists. Our viewpoint on such issues, was beautifully captured in a peer-reviewed paper by a non-IDer, which I mention here: Perfect architectures which scream design. I can appreciate then the anger of the EBers toward the IDers that no empirical product is delivered, but I hope it is evident the IDers have equal disdain for demands for empirical dis-proofs of square circles.
So I suppose I’m trying to inform you up front what you will never see from IDers and what you may possibly see from IDers. Rather than leaving us an irreconcilable impasse about whether there was an intelligence at the root of existence, I simply extend an olive branch, namely the search for recapitulating some amounts of phylogeny in the lab. It’s a heretical evolutionary idea, and I would suppose such heresy might actually pique your interest.
At least in that regard we can find something of mutual interest to both of us, and which will move the research into evolution forward.
Salvador
PS
I’ll be leaving for the weekend shortly, I regret I can only participate sporadically if at all over the next few days.
Comment by Salvador T. Cordova, IDEA GMU — July 14, 2006 @ 1:03 pm
PvM
I can appreciate that dissilusionment with authority figures can cause severe emotional trauma. However please do not “throw the baby out the the bathwater.” The foundational issue is that a priori excluding any intelligent cause results in force fitting data into non-intelligent models, whether or not there is any intelligent cause.
Behe proposes Irreducible Complexity with an intelligent cause as better fitting data than Darwin’s model or Neo-Darwinian Random Mutation & Natural Selection with a non-intelligent cause. Please return to the thread focusing on Behe’s IC.
Allan, Sugest addressing Behe’s detailed responses to critics. See:
A Response to Critics of Darwin’s Black Box
In Defense of the Irreducibility of the Blood Clotting Cascade:
Response to Russell Doolittle, Ken Miller and Keith Robison
The Lamest Attempt Yet to Answer the Challenge Irreducible Complexity Poses for Darwinian Evolution
PvM Rather than hijack this list, if you wish to explore degeneracy and redundancy, please post your definitions and questions elsewhere. [E.g., Sheehan Physical Chemistry, 2nd ed, McGraw Hill (2003), and Yockey (2005, p15) give conflicting definitions.]
Comment by David L. Hagen — July 14, 2006 @ 1:04 pm
LOL! Could you give an example of a scientific study that demonstrates “force fitting data into non-intelligent models”???
…perhaps showing how any study of mutations or genetics that forces their data into a model, and assumes a priori that a Designer specified the observed results to occur, is “force fitting” their data…
… or, heck, any study from any field of biology (evo-devo, paleontology, comparative anatomy) that “force fits” their data…
Comment by Dan — July 14, 2006 @ 1:19 pm
Again, you agreed less than twenty-four hours ago that Darwin’s Black Box has nothing to do with the major part of evolutionary theory. You have to realize that goes both ways. It doesn’t affect most of current evolutionary research, but also most of current evolutionary research does not address his thesis and therefore is utterly irrelevant in considering appropriate revisions of his work. He most definitely never addresses phylogeny; except to say that there is a good deal of sound research done in that field.
The evolution of biochemical pathways, which is the point he does address, has made minimalistic progress in the last ten years. He discusses this “progress” in his afterward, and you claimed yesterday you had no quarrel with our extremely poor opinion of it.
It really would help if you had a logical basis for your “public shaming”. After all your talk about the necessity for sound bases to arguments and the weakness even of strong forms of the argument from analogy, choosing a property (the number of changes between two editions of a popular book) that is both non-causal and has not been shown to be directly related to the issue under consideration (scientific integrity and care for accuracy), and then acting as if two examples (chosen by convenience) will demonstrate your point only makes it appear you have a deep-running double standard.
My “confidence level” in intelligent design has been based more on the complete illogicity, irrationality and utter vacuity of most of the criticisms of ID that I hear than from any sort of reliance on Behe or Dembski’s work. In a way, I rely on you people to help me see the flaws in intelligent design theory– and I agree with Allen that critics can be your best friends. But if the critics do such a poor job coming up with any argument of interest, you begin to wonder if the theory being attacked is stronger than you thought.
Back when I was a sophomore I remember Michael Behe coming to Cornell, by invitation of the Biology Department and ACH. He gave a careful and fully scientific presentation, followed by an extensive Q&A or “public discussion” in which large contingent of the Cornell biology department participated. I hadn’t studied much about ID yet then, and knew nothing about the debate. What I remember most from that evening is that he gave a reasoned, scientific presentation and an even-toned response to all his critics, and they –many of whom had lost their cool before the evening was half over– had primarily arguments from emotion. Maybe only arguments from emotion; as far as a remember, no sound logical or scientific critique was presented that night.
You’ve had ten years. Is that all you can come up with?
[for those not from Cornell; I’m not shouting, or mad. Just earnest :)]
I do agree that we should do more empirical research, write more papers and publish more books. Every aspect of ID should be thoroughly tested. Labwork is slow, though, and doesn’t usually like to be hurried…
Comment by Hannah — July 14, 2006 @ 1:28 pm
…and along the lines of thanking one’s critics, I should say that I’m very grateful for the time that many people here at Cornell– especially Allen, Tim, and Dan– have spent debating these issues with me, letting me know when I said something particularly stupid, and “setting me straight” on a thousand different issues. Much of what I know in this debate I learned from you. Thank you, and thanks for the patience you’ve shown even when I made you absolutely certain you hated me.
Comment by Hannah — July 14, 2006 @ 1:37 pm
Hi, Hannah:
I’m just not particularly sanguine on the assumption that this will actually happen, give the history of such research efforts since 1996.I concede that my blanket characterization of ID on the basis of a comparison of single cases (OoS vs. DBB) was perhaps a bit over-extended (and, indeed, was essentially an argument by analogy…or, rather, comparison, which is basically the same thing). And I appreciate your concession that
BTW, I didn’t attend Behe’s presentation to the biology department, only his presentation in Will Provine’s evolution class. But I stand by a question that I have implicitly asked several times: why, when he was given a golden opportunity to update the arguments and evidence for his ideas in the second (i.e. “anniversary”) edition of DBB, did he not change a single word in the text, and start off the Afterword with “…there is very little of the origina text that I would change if I wrote it today.” (pg. 255). Really? Why not address the critics, the way Darwin did? Wouldn’t this new edition be the ideal venue? And if not, why not?
Comment by Allen MacNeill — July 14, 2006 @ 1:45 pm
Hannah,
You’re absolutely welcome - and likewise, I appreciate your near-infinite patience when discussions get heated that I’ve said rash things out of frustration.
Comment by Dan — July 14, 2006 @ 1:50 pm
Hannah:
On the contrary, I both admire and appreciate you very much, not the least because of your passionate search for clarity on these issues and your defense of logical argument as the means for accomplishing it. As I have said many times, I have far greater respect for an opponent of my views who defends them with logic and with vigor, than for a supporter of my views who sits idly by and does nothing at all.
As my fencing master, Adam Adrian Crown, has said, a true fencer (from the word for “defense”, of course) is “gracious and dignified in defeat, magnanimous and humble in victory.” What we seek is to “…improve our society by promoting the “All for one and one for all” spirit…that emphasizes respect, cooperation, honesty, fairness and personal responsibility.”
Comment by Allen MacNeill — July 14, 2006 @ 1:52 pm
Allen re My #6 and your #7, #8
In Road Kill, Ch 7, Behe addresses the complexity of ATP synthesis and the challenge of population modeling. Biotic energy like ATP is critical for biotic life. Where are the detailed models showing that it can be realistically formed within the Universal Probabilty Bound of 1 in 10^120?
In Ch 3, Behe addresses the flagilum. Since then,
N. J. Matzke (2003) Evolution in (Brownian) space: a model for the origin of the bacterial flagellum proposes detailed evolutionary scenarios for the flagelum. However, On Evolutionary Explanations observes:
Do you know of any population modeling for each step showing that the combined sequence from beginning to end is less than the Universal Probability Bound? (I.e., including all relevant population models such as Sanford (2005) reviews).
If not, that might be a suitable challenge for your premier institution and funding. You are welcome to use all naturalistic models and forces. Once that is satisfactorly demonstrated, realistically quantifying abiogenesis of the first self replicating cell including photosynthesis within the UPB might be a suitable subsequent challenge. However, till then, in light of Hoyle (1999) Mathematics of Evolution, and Sanford (2005) Genomic Entropy etc., I remain skeptical. (And yes I will explore predictive theories for ID outside of my larger responsibilities.)
Comment by David L. Hagen — July 14, 2006 @ 2:05 pm
Jonathan Bartlett remarked
Sure it is. But in the absence of reliable and carefully justified quantitative data on just how much “time, chance, and population resources” is necessary to get to some unspecified end point from an unspecified starting point, appeals to intuition are merely appeals to ignorance.RBH
Comment by Richard B. Hoppe — July 14, 2006 @ 2:17 pm
David (comment 28),
If I may jump in yet again…
It sounds like you expect someone to respond with a detailed accounting of every step for a series of molecular events in the evolution of some feature. Sorry, but I know I don’t have an example where we know everything behind a feature’s evolution, and I admit, I haven’t read Sanford’s nor Hoyle’s books.
Nonetheless, there are many such studies that use population modeling, and feasibility of navigating the fitness landscapes in divergent, (Evolutionary Potential of a Duplicated Repressor-Operator Pair: Simulating Pathways Using Mutation Data) and directional (In vivo molecular evolution reveals biophysical origins of organismal fitness) Selection processes.
Other studies have shown such phenomena in computer modeling studies (The evolutionary origin of complex features), in human genetics studies (Natural selection on protein-coding genes in the human genome), and in transcriptional regulation(Evolutionary Dynamics of Prokaryotic Transcriptional Regulatory Networks).
And that’s just the few studies I’ve come across and bookmarked (at Spurl.net) in the last few months - it’s far from an exhaustive list - so I’m rather sure that your skepticism is based solely on taking Sanford and Hoyle’s claims (whatever they are) very unskeptically, and a weak understanding of the literature in biochemistry and cell biology. Perhaps those fields can be faulted for not having explained this topic to the public better, but the molecular basis for evolution is a relatively new avenue for biology…
Comment by Dan — July 14, 2006 @ 2:40 pm
More thoughts on probability and fitness landscapes regarding the molecular basis of evolution:
Mark from Good Math, Bad Math just got done commenting on one of the articles I just linked to (comment 30) and blogged on, and a commenter (Bob Hawkins) had a very relevant and insightful observation:
Indeed - the genome is clearly an extremely robust and plastic repository of hereditary information, and is adept at both being able to retain/conserve necessary data/sequences and change in n- directions.
Comment by Dan — July 14, 2006 @ 3:16 pm
Hannah wrote:
Could you please provide a list of some of these criticisms of ID you say are so lame?Comment by alienward — July 14, 2006 @ 5:12 pm
Indeed, that would be interesting to see. In particular, Hannah, please explain why asking for empirical and parsimonious evidence for ID (which ID is currently lacking) is lame…
Comment by Dan — July 14, 2006 @ 5:28 pm
Dembski, addressing the Matzke paper linked above.
Comment by todd — July 14, 2006 @ 6:19 pm
From todd’s quote of Dembsky:
In essence evolutionary theory is untestable as well. How do we test that blind chemical reactions are actually building successively more complex bio-machines over very long periods of time? We can’t. We can only guess. How some chemicals self organized into replicating bio-machines which then ever after converted other chemcials into more and more complex nano-bio-technology and bio-machines is on the face of it an indredibley unlikely story to believe in. Yet that story is preferred as the rational story in today’s academic environment.
We can look at a plant in our yard and wonder how that plant came into existence. We can learn that it came from a seed. We then wonder where the seed came from. We learn if comes from the plant. We then wonder where the original seed and plant comes from. We are then told that the plant and seed evolved over time from a single celled life form. We then wonder how a single cell life form or multiple cell life form can make a seed. A seed contains the design schematics for every part of the plant. We are told that plants and seeds evolved over a very long period of time. We wonder if time has some special ability to make seeds. We are told that nature is able to build seeds and plants by time and mutation and natural selection. How does a thing which is not a seed mutate into a seed? A seed is a schematic for the design of every part of a plant. The mutation of the thing that was not a seed into a seed would seem to violate the precondition of evolutionary theory prime directive # 1 i.e unguidedness. Before the seed exists what would be necessary to exist in order for the seed to be the next step in an evolutionary mutative process? How does something go from being not-a-seed to a seed without the purpose of building a plant?
Comment by Neo Avatar — July 14, 2006 @ 8:10 pm
Hannah writes,
My “confidence level” in intelligent design has been based more on the complete illogicity, irrationality and utter vacuity of most of the criticisms of ID that I hear than from any sort of reliance on Behe or Dembski’s work. In a way, I rely on you people to help me see the flaws in intelligent design theory– and I agree with Allen that critics can be your best friends. But if the critics do such a poor job coming up with any argument of interest, you begin to wonder if the theory being attacked is stronger than you thought.
Well, if you actually want to be taken seriously when you say things like this, you have to deal with the serious critiques. For example:
Bottaro, Andrea, Inlay, Matt A., and Matzke, Nicholas J. (2006). “Immunology in the spotlight at the Dover ‘Intelligent Design’ trial.” Nature Immunology. 7(5), 433-435. May 2005. (Subscription no longer required: DOI | Journal | Google Scholar | PubMed | Supplementary Material | Annotated Immune System Evolution Bibliography | Longer, Unannotated Immune System Evolution Bibliography)
Matt Young and Taner Edis, eds. (2004, 2006). Why Intelligent Design Fails: A Scientific Critique of the New Creationism. Rutgers University Press. Book website, Table of Contents, Preface, etc.
Speaking of being serious, isn’t it a little odd that the discussion on this course blog isn’t focused on whether or not Behe’s irreducible complexity argument makes any sense? Isn’t that the key issue? Or do we just take what one biochemist says about evolution on faith?
Comment by nmatzke — July 14, 2006 @ 10:24 pm
Darn links are putting me in the spam buffer again…how’s a guy supposed to cite his sources ’round these parts?
Comment by nmatzke — July 14, 2006 @ 10:25 pm
Hannah,
I too agree with the sentiment “is that all you can come with” but maybe for slightly different reasons. I have no interest in defending ID as a separate scientific discipline but it certainly uses scientific tools to make its conclusions and I haven’t found anything here or anywhere else that undermines many of those conclusions. Most of the discussion I find irrelevant to the basic issues. The most specious is whether ID is a science of not.
As I have said earlier, ID or the techniques that it uses, is mainly applied to OOL issues and also to what some have called “novo-evolution” or the origin of new or complex biological structures or body parts and systems, many of which arrived very rapidly on the scene during the Cambrian Explosion. Essentially ID deals with low probability events and as the probability of the biological event gets higher, people in ID seem willing to support a naturalistic explanation if there is evidence for it. For example, I do not think many ID proponents would object too strongly to much of the speciation mechanisms that lead to species diversity presented in a typical text book on evolutionary biology. It is not something they really care about in terms of the ID vs. NDE debate. What they care about is the low probability events.
However, those who support a non NDE answer to most of these low probability events see no evidence from those who adhere to NDE other than rhetoric (especially technical jargon), wishful speculation or some trivially related findings. It is common to see in evolutionary biology articles the words “it evolved” and it is then left to the reader to infer that some how this happened or must have happened through an NDE process at some time in the distant past. It is also common to find a long list of qualifiers in these articles such as “might, may, plausible, suggest, speculation, seems, puzzle, caveat, missing, difficult, is understood to be, is considered, etc.” when referring to these past evolutionary events. These explanations often have a name, “Just so Stories.” It seems evolutionary biology is one science where one’s imagination counts as evidence.
Behe lays out several complex processes which seem to defy a stepwise gradual approach for evolution. I have not seen any reasonable answers which doesn’t invoke some magical terms like “co-option and preadaptation” or give some irrelevant criticism to undermine his credibility.
Let me take the one that many evolutionary biologist seem to think has been solved, the evolution of the eye. From what I understand, most if not all of the eyes first appeared during the Cambrian Explosion. I use this term because James Valentine uses this term and it refers to a relatively short geological period of time, 515 to 530 million years ago. There were several different types of eyes and some are somewhat similar but others are quite different and there have been improvements since the Cambrian Explosion but essentially no new types of eyes. Valentine also denies that a NDE process can explain the Cambrian Explosion though I haven’t seen him say anything specific about the eye.
After reading Behe’s description of how the eye works, I am just amazed that anyone can think that these various eyes just evolved over this short of time by a chance process. The proteins involved are very complex and this very tightly controlled finely tuned process just screams design. Even if these complex proteins could somehow have evolved separately, it just begs the question of how they were then assembled in such a “remarkable” way. So it is not only the component parts that defy imagination on how they originated but it is the assembly instructions for it all that is really remarkable. Saying that each species had the Pax6 gene just begs the question of where did this very complex DNA sequence come from and why. And what else is needed besides this gene.
The answer is obviously “it evolved.” Yeah, and how did the assembly instructions evolve?
I have found no answer the NDE people give that convincingly answers the questions of novo-evolution and they have no clue about OOL. The answers make great speculation so yes, is that all they have?
Comment by J. Cosgrove — July 14, 2006 @ 11:20 pm
The argument at the beginning of this thread ( inference from the number of revisions in two popular books) makes a lovely exhibit A. The “ID’s aim is to turn America into a theocracy” and “ID is wrong because Behe/Johnson/Dembski (insert name of choice here) is an awful person” follow close behind that, and for a fourth exhibit consider “ID is a science-stopper!”. Add to that the various demarcation arguments based on methodological naturalism, and then some of Miller’s co-optive mechanisms.
Those are just a (very) few of the most egregiously illogical examples.
You’ll notice the importance of more of it is the only point I conceded above (though I do hold ID currently has a fully empirical basis).
That was the focus of our Thursday night discussion, which I haven’t had time to write about here. But you ought to know that your paper was not forgotten.
Comment by Hannah — July 15, 2006 @ 6:57 am
Comment by Mark Frank — July 15, 2006 @ 9:10 am
Re 40 above. I am sorry - the posting did not reflect the preview! I mean’t to make this comment about the quote in 40.
This neatly encapsulates some of the things I find most disturbing about the design inference.
1) Talking about the probability of a past event as though it were a given objective property of the event independent of the observer. What was the probability of Hurricane Katrina flooding New Orleans? It all depends when you made the assessment, what you knew when you made the assessment, and what exactly counts as the event. Does it mean the hurricane expert in 2004 estimating the probability of some hurricane leading to flooding in New Orleans in 2005? Or the met office forecaster 24 hours before it happened? Or someone standing on the levee two minutes beforehand?
2) Using the ambiguity in 1 so that when presented with a neo-darwinian model at one level of detail explaining that it does not allow you to calculate the “true” probability and demanding yet more detail until the modeller is unable to provide it (such a point must always come).
3) Then deducing that the ND model is wildly improbable and therefore the explanation must be design. This is the big leap ….
Take an analogy. Suppose I doubt current physics as an adequate explanation of for the creation and appearance of comets. What an improbable coincidence that they should avoid the orbits of other major stellar bodies and that they should appear at such meaningful periods (Halley’s comet should appear with just the frequency of a normal human lifetime). I propose that in fact a designer created them and put them in their orbits. Rubbish say the astronomers - nothing could be more established than modern physics. Aha - I say - you only have the vaguest idea of how comets are created or how they got into their orbits. Give me the detail and then we can assess the probability of your explanation. All you can give me is “just-so-stories” about how comets were created.
Comment by Mark Frank — July 15, 2006 @ 9:13 am
Hannah (comment39):
I don’t object to opposing arguments for “A”; perhaps “B” is a slight exaggeration (the Discovery Institute, at least, IS interested in a resurgence of religion); “C” - no, we’re not saying their wrong because they’re “awful,” we’re saying they’re awful because they’re so wrong and don’t care that they’re wrong: their agenda supercedes their interest in intellectual honesty; and on “D,” if the Design Inference were not a “science-stopper,” shouldn’t it be easy to study this inference, make further hypotheses, and actually conduct science?
Instead, IDers have failed utterly at coming up with a conceivable way to confirm their Design Inference and distinguish it from evolutionary theory. Whine about demarcation you want when your views are labeled “science-stopper” or “unfalsifiable,” but until you actually “get on your hands” and look for any empirical evidence to support your claims, your objections will remain hollow.
Comment by Dan — July 15, 2006 @ 11:40 am
J Cosgrove said: “Essentially ID deals with low probability events and as the probability of the biological event gets higher, people in ID seem willing to support a naturalistic explanation if there is evidence for it.”
Doesn’t it seem unusual that ID looks better the less you know and then weakens in the face of observable natual evidence. You have to remember, much of what we now consider basic fact used to be considered almost unknowable. What makes you think this chain of natural explaations will now somehow fail, when it has proved so successful over time?
You thinking seems totally illogical to me.
Comment by Mike Hannigan — July 15, 2006 @ 12:08 pm
Hannah wrote:
Do you really consider those quotes to be criticisms of ID? The only thing in that whole paragraph that actually is a criticism is the last three words “Miller’s co-optive mechanisms”. What about that is based on “complete illogicity, irrationality and utter vacuity”?Comment by alienward — July 15, 2006 @ 12:51 pm
Let me illustrate why I think this demand has some flaws. There is no lab work or experiment which will disprove the existence of square circles. It would be unfair to expect it. There is a parallel consideration at play here regarding “lab work” to disprove RMNS or Blind Watchmakers are the prime-movers of complex features in evolution!
Consider we now have computer viruses that self-mutate as a defense mechanism to improve its chances survival by eluding detection. It resorts to using random mutation as a survival strategy. Would one argue the fact random mutation exists in a computer virus is proof there is no need for its design or that it proves such things can emerge from much much simpler pre-cursors through blind watchmaker processes? It is a non-sequitur (conclusions irrelevant or don’t follow from the premises). But then to demand “empirical proof” of this non-sequitur is an even worse non-sequitur, and therefore illogical demand. The same issue of demanding “lab work” to disprove Blind Watchmaker evolution applies here.
What has happened with evolutionary biology is that they don’t realize that major descriptions of their process could be inherently self-contradictory. It is becoming blatantly apparent in Origin of Life as I pointed out Stochastic Process, Deterministic Processes, Square Circles.
We are getting close to the point of seeing it with respect to organic evolution (evolution after the progenitor(s), after the first life or lives ).
The presumption of non design is infecting the mechanistic description of evolution. It should be readily apparent if large scale marcoevolutions are happening it was more likely through pre-programming. That pre-programming may be discoverable, and if EBers would be a little more welcoming to IDers by inviting them to participate in the search of pre-programming the evo departments around the nation would possibly be growing by leaps and bounds. It would be a project of mutual interest to EBers, IDers, and even (gasp) flood-believing YECers like myself.
If one thinks intelligence is superfluous to the issue of pre-programmed evolution, fine. We can describe the process purely mechanistically just as we can describe the evolution of self-mutating computer viruses mechanistically without reference to the original intelligence which created it. I don’t have as much problem with that.
Salvador
PS
I thought the articles at your website were fine, though I disagree at some points. I’m sorry my postings will be sporadic this weekend.
Comment by Salvador T. Cordova, IDEA GMU — July 15, 2006 @ 12:56 pm
As I think I made pretty clear above, they aren’t examples of the best logical reasoning I’ve seen from your side, but a small sampling of the oft-repeated worst. To avoid making it unnecessarily personal I chose to avoid most examples from this website; but each of the others were given by otherwise rational people (all of them people affiliated with our biology department) as good and sufficient reasons for why ID theory should be rejected.
Comment by Hannah — July 15, 2006 @ 1:16 pm
Salvador,
We’re not asking you to disprove square circles. We’re asking for a test that ID as a theory explains, but evolution does not. This is what we’re talking about with regards to ID’s utter vacuity - ID has no research program, either in the field or in the lab; ID has no research funding; no data, nothing. Only “thought experiments,” speculation, and the Wedge agenda.
Yes, disproving evolution would help your case, but that would not “prove” ID - to use a little bit of simple logic: disproving theory “A” does not prove theory “B.”
But of course your “square circles” issue is appropriate if we’re going to talk about Evolution instead of ID: indeed, just as we’ve never seen square circles, we’ve yet to see the rabbit fossil in the Burgess Shale, or anything else that would falsify evolution.
If your problem is with the prerequisite for empirical evidence, then too bad - that’s the prerequisite for science itself. Sure, you can admit that ID is nonscientific, thereby bypassing the need for hard data, but no, most IDers insist that ID is science. The point: pick one - call ID science and get some incontrovertable evidence, or stop trying to pretend that you’re pet theory is science.
With regards to stochastic and deterministic processes - what processes are you referring to, specifically? (Please dispense with the hand-waiving)
Example?
More and more, as I read books like Endless Forms Most Beautiful and others, we’re seeing that the only differences between “macro” and “micro” evolution are the timeframes and the manner in which change is occurring. For instance, between evo-devo and the paleontology, the “walls” between vertebrate groups (fish, amphibians, reptiles, birds, mammals) are dissolving. Not to mention the walls between the bilateral animal phyla.
So, where is the presumption of non-design infecting biology in anything but a very positive way?
Sounds reasonable - and yet, we can trace the origin of these computer viruses to it’s “original intelligence” - where is even a hint of this supposed “original intelligence” for life?
Comment by Dan — July 15, 2006 @ 1:22 pm
Hannah,
So, would it be fair to say that you’re selecting a few arguments against ID that you find “weak,” and standing by your ID opinions in the face of “good” arguments? (or even ignoring them?)
Of course as I said, I disagree with your views of these “weak” arguments to some degree, but why do you get to pick and choose what criticisms of ID to “debunk”? Why not be intellectually honest and admit that ID is scientifically vacuous, like MikeGene has done? That, at least, would earn a greater measure of respect from the science community.
Comment by Dan — July 15, 2006 @ 1:31 pm
To follow up on that last thought, where I said:
I don’t want to make it sound like ID-related concepts, and theism in general, aren’t useful views. The point is that they’re nonscientific. However, a very reasonable claim can be made that nonscientific views are being devalued in this era where reductionist science has been so overwhelmingly successful. Science is extremely valuable, true, but there are other valuable ways of lookiing at our world and our society, that I don’t want to debase.
But let’s call these different views what they are, shall we? Scientific, on the one hand, which helps us understand our reality; and cultural, which help us give meaning to this understanding.
Sorry, I know, I’m digressing here, towards my view of the root of the problem of ID, which is so eloquently formulated as the Wedge document. Bottom line is that a theistic worldview has its use for society, but not for science.
Comment by Dan — July 15, 2006 @ 1:41 pm
No; Alienward asked for examples of criticisms I found particularly lame; I complied. It wasn’t really necessary, though, since we have examples on this thread as well.
No; although I’ll readily acknowlege that there are better arguments than those; I have yet to find any that are at all convincing in a logical way. I know you think I ought to have found some of them convincing–even as you think some of these are logical– but whenever you’ve asked I’ve given you extensive deconstructions as to why I reject particular arguments. Since your response is often not more than “your standards are too high” I’m not quite sure what more you can expect of me.
Be fair, Dan. We’ve spent a great deal of time over the past six months arguing. When have I ever shied away from criticisms I didn’t like?Comment by Hannah — July 15, 2006 @ 1:57 pm
The laws of physics, give a hint. I pointed it out in Stealth ID Classic: The Cosmological Anthropic Principle.
If you wish not to even consider ID until you see such a Designer in person, I respect that. But for the record, I don’t disparage any one for hoping or wanting an Ultimate Designer to be as real to the human experience as the air we breathe. There are many time I wish that were true myself.
Whether ID qualifies as empirical science in your eyes is a side issue to me personally, but applying the same standards to evolutionary theory that you wish to impose on ID might disqualify evolutionary theory as well from being empirical.
Paul McHugh, Johns Hopkins Professor of Medicine quotes Ernst Mayr:
If evolutionary biology is empirical science, then by the same standard ID could be consider empirical science.
Of interest to me is removing the impression in scientific classrooms that purely blind purposeless forces account for the evolution of life from chemical precursors. Assertions that there is no need for design from molecules to man is premature at best, and possibly wrong at worst. Even Darwin began with an assumption of a specially created progenitor.
One can describe the mechanistic details of some of the evolution, but care should be taken to point out that it doesn’t warrant rejecting design inferences somewhere in the pipeline.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 15, 2006 @ 2:06 pm
Hannah,
Did you not say:
??? This, to me, clearly implies the use of such logic as “well, some criticisms of ID don’t hold water with me, so I must be on to something.”
Yes, however, you’re right in that you don’t shy away from criticism - sorry about that - but you do obstinentely stand in the face of requests for a way to test ID; empirical data; or anything that would make ID non-vacuous. And all through that, not a single example of real research, real data, or anything that we can call science to discuss on your end.
And yet, you still claim that ID is science, that ID passes the “demarcation” test, etc. - all completely untenable claims. Why?
Comment by Dan — July 15, 2006 @ 2:13 pm
Salvador,
Ah, yes, the Anthropic Principle. You do realize that the AP is a personification of nature - an a priori descriptive construct that we have superimposed upon nature - don’t you?
Nor do I - but that is a nonscientific value judgement, not an observation-laden fact.
LOL - You keep thinking that if you like. Perhaps more misguided is:
It’s abundantly clear that you’re not familiar with the scientific literature. Again, please, address any specific study that I’ve sited here or on my blog, and offer an example of how said empirical data is in any way better explained by ID than evolution.
Thats true - but the burden of proof is on the positive data - in the absense of evidence for intelligently designed features, despite searching for purposefully-directed processes for so long, one must begin to start working with the conclusion that such processes are non-existent. Especially when the research programs that rely on evolution as an underlying assumption (all of the medical R&D fields and more) have been so tremendously successful.
Comment by Dan — July 15, 2006 @ 2:27 pm
Everyone is stuck in the rut of speculation on the subject of evolution. We often fail to notice the resemblance of Darwin’s ‘natural _selection_’, as a term, to the language of design. It’s another ’something designed it all’ phraseology. It’s a sign noone really knows what they are talking about.
For some hard data on history and evolution consider my http://history-and-evolution.com and/or the issues of the Axial Age.
Darwinists haven’t the foggiest notion of what real evolution is like, reducing everything to microevolution.
Comment by John Landon — July 15, 2006 @ 2:52 pm
Hannah wrote:
Wow, the biology department at Cornell only makes criticisms of ID based on whines like “IDists are theocrats and they’re all bad people.” Does this have anything to do with why you didn’t answer my second question? You won’t answer “What about that [Miller’s co-optive mechanisms] is based on “complete illogicity, irrationality and utter vacuity”?” because he’s with Brown?Comment by alienward — July 15, 2006 @ 3:55 pm
You’re invited to refute the Barrow’s interpretation of the Schrodinger equation on that weblog rather than give glib straw man dismissals. You asked for a hint of an intelligence, I’d say Barrow gave more than a hint.
First of all saying “said empirical data” is not quite accurate. It mis-characterizes what was actually there because what was actually there is loaded with inferences that are circularly justified (like phylogenies). You are aware that convergence, HGT, and especially common design are challenges to phylogenies. You’re “empirical explanation” then is loaded with assumption and inference. I have no problem with inferences or working assumptions, but if one can claim that framework as empirical one can claim ID as empirical.
So I would recommend you qualify your description of that section of your weblog as being “empirical” in light of the fact it has presumptuous inferences mixed with it.
ID explains evolutionary scenarios better than blind watchmaker processes in the sense it can characterize what are dead ends or invalid characterizations of ancestral precursors related to their descendants.
For example, in information science an Mp3 file is limited in what it can really decompress into. A 1 meg Mp3 might be able to decompress to a 10 meg WAV file, but the actual information content in the 10 meg WAV file is really only 1 meg (as defined by the Mp3 file).
In like manner the descendants of a progenitor can be no more information rich than the ancestor. It may have more base pairs (analogous to WAV files having more bytes than the ancestor Mp3 which generated it), but it really is not more information rich (information here being CSI, not just Shannon information).
Because of information conservation principles, blind watchmaker processes will be guaranteed to be characterizing the information evolution improperly. That will thus make the characterization of the ancestor progenitors incorrect, and that why the ID perspective of information conservation is a superior framework to characterizing :
1. the ancestral progenitor
2. the limits of change and evolution for the descendants of the progenitor
For example in one article you point to:
that only explains one part, it does not characterize the context where the network topology originated in the first place.
Let me suggest something from information principles: the origin of the topology isn’t rooted in a process describable only by low information content deterministic or stochastic laws with general boundary conditions. The source of the topology is either a more information rich pre-cursor artifact or an intelligent designer.
Finally, the researchers pointed out for evolution in the lab to progress it must be under certain constraints. It is reasonable to see, comparable levels of constraints must be present for evolution to move forward in the natural world if such constraints are necessary in the lab. In fact, they give an idea of how tightly those constraints must be, because they describe their lab simulation of such necessary constraints as having to be “engineered”:
Well, perhaps out of courtesy to this weblog, further discussion of specifics should be discussed at your weblog, and not here.
I felt however, that Dan’s question was of interest to some readers, and thus I answered to a small extent here.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 15, 2006 @ 4:04 pm
Alright, I give up. I’ve been trying pretty hard to avoid making inferences to a total lack of reading comprehension, but it is becoming increasingly difficult. Will you please reread my comments and see if you can figure out what I am and am not saying? If you repost an honest question I’ll do what I can to answer it.
Comment by Hannah — July 15, 2006 @ 4:07 pm
Well, until you grapple seriously with stuff like this, and the scientific literature that it is based on, then you won’t understand the real reasons so many scientists are skeptical of ID, and you will never have any chance of making a convincing case for ID.
So if you actually want to attempt to make ID rigorous, rather than having ID just be a mutant wing of apologetics that it currently is, your path is clear. Until you do it you’re not really even serious.
Comment by Nick (Matzke) — July 15, 2006 @ 4:18 pm
I’ll readily agree that– in a logical sense– just because the only arguments put forward to support an idea are unsound doesn’t mean the idea itself is untrue; and even if the only arguments given against another idea are faulty doesn’t mean that idea is true. And I know I’m supposed to be critical of ID on my own; without your help in coming up with sound arguments, so I try to be. But one’s confidence level in something does increase– involuntarily or not– if there are as many critics as ID has and none of them gives any particularly interesting arguments.
Another concession: I’m sure there are lots of arguments far better than the ones I’ve read; I’m an undergrad and don’t pretend to have made any sort of comphrehensive survey of the literature. That’s another reason why it’s a bad idea to write appeals to emotion or obviously faulty arguments– they get to be so many that they obscure the real arguments, and make it impossible to find them.
Is this a rhetorical question? I’m perfectly ready to defend them, as you know; your position is the one that seems to me untenable. Should we go over either of those issues again?
I’m feeling guilty about taking over Josh’s thread, though, so if you do want to discuss it, perhaps we can do so elsewhere?
Comment by Hannah — July 15, 2006 @ 4:40 pm
Salvador,
For one, I imagine that commenting at the UD would be futile - I ventured over there several times over the past year, only to have my (very reasonable, IMO) comments deleted, and regardless, I have a very low opinion of the normal UD crew, to be bluntly honest.
However, looking at the original post itself that you link to, I’m not a mathematician, nor a physicist, but the following claim seems to be the central theme:
That has to be the most ridiculous example of dubious physics I’ve heard of in a long, long time. I don’t even know where to begin to address that, and I find it alarming that any serious physicists or mathematicians are seriously making prognosticating that such an entity is “inevitable,” or even possible.
Sorry Sal, but you can rant all you want about your lunacy, but I’m going to start ignoring you now, before I lose my patience and start making rash conclusions of my own.
Comment by Dan — July 15, 2006 @ 4:41 pm
What?! Demanding that a theory have empirical data, and/or be capable of actually accomplishing something outside of “thought experiments,” to be considered science is an untenable demand???
Wow… as with Salvador, I simply don’t know where to begin picking my jaw up off the floor. Do you really think that ID’s hand-waivy concepts (IC, CSI, the EF) qualify as science in the absense of hard experimental data??? Have you no understanding of what constitutes science???
Sure, I’d be happy to take it to the TDP, or Migrations, or elsewhere - since we’re talking about the evidence for ID, which is more your area than mine, you’d like to start it off at TDP?
Comment by Dan — July 15, 2006 @ 4:54 pm
Hannah wrote:
Ok, I’ll repost my honest question – for the third time. What about “Miller’s co-optive mechanisms” is based on “complete illogicity, irrationality and utter vacuity”?Comment by alienward — July 15, 2006 @ 9:13 pm
Sal confuses convergence again and its impact on phylogenies
You are aware that convergence, HGT, and especially common design are challenges to phylogenies.
Common design is a challenge to nothing as there is not even such a thing, at least not in the realm of science. HGT and convergence are not challenges to phylogenies as much as complications in restoring the correct phylogenies. Of course, convergences can be quite well dealt with by adding additional information
So far Sal has, not surprisingly, failed to explain the vaste amounts of consistent and coherent data for common descent.
Only by picking some careful quotes and a less than stellar understanding of scientific concepts does Sal attempt to instill doubt where no doubt exists.
If Sal were to familiarize himself with evolutionary theory, phylogenetic reconstruction and the vaste amounts of supporting evidence for common descent then we could perhaps discuss his objections in a more fruitful manner. Until then it seems that they are mostly arguments from ignorance or at least unfamiliarity.
Now as an Ex Young Earth Creationist, I do understand Sal’s position. Anything even remotely problematic for a particular position is blown out of proportions while the consistent data are being ignored.
Such is the power of faith. Having heard of W Dean’s latest book on authoritarianism, I am starting to understand how the ‘fear of losing one’s religion’ can easily lead one to accept authoritarian positions, leading to an unwillingness to consider contrarian data. I have found Dean’s analysis particular insightful and see some applicability to creationism where fear of atheism is created through a conflation of naturalism and methodological naturalism (See Johnson and Lamoureux’s devastating analysis of Johnson’s position). This fear can lead some to search for authoritarians who are willing to present a safe heaven.
I see ID to a large extent fitting the bill quite accurately, providing creationism with a thin veil of scientific relevance.
Comment by PvM — July 15, 2006 @ 10:16 pm
I’m afraid Miller’s objections don’t even rise to the level “complete illogicity, irrationality and utter vacuity” but descend to outright misrepresentation, and misrepresentation under oath in a landmark trial, Kitzmiller v Dover
See: Ken Miller’s Strawman
Comment by Salvador T. Cordova, IDEA GMU — July 16, 2006 @ 1:15 pm
Alienward:
I should have been more courteous to you upthread. Sorry about that.
Those I’ve seen appear to be untestable, purely speculative, and with little connection to the real world– the sort of thing that would look halfway reasonable only if you really desperately want to be convinced. That’s aside from the fact that he has a tendency to misrepresent and to attack straw man arguments.
The qualifier “some” in my first statement is because I haven’t evaluated all of Miller’s co-optive mechanisms; the ones I haven’t read might be better. Someone recommended his analysis of blood clotting IC, and I’m planning to get to that sometime this weekend.
Let’s make this the end of this tangent. Future comments on this thread should have some connection to the questions Josh brings up in his orginal post.
Comment by Hannah — July 16, 2006 @ 1:34 pm
Dan seems to suggest evolutionary theory is as empirical as the field of chemistry (which is, by the way, one of Hannah’s majors). But this is not the case, thus he should be reluctant to call ID hand-wavy lest he reject the field he promotes:
Dan should then perhaps reconsider how “empirical” the field he is defending really is.
As I pointed out with the example of a self-mutating computer virus, one can empirically demonstrate it’s evolution in the lab, but it’s fullest context is better understood from an ID perspective.
One is far less inclined to make unwarranted assertions that it self-organized, and from an ID perspective, one is in a better position to justify the architecture of the ancestral versions of the virus in relation to its descendants.
If biology is governed by the same laws of information science that govern self-mutating computer viruses, then ID is a superior perspective just based on it’s information conservation principles alone.
It is through this ID conception that ancestors and descendants can be more accurately described, because if an evolutionary scenario violates the principles of information science, we know we can rule it out immediately. Science is not benefited by wasting time chasing after perpetual motion machines or justifying epicycles.
As far as hard empirical evidence consistent with ID theory, look at the law of biogenesis and experimental confirmation of that law. If one admits Mayr characterization of what counts as “empirical” then all repetitions of Pasteur’s famous law-of-biogenesis experiments qualifies as hard empirical data.
I should point out, one of Darwin’s supporters, Haeckel presumed evolutionary theory was supported by assuming spontaneous generation was possible. When empirical data destroyed his idea, he just brushed it aside.
Well, we know on whose side the empirical data has fallen, don’t we? And as I pointed out, Darwin accepted the special creation of the first life. If Darwin said it, perhaps you should believe it (just kidding).
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 16, 2006 @ 1:58 pm
Sal’s quote of Haeckel shows how present knowledge may lead one erroneously to a path of the supernatural. Heck, Newton himself argued that the action at distance of gravity required the supernatural interventions.
Do we want to get stuck in our ignorance or do the hard science ID refuses to engage in?
Sal As I pointed out with the example of a self-mutating computer virus, one can empirically demonstrate it’s evolution in the lab, but it’s fullest context is better understood from an ID perspective.
A meaningless assertion and contradicted by fact and logic. ID provides no explanation or understanding, it merely insists that if we do not know how something arose to a sufficient level of detail we must call it designed.
Sal One is far less inclined to make unwarranted assertions that it self-organized, and from an ID perspective, one is in a better position to justify the architecture of the ancestral versions of the virus in relation to its descendants.
Again fully begging the question. If Sal were right we would have seen by now fruitful applications of this superior thinking of ID. Instead we see how ID hides in ignorance and is unable and even unwilling to provide pathways, mechanisms etc.
Sal If biology is governed by the same laws of information science that govern self-mutating computer viruses, then ID is a superior perspective just based on it’s information conservation principles alone.
Again the information conservation principles of ID are not about conservation. So far these ID principles have led to nothing scientific and in fact their insistance that they show that evolution or Darwinian evolution is impossible indicate how they go against empirical evidence and logic.
If natural law is relevant to evolution, ID’s role is over since it relies on elimination of regularity and chance.
In other words, Sal’s vacuous claims (and I doubt he will support them since his past performance in this area, despite the rules of engagement of this board, have been dismal) indicate that ID fails to be scientifically relevant and Sal’s suggestion that natural law supports ID are plainly illogical since ID relies on rejection of natural law and chance processes.
Information theoretical principles indeed are relevant to evolution and the hard scientific work in these areas has unravelled many components of evolution such as the origin of complex information via the natural processes of selection and varation (Schneider, Adami et al, Lenski et al) or the degeneracy, scale free nature, modularity and evolvability of the genome (Fontana, Schuster, Wagner and countless others).
In other words, information theory has shown itself to be quite relevant to science and thus fails to be relevant to ID, despite Sal’s vacuous claims to the contrary.
The proof is in the pudding and the data show zero scientific contributions in this area from ID.
Zero…
Comment by PvM — July 16, 2006 @ 2:32 pm
Salvador,
Oh, the type of data biology collects is different from chemistry, for sure. But it’s no less empirical.
How??? I charge that this is a nonsense statement, and I’ve discussed computer virus-like simulations of reducible evolution before.
No - these evolution modeling programs work under no purposeful directives whatsoever, which ID predicts they would, other than competition for finite resources. But please, provide even just one example of a study backing up your claims - not your bogus UD psychophantic links.
And also, please cite an example anywhere of informatics approaches to biology, demonstrating Design, and actually backing up a claim by verifying the math with empirical observation.
On all of these counts, no such studies exist.
And nice quote of Haeckel - but that was pre-Pasteur, was it not? Are you going to quote someone pre-Copernicus to back up claims of geocentrism, too?
LOL You’re a joke.
Comment by Dan — July 16, 2006 @ 2:39 pm
Come on Sal, a minor mistake by Miller hardly supports your claims (does anyone see an emerging theme here?).
Miller’s examples of co-option undermine not only the claims about irreducible complexity by Behe and Dembski but also show how ID has to ignore scientific pathways and thus render itself scientifically irrelevant.
It’s refreshening to me that the people on this board recognize the vacuity of the UD responses. In fact has anyone noticed how lately Dembski and others seem to have abandoned to be seen as serious science?
Such is the inevitable future of an approach from ignorance combined with a weak form of logic namely an argument from analogy.
Combine this with the inevitable argument from authority found amongst ID supporters and one quickly comes to realize that ID shows all the failings and lead to the conclusion that ID is scientifically vacuous.
If Sal could be encouraged to attempt to support his claims, all this would become even more visible. Hence, I am not too surprised by his obvious reluctance in this area. Caught between rock and a hard place, Sal has no choice but to ignore the valid rebuttals and objections to his claims.
Luskin’s ‘response’ is not about a scientific rejection of Miller but rather the attempts by the Discovery Institute to trivialize the Dover Kitzmiller ruling by attempting to taint the testimony and the expert witnesses.
Miller dismantled much of ID’s claims and particularly Behe’s claims. A good example is that Behe was forced to move the goal posts from function to ‘original function’ to avoid falsification by real evolutionary pathways such as the all to prevalent co-option.
As is the case on this board, Sal’s comments are lacking much in supporting evidence and logic and while he can avoid responding on UD, this board with its rules of engagement is far less forgiving to those making unwarranted, unsupported, fallacious or illogical claims.
Just for the record, I continue to invoke the rules of engagement of this board and expect Sal to either support his claims of ‘fact’ or abandon them. Either he abandons them explicitly or his forfeits them by default. Either way works for me.
How do the esteemed people of this board see Sal’s avoidance of the rules of engagement of this board?
How does such behavior reflect on Intelligent Design?
Comment by PvM — July 16, 2006 @ 2:45 pm
(hannah, I missed your earlier comments about getting back to Josh’s post, let me make amends):
OK, getting back to Josh’s question:
Your comment here, Josh, has a lot of merit, but if you’ll indulge the following considerations, I would be grateful.
From a scientific viewpoint, IC has value in pointing out that in the evolution of complex systems, the normal mode of evolution via natural selection would more likely have to be indirect, not direct, that is through co-option. (like the cilia exmple you described).
From a probability viewpoint however, co-option is possibly not any more likely than random chance. For example, in general, what’s the chance you can reuse something for new purposes versus not being able to use it at all? What’s the chance you can re-use parts of your own passwords to figure out someone else’s? Those are the problem with co-option! Even if the parts are available, making them integrate into an existing architecture or finding a new uses (like for cilia) is not so easy!
On a larger scale we can definitely see this. How do we envision co-option of a 2-chambered heart into a 3-chambered heart, even though most of the necessary proteins are already there? The intermediate steps would normally be lethal to the organism. Many other examples abound, too numerous to mention…..
These intuitions were formalized by Bill Dembski’s Displacement Theorem.
You’ll get something of the lite version of Dembski’s ideas in your current reading.
regards,
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 16, 2006 @ 2:48 pm
PvM,
Indeed… and that is the sort of intellectual dishonesty that so annoys me, whether it comes from Sal or others.
Hear, Hear!
Comment by Dan — July 16, 2006 @ 2:49 pm
Sal,
Um, no. Bridgham et al. demonstrated the feasibility of co-option - the result of course was more of Behe moving the goalposts.
Comment by Dan — July 16, 2006 @ 2:53 pm
Dan, PvM–
Would you both re-read the ground rules?
Update: Especially the first and fourth in the original set and the last on the amendment.
Comment by Hannah — July 16, 2006 @ 2:59 pm
Hannah, I appreciate your dilligence so I would like to apologize if my stance has given the impression that I am using ad hominem arguments when in fact I am working under the rule of engagement which allows one to ask someone to support its claims of fact with logic and/or supporting evidence.
I am pointing out that Sal has so far failed to follow these rules.
As a scientist and christian I hold people to high standards and I am extremely sensitive to ad hominem arguments. In this case my insistance that Sal supports his claims seem well within the rules of engagement of this board.
Sal
From a scientific viewpoint, IC has value in pointing out that in the evolution of complex systems, the normal mode of evolution via natural selection would more likely have to be indirect, not direct, that is through co-option. (like the cilia exmple you described).
In other words, ID is mostly vacuous here as it 1) argues strawmen 2) attacks selection as the sole relevant mechanism of evolution.
IFF Sal is correct, IC has no relevance to Intelligent Design and he himself seems to be moving away from such a position as well.
Sal
From a probability viewpoint however, co-option is possibly not any more likely than random chance.
Totally begging the question. In fact, I argue that co-option is quite different from ‘random chance’.
Sal
For example, in general, what’s the chance you can reuse something for new purposes versus not being able to use it at all? What’s the chance you can re-use parts of your own passwords to figure out someone else’s? Those are the problem with co-option! Even if the parts are available, making them integrate into an existing architecture or finding a new uses (like for cilia) is not so easy!
Notice the hand waving and total lack of supporting calculations. In fact Sal suggests that co-option would not be expected from a technology perspective and yet we see countless evidences of co-option in biology. In other words, once again science strongly suggests that ID has once again been falsified. At least, the claims Sal has made about ID. I should note that he has yet to show that these claims follow from the basic premises of intelligent design. Nevertheless, ignoring for the moment the shakey foundations of Sal’s claims, one can conclude that contrary to Sal’s ‘predictions’ evolution shows evidence of degeneracy (more than redundancy) and co-option. Both, Sal argues are not to be expected from a technology or at least Sal’s ID perspective.
Sal On a larger scale we can definitely see this. How do we envision co-option of a 2-chambered heart into a 3-chambered heart, even though most of the necessary proteins are already there? The intermediate steps would normally be lethal to the organism. Many other examples abound, too numerous to mention…..
Ah, the classic argument from ignorance combined with unsupported claims about the probabilities of intermediates.
SalThese intuitions were formalized by Bill Dembski’s Displacement Theorem.
Dembski formalized little in this area. His displacement theorem is as much a problem for ID as it is for science. In other words, it really isn’t.
You’ll get something of the lite version of Dembski’s ideas in your current reading.
On Pandasthumb I have shown how Dembski’s arguments are flawed in that under the No Free Lunch theorems, random search is trivially simple. More recently Erik Tellgren has extended this to show that evolution on a multidimensional fitness function is trivial as well, combining the random search findings with the work by Gavrilets.
As others on this board already have argued, the higher the dimension of the fitness function (in other words, the more independent parameters to search), the simpler finding neutral and selective pathways becomes.
This may seem self contradictory but in fact follows from both logic and theoretical foundations. In other words, random search, No Free Lunch theorems all end up showing how evolution has been so succesful, contrary to the claims of ID based on a flawed ‘displacement theorem’.
I cannot emphasize this strongly enough namely that Dembski’s claims rather than providing a solid argument against evolution, have turned out to be strenghtening evolutionary theory.
In other words, the hopes of ID on Dembski’s work providing a better foundation for ID have been mostly turned into pipe dreams.
Remember:
Complex Specified Information (CSI) is not a reliable indicator of design
The explanatory filter is useless because of false positives
The law of conservation of CSI is neither a law nor a conservation theorem
No Free Lunch theorems show how random search is trivial
Displacement theorems provide similar challenges to ID as it does to evolutionary theory. Or perhaps better stated, if the claim is that ID can circumvent displacement theorems then so can natural processes.
I hope in the next week to explore these findings in more depth. Needless to say, I intend to show how the foundations of ID are fundamentally flawed, and how its conclucions rather than showing evidence against evolutionary theory, end up strengthening the evolutionary theories while on the other hand ID remains fully empty-handed.
So let’s abandon the urge to appeal to authority to Dembski and look at Dembski’s actual claims and how they simply do not hold up under scrutiny but rather end up being not dissimilar from ‘jello’ as one mathematician observed.
In addition to showing the problems with ID, I also intend to show that science has found quite a solid foundation for such ‘enigmatic’ issues as convergence, robustness, evolvability which all are reducible to quite simple processes of law and chance.
May I invite ID proponents who still believe that there are ways to recover the ID argument, present their claims and supporting evidence and/or logical foundations.
In other words, I am invoking once again the rules of engagement of this board and challenge those who have made claims of ‘fact’ to support them vigorously and rigorously.
In the mean time, I will be more than happy to do so myself.
Comment by PvM — July 16, 2006 @ 4:02 pm
Don, intellectual dishonesty is too strong a term and unsupportable. Honesty, dishonesty, lying are all concepts which require a level of evidence seldomly achievable.
Let’s focus on the scientific vacuity rather which points out the lack of a scientific foundation for the claims.
I believe that Sal and other IDers are truly believing that Dembski’s claims and arguments are relevant to the issues. Which is why 1) encouraging them to explore their claims in more depth and see where the lead and 2) showing the scientific irrelevance of ID are powerful ways to explore the concepts of ID.
Invoking the rules of engagement of the board provide for a powerful mechanism to explore the depth to which claims can be supported by logic, empirical evidence and even theoretical foundations.
This board is one of the few which explicitly provides a rule which when invoked properly can actual lead to resolution of claims of fact as either factual or fictional.
Comment by PvM — July 16, 2006 @ 4:08 pm
Josh may be passingly interested in the computer work regarding IC. I’m sorry it gets technical, but I can’t let a particular supposed “dis-proof” of IC slide which was offered by Dan.
Dan wrote regard IC and computer disproofs:
Dan refers to the work of Adami, Lenski, etc. using a program called Avida to create the appearance of co-option, and thus it gave a superficial appearance that Behe was refuted.
I demonstrate that Adami and Lenski’s “dis-proof” of co-option relies on equivocating the normal conceptions of complexity, selection, life and reproduction — effectively creating a straw-man misrepresentation of Behe’s argument and coupling it with numerous tautologies and non-sequiturs being offered as “proofs”.
See my comments at
Tautologies and Theatrics (part 1): adventures in Avida.
The program Avida, which Dan upholds as dis-confirmation of Behe, could also be used to argue that creatures could be put through a cycle of resurrection and death through extreme dosages of radiation. Let me pose this to Dan, how empirical is that?
I would caution accepting results by the promoters of Avida or similar evolutionary algorithms to refute Behe. The are disingenuous at best.
Salvador
PS
By the way, Avida version 1.6 has fix that is traceable to me. If I had my way, though, getting the whole thing fixed would end up ending the project because it is in such definitional disarray.
Comment by Salvador T. Cordova, IDEA GMU — July 16, 2006 @ 4:26 pm
Sal asked an interesting question on the evolution of a two chambered heart into a three chambered heart. The following may be relevant
Recent work in biofluid dynamics suggests that the early embryonic heart beat does not pump blood for the purpose of convective transport, but rather it aids in the shaping and maturation of the developing heart.Hove et al. describe the presence of high-shear vortical flow at two important stages of heart development. When flow was occluded at either inflow or outflow tracts, the heart did not develop properly.The embryonic vertebrate heart develops from a simple peristaltic pump into a two, three and four chambered heart. The development of the mammalian embryonic heart mirrors the evolution of the heart from the early vertebrate ancestor to higher vertebrates. This suggests that much insight can be gained by studying heart development in an evolutionary context. My future research will focus on the three questions outlined below:
What’s ID’s explanation for these hearts? Why?
Comment by PvM — July 16, 2006 @ 4:27 pm
Yes, and embryonic development is more properly described by pre-programmed control and mediation than by the metaphor of natural selection. Natural selection is an inappropriate metaphor to describe the process of embryonic development.
Embryonic development is a beautiful illustration of how IC might evolve, namely, under programmed control!
Which leads to a different way of looking at this
By way of extension one would properly argue natural selection was not an appropriate metaphor for the evolution of the heart either. And this is consistent with Behe’s ideas.
The above author did not intend the interpretation I just gave, but that’s what comes to mind for me.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 16, 2006 @ 4:42 pm
I invoke the rules of engagement and ask Sal to support his follow claim
Yes, and embryonic development is more properly described by pre-programmed control and mediation than by the metaphor of natural selection. Natural selection is an inappropriate metaphor to describe the process of embryonic development.
Embryonic development is a beautiful illustration of how IC might evolve, namely, under programmed control!
Remember that IF embryonic development can explain the evolution of the heart then ID is effectively blocked since we now have a natural pathway to explain the system.
Remember that ID is inherently an eliminative argument which states that design can be inferred by eliminating all known (and unknown) regularity and chance explanations and providing a specification.
The specification in biology is merely ‘function’, something which is a fundamental concept of evolutionary theory.
Note how Sal moves the goalposts from evolutionary mechanisms to ’selection’? In other words
1. Sal artificially limits evolution to ’selection’
2. Sal provides no support for his claims that embryonic development is better understood by ID
3. Sal ignores that once regular pathways exist, ID is effectively blocked from making its design inference
4. Arguments from analogy as the weakest form of arguments especially when one can show that the analogies quickly fail (robustness versus degeneracy comes to mind).
Remember that Sal’s original argument was about
How do we envision co-option of a 2-chambered heart into a 3-chambered heart, even though most of the necessary proteins are already there?
I believe I have given the answer to this question. As to whether evolutionary theory provides a better explanation than ID, let me point out that logic rejects ID and that ID fails to present any explanations as to how the two and three chambered hearts arose.
So let’s get to the specifics Sal. It’s time to support your claims.
Comment by PvM — July 16, 2006 @ 4:56 pm
If Sal btw accepts that ontogeny recapitulates phylogeny then he and Haeckel seem to have much in common :-)
As far as natural selection it seems to me that this is almost trivially self evident as the following points out
Functionally linked to adaptations for gas exchange (oxygen uptake) are circulatory changes. In using skin, lungs and mouth lining as gas exchange surfaces, amphibians send both oxygenated and deoxygenated blood back to their hearts, unlike most fishes which return only deoxygenated blood to the heart. This makes the separation of these two types of blood advantageous, for an organism needs to send only oxygenated blood to the tissues and only deoxygenated blood to gas exchange sites. Amphibians have separated the single atrium into two atria, right and left, with a septum. This is referred to as a 3-chambered heart. Unfortunately, the ventricle is not separated and a certain amount of admixture of the two bloods occurs here. Reptiles all still have 3-chambered hearts, only with better-developed septa than seen in amphibian hearts. In snakes, lizards and turtles, the septum extends well into the ventricle, resulting in better separation of oxygenated and deoxygenated bloods. In the crocodilians, only the merest opening is left between right and left ventricles, resulting in a heart that is (for all intents and purposes) 4-chambered! This situation keeps the two blood types well separated, a much better situation for an active organism with high metabolic demands.
Combine this with the phylogenetic data showing once again strong support for common descent and once again it seems that science has the upper hand here.
Now does science understand all the pathways taken by evolution when it comes to the evolution of the heart? I doubt it but as is with so many examples quoted by ID, science is closing in on answers and is scientifically fruitful
Comment by PvM — July 16, 2006 @ 5:06 pm
Sal, your distraction with your comments on Avida are irrelevant. Even though you contributed to a minor bug in Avida 1.6, it has done little to improve your arguments why Avida should be rejected.
If you really want to discuss Avida and your flawed arguments then I would encourage a separate thread as we would not want to distract from the real discussion topic. We may even bore most of the contributors with such a discussion, which has taken place many times already in other venues with similar results.
Comment by PvM — July 16, 2006 @ 5:09 pm
SalThe program Avida, which Dan upholds as dis-confirmation of Behe, could also be used to argue that creatures could be put through a cycle of resurrection and death through extreme dosages of radiation. Let me pose this to Dan, how empirical is that?
It isn’t and really that is not what Sal has done. What Sal has done is not radiation but yanking up the mutation rates. Anyone familiar with mutations should realize that there is a fundamental difference between mutations caused by biological mechanisms and mutations under strong radiation.
So what Sal has shown is that Avida under strong point mutations (sometimes called cosmic ray mutations) behaves in a manner which he considers unrealistic. What Sal has shown is that Avida may be unrealistic at high mutation rates. However this does not negate that simple processes of selection and mutation can indeed generate IC systems and CSI.
That’s all that matters. Now it is up to ID to show that such processes are unlikely in real life. So far that’s where ID has fully failed.
Avida mentions the followin
There is an erroneous note in the default “genesis” file distributed with Avida 1.x. The line specifying point mutation rate has a comment (x10^-6), implying that the user value is multiplied by this quantity before application. This is in error; the specified point mutation is used as-is as a probability. This erroneous comment has been removed in Avida 2.x releases.
What Sal saw as replication was clearly not
Explanation: Put simply, the population was dead. What Mr. Cordoba observed was slow, random activity of non- replicating random strings.
and
Conclusion: Mr. Cordova has experimentally demonstrated that there is in no mechanism protecting genomes from randomization by killing the ancestor organism with a high mutation rate and observing the “brownian motion” activity of dead, random, sequences of computer instructions.
Case closed I’d say.
Comment by PvM — July 16, 2006 @ 5:25 pm
I do not. Any further suggestions to that effect would also be erroneous. However, I can understand why I might be perceived as doing so.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 16, 2006 @ 5:30 pm
Pvm:
Even an amateur evolutionary biologist would look at a the problem Sal has proposed, in regards to the chambered heart, and quickly check the phylogenetic data. Wow, big surprise, the two match up! Now that is what science is supposed to do. You observe something unusual, make a hypothesis, gather the data, analyze it and form a conclusion. The fact that the types of o2 exchange systems matches up with the phylogentic data is a powerful rebuttal to those still saying this system is IC.
Comment by Mike Hannigan — July 16, 2006 @ 5:36 pm
Sal has explained what he is NOT doing but perhaps he can help us understand why Haeckel’s argument played such a role in Sal’s conclusion that the heart evolution implicates ID?
The fact that the mammal heart goes through very similar pathways as evolution seems to have taken surely seems quite a relevant observation.
How does ID explain this?
Comment by PvM — July 16, 2006 @ 6:05 pm
An excellent though simplistic overview of the evolution of the heart can be found at
Replace DOT with period (”.”)
libraryDOTthinkquestDOTorg/C003758/Development/heart_evolution.htm
Carl Zimmer explains in other article the evolution of the heart
“The Hidden Unity of hearts”
ZimmerOver the past several years, scientists have gone a long way toward figuring out how this complex and vital organ evolved. By comparing the hearts of living animals and unlocking the genes that build them, they have found that while there may be no physiological truth to the expression “my heart is in my throat,” that may be exactly where hearts began. They’ve also discovered that the change from simple tube to complex, chambered organ may have happened in an evolutionary flash.
From past to present understanding
ZimmerFor decades, biologists assumed that all these hearts, which look so different from one another, had evolved independently. But in recent years, research on how genes orchestrate the development of hearts within embryos has revealed a hidden unity. In the laboratory, scientists alter or remove particular genes in animals and then look at the consequences in the developing embryo. The deformities that result from these experiments help the researchers figure out a particular gene’s usual role in development.
In other words, while science initially was led to believe, due to incomplete information (read ignorance) to conclude independent origins for the hearts, science now uncovers a strongely unifying principle.
Zimmer provides some interesting data
“Fortunately, that turned out to be a false worry,” says Fishman. His team and others have found more than a hundred genes involved in heart development. After tinman-like genes have finished creating a simple tube, these other genes switch on, transforming the tube into the complex organ we’re familiar with. And some of the genes took Fishman by surprise. By knocking out a single one of them, his group could create a heart that was missing its ventricle but was otherwise normal; knocking out a different one produced a heart that was missing valves but nothing else. These genes seemed to be in charge of little modules of genes that worked together to build specific parts of the heart. Fishman ended up finding about a dozen heart-module genes. “It was more than we could have hoped for,” says the geneticist. “It meant we could dissect organ development, because we had individual elements that could be removed.”
Fishman also realized that the way these heart-module genes work in living fish might hold a clue to the evolution of vertebrate hearts. It’s possible that the complex, chambered heart didn’t change gradually, with many genes evolving minor mutations that changed their functions. Instead, each of the heart modules may have existed in earlier vertebrates, where they performed other, still unknown jobs. Merely by tinkering with the master gene that controlled a module, evolution could have quickly invented a new structure for the heart. To picture the difference between these two kinds of evolution, imagine building a concrete bridge. If you build it by adding sand grains one at a time, it will take a lot longer than if you assemble it from large prefabricated blocks.
Seems that co-option is hardly that hard to understand from an evolutionary perspective. And this was in 2000. One can only imagine what science can discover in 6 more years.
So fast forward to 2006
So how much resemblance does the heart of Drosophila bear to that of the human, and how reasonable a model can it provide of the dilated cardiomyopathies? Much of the cellular machinery of heart cells is the same between these species, even though they are presumed to have diverged at the invertebrate–vertebrate junction >500 million years ago (Mya) and may have arrived at their hearts by convergent evolution not from a shared ancestral heart. Orthologous genes direct cardiac cell fate decisions (e.g., nkx 2.5) and the generation of the contractile sarcomeres (9, 10). It is reasonable to presume that important molecular pathways related to contractility are shared and, as Wolf et al. (4) demonstrate, that mutations of sarcomeric proteins do lead to diminished contractile function and cardiac enlargement.
Concluding
These studies are yet more proof of the power of genetics to reveal the function of key genes in the intact animal and to help to identify key functional elements, in this case at the level of organ physiology, that most integrative and clinically relevant of sciences.
Fabrizio C. Serluca, and Mark C. Fishman Big, bad hearts: From flies to man PNAS | March 14, 2006 | vol. 103 | no. 11 | 3947-3948
Remind me again what ID has contributed to understanding the evolution of the heart, other than arguing it is somehow IC and/or cannot have evolved?
Comment by PvM — July 16, 2006 @ 6:24 pm
PvM,
I’m afraid you’re arguments are a subtle equivocatoin of the real question in hand.
Even if the parts are available, IC poses a barrier for the assembly of the parts. I already pointed out that having copted parts of someone else’s password (like alphabetic letters) doesn’t necessarily make it any easier to use your password to break someone else’s.
Your voluminious posts above are therefore irrelevant to Behe’s thesis, as commmon ancestry is a working assumption.
Also when you ask, “how does ID explain that?”, you are subtly insinuating a domain which may not be applicable thus giving the impression it failed to answer a question it was not intended to answer. It’s like asking how does the periodic table explain the orbit of planets, in an attempt to discredit the periodic table.
ID is limited in what it says about manufacturing details, except to say which supposed manufacturing processes are invalid (like natural selection for evolution of large scale IC).
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 16, 2006 @ 8:02 pm
SalI’m afraid you’re arguments are a subtle equivocatoin (sic) of the real question in hand.
I disagree, my arguments go to the heart of the argument or real question. But let’s see where Sal is going to take us here
Sal
Even if the parts are available, IC poses a barrier for the assembly of the parts. I already pointed out that having copted parts of someone else’s password (like alphabetic letters) doesn’t necessarily make it any easier to use your password to break someone else’s.
As analogy is a very weak argument, it is insufficient to point to systems which cannot and did not evolved as evidence against evolution. Sure, there may be real objections to evolution in the form of IC structures but the conclusion is that IC itself is not a sufficient condition. Worse, ID, lacking any scientifically relevant contribution to understanding IC systems, remains empty handed.
Your voluminious posts above are therefore irrelevant to Behe’s thesis, as commmon ancestry is a working assumption.
Cool, we assume common ancestry based on extensive evidence and find consistencies time after time. Not bad for common descent. Such is how hypotheses work Sal.
Also when you ask, “how does ID explain that?”, you are subtly insinuating a domain which may not be applicable thus giving the impression it failed to answer a question it was not intended to answer. It’s like asking how does the periodic table explain the orbit of planets, in an attempt to discredit the periodic table.
In other words, ID does not really explain anything in biology because it is not meant to explain it? Please explain what ID has to contribute to our scientific knowledge in an ID relevant manner?
ID is limited in what it says about manufacturing details, except to say which supposed manufacturing processes are invalid (like natural selection for evolution of large scale IC).
So ID is mostly a negative argument, lacks in its own scientific explanations and argues, without much luck, how natural selection is sometimes unable to explain a particular feature. Seems that ID as such is of little interest and relevance to evolutionary theory.
So Sal, do I represent your argument correctly that ID is mostly about showing the incompleteness of natural selection as the sole explanation of evolution?
If so, most scientists all the way back to Darwin would agree with ID.
Is this all ID is about really? And why should I accept your assertion that ID is not about explaining the how, when, etc for systems it claims have been designed? Science does it all the time for criminology, archaeology etc.
Is ID so limited in its claims and applicability that it has reduced itself to irrelevance?
Comment by PvM — July 16, 2006 @ 8:17 pm
May I also ask my esteemed colleague Sal to explain why he considers my arguments to be equivocation?
Anything specific?
It seems that this claim of fact could benefit from the rule of engagement of the board which allows me to insist that Sal
Both statements of fact and statements of opinion may be challenged by anyone, so long as the challenge takes place within a reasonable length of time (and please remember, time online passes much more swiftly than time in the real world; three days is a virtual eternity).
• If a statement of fact is challenged, the person challenged should make a good faith effort to either provide supporting evidence or make a logical argument as to why such supporting evidence is unnecessary.
I may have overestimated ID’s ability to provide explanations for so called designed systems but to call this equivocation seems to be illogical.
Perhaps I have unearthed, in an indirect manner, that which Del Ratzsch argued earlier
“I do not wish to play down or denigrate what Dembski has done. There is much of value in the Design Inference. But I think that some aspects of even the limited task Dembski set for himself still remains to be tamed.” “That Dembski is not employing the robust, standard, agency-derived conception of design that most of his supporters and many of his critics have assumed seems clear.
Del Ratzsch Nature design and science
Or Wimmsat?
Unfortunately “popular” presentations of “Intelligent Design” have tended to give the impression that it rested solely on mathematical demonstrations. Anyone who could have succeeded in showing that natural selection is incapable of generating biological structures according to standards from mathematics or logic would have constructed a mathematical proof that would have dwarfed Godel’s famous Undecideability theorem in importance. As one who read Dembski’s original manuscript for his first book, found much to like in it, and had appreciative remarks on the dust jacket of the first printing, I can say categorically that Demski surely has shown no such thing, and i call upon him as a mathematician to deny and clarify the implications of this advertising copy.
Wimsatt on Yahoo Evolutionary Psychology discussion group
If I remember correctly, Wimsatt used to be Paul Nelson’s thesis advisor.
Comment by PvM — July 16, 2006 @ 8:35 pm
I can appreciate your viewpoint here. Indeed there is evolution at the level of the phenotype which we know can be inherited outside the genome. The relation of genome to phenome is now a very hot topic!
Mary Jane West-Eberhard has a good book on developmental plasticity. Certainly we see large morphological changes through environmental influence being stored into the organism.
I would not be surprised to see entire IC systems being expressed and then suppressed based on environmental stresses. I would not be surprised if significant portions of this information were stored in the phenome (as West-Ebberhards work would suggest). But would this really be an explanation in terms of blind processes, or would pre-designed adaptive strategies be a better explanation?
As I pointed out, self-mutating computer viruses have “randomness” incorporated into them as part of an adaptive strategy. Upon seeing the novel features of a self-mutated virus, would we presume no design? Hopefully not….
As a preliminary, consider the following illustration: a song can be rendered in numerous ways by artists, adapted to different contexts, but there is still fundamentally one archetype, the song. One has a basic pattern, and there are infinite variations, but within limits. A more rigid example of this is a 1 meg Mp3 which can be decompressed into billions of descendant 10 meg WAV files. Each of the WAV files will be different, but they retain the basic information.
This idea of decompression of a basic form may well be extensible to proteins, and is a topic of research. Michael Denton had a peer-reviewed paper in the journal of theoretical biology related to this very idea: The Protein Folds as Platonic Forms: New Support for the Pre-Darwinian Conception of Evolution . Denton thus asserts a very anti-Darwinian view of biology in favor of one where teleology and physics are primary.
Thus it is very possible an organism needing to adapt may have at it’s disposal the ability to create astonishing phenotype changes, even novel proteins, but only within definable platonic limits.
A pre-designed adaptive architecture then might be a far more appropriate metaphor for evolution than natural selection. It is like a fundamental archetype (song or Mp3 file) with many possible valid variations within limits.
I point this out to say one must be careful that one’s perception of phenotype evolution is not being colored by a pre-conception. Looking at the capacity of self-mutating computer virus to mutate novelty should not imply there was no foresight by a designer, nor that a designer is not needed for the virus, nor that all of it’s features can come about from the process of self-mutation.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 16, 2006 @ 11:09 pm
Sal argues
This idea of decompression of a basic form may well be extensible to proteins, and is a topic of research. Michael Denton had a peer-reviewed paper in the journal of theoretical biology related to this very idea: The Protein Folds as Platonic Forms: New Support for the Pre-Darwinian Conception of Evolution . Denton thus asserts a very anti-Darwinian view of biology in favor of one where teleology and physics are primary.
In other words, Denton invalidates ID since he shows that regularity processes can explain the form of proteins. Sal’s confusion lies in the presumption that selection is the only relevant process in evolution. In fact, as Ruse, Ayala and others have shown, evolutionary processes, especially when constrained by history, and physics are very teleological. Of course, we should not confuse this teleology with the concept of intelligent design as this concept relies on the rejection of regularity (physics) and chance processes.
Sal once again shows how empty the concept of ID really is as his own references fully reject ID’s approaches.
Now it may be tempting to claim that Denton’s paper is relevant to ID but it really isn’t unless we limit ID to Sal’s interpretation of that which shows how selection is insufficient to explain evolution. But that is something with which most of us can easily agree.
It is also quite ironic that creationists are still arguing that since the genetic code is not linked to physics/chemistry, science cannot explain its origin and evolution. Now that science has identified the chemical processes that have guided the origin and evolution of the genetic code, said existence of such processes is suddenly argued to also be evidence of design.
Seems that anything goes but simple logic clearly has to reject ID’s claims since ID is based on the elimination of chance and regularity and remember that regularity includes natural law.
So what’s the relevance of these platonic forms?
Ironically they help understand why convergence seems to be quite prevalent in evolution, once again blocking an ID claim.
I have shown the results of this paper before and it seems that Sal may have missed these scientific findings, so let me explain:
Information Theory of Complex Networks: on evolution and architectural constraints
Ricard V. Sole and Sergi Valverde
Complex networks display heterogeneous structures that result from different mechanisms of evolution (Sol´e et al., 2002). Some are created through multiplicative processes while others seem to be well described in terms of optimization mechanisms. Our study indicates that the possible universe of complex networks is actually rather constrained. Networks display scale-free architecture but also small assortativeness. The search algorithm, instead of assuming the presence of a given predefined mechanism of network growth, simply searches for candidate solutions to an optimization algoritm trying to approach simultaneously some amount of network heterogeneity and correlations. The result is that indeed networks are scale-free and involve low degree of correlations, but such situation is constrained to a well-defined domain. This domain is remarkably similar to the one inhabited by real graphs. Outside this domain, it is not feasible to find graphs simultaneously satisfying the two requirements.
and
Such a constrained set of possibilities fits very well the view of evolution as strongly dominated by intrinsic constraints (Jacob, 1976; Alberch, 1989; Kau man, 1993; Goodwin, 1994; see also Gould, 2003 for a critical discussion). Under this view, the outcome of evolutionary searches would be not any possible architecture from the set of possible patterns but a choice from a narrow subset of attainable structures. In this context, in spite of the contingencies intrinsic to evolutionary dynamics and history, the same basic repertoire of architectural motifs would be observable if the tape of evolution were rewound and played again (and this includes the evolution of technology).
I will refrain from asking how ID explains all this, seems that ID is not really about such trivial things and so I will point out that although some have argued that convergence is a problem for evolutionary theory, evolutionary theorists have done excellent work in showing how simple mechanisms can help explain the existence of convergence.
Seems to me another ID prediction bit the dust. But since ID is not in the business of making predictions, I am not sure what has been shown here other than that evolutionary science rocks…
I doubt that few realize the relevance and importance of constraints on evolution. Michael Ruse has pointed out how such processes help much better understand the history of evolution.
All this is based on solid information theoretic approaches which once again show how evolutionary processes are quite capable of explaining the many features found in the biology.
Comment by PvM — July 16, 2006 @ 11:31 pm
Hannah writes,
C’mon, Hannah, you can do better than this. I didn’t want to do this, but…There is a well-tested hypothesis for the origin of rearranging receptors in the immune system — a feature that Behe specifically declared was IC and unevolvable in Darwin’s Black Box. How did the next 10 years play out?
The question you have to answer, Hannah, is why any of these hard working, prolific-publishing evolutionary immunologists should take you seriously when you, and Behe, dismiss with mere hand-waving their painstaking work, published in Nature and Science, explicitly based upon evolution and confirming an explicit evolutionary hypothesis?
Hannah’s claims that evolutionary cooption hypotheses for the origin of IC systems are “untestable, purely speculative, and [have] little connection to the real world” are directly and completely refuted by the evolutionary immunologists. Kenneth Miller and Eric Rothschild showed this work to the judge, and that was the final blow to Behe’s credibility in court. Do you really expect scientists and educators to follow Behe’s advice and just give up this productive research, and replace it with “Poof, a miracle occurred!” If so, you’re the ones with “little connection to the real world.”
Comment by nmatzke — July 17, 2006 @ 12:07 am
Nick, I think you are not being completely fair here as you are arguing your case almost like the ACLU lawyers in Dover vs. Kitzmiller. They resorted to equivocation with some court room theater added. Thus, your invitation to Hannah to take the “clear path” you set for her, will probably be met with skepticism. I invite her however, to read the list of “proofs” you gave, but to read it in light of what I am about to share.
This document should help set the record straight: A Response to the Opinion of the Court in Kitzmiller vs Dover Area School District
There are two meanings of immune system evolution:
1. phylogenetic history (lawyers)
2. account in terms of natural selection and random mutation (Behe)
And also, the phylogenetic histories assumed Darwinian evolution was true. They did not demonstrate it. Thus in order to argue that these documents prove Darwinian evolution was demonstrated for the immune system, the lawyers thus resorted to equivocation, circular reasoning combined with to make a non-sequitur. One of the most brilliant legal maneuvers I’d ever seen.
The lawyers used examples of #1 to pretend #2 was actually solved. Such tactics are disingenuous at best, especially if the party making the equivocation knows they are making an equivocation.
Furthermore, Jones uncritically accepted Miller’s misrepresentations of Behe’s own theory.
Behe describes it in more detail:
Salvador
PS
I personally know one professor of cellular biology with a specialty in immuno- pharmacology who had her fill of Darwinian speculations and equivocated “evidence” regarding the immune system. She jumped ship 6 years ago (see Caroline Crocker).
Comment by Salvador T. Cordova, IDEA GMU — July 17, 2006 @ 1:39 am
On UD, a contributor asks if I am familiar with the demarcation problem. So let me point out that I am not as much arguing that ID is unscientific but rather scientifically vacuous.
And yes, I am aware of the demarcation problem which says that defining what is science may be complex. Nevertheless, this hardly means that it is impossible to identify that which is not science.
Personally I have found the observation that ID is scientifically vacuous or irrelevant to be much more defensible than arguing that it is not scientific as the argument becomes more a posteriori and avoids the accusation that science rejects design a priori.
I am still inviting ID proponents to explain why my observations are erroneous. Could anyone point to non-trivial ID relevant contributions of ID to scientific knowledge. Sal seems to suggest that ID is not in the business in explaining systems identified as design, which seems to me a bit self defeating.
Comment by PvM — July 17, 2006 @ 2:22 am
Why the overwhelming tendency on this board to cut out qualifiers? They aren’t extraneous words; each of them has a meaning. I thought I made very clear that my criticism was limited to some of Ken Miller’s co-optive mechanisms, i.e, the ones brought up in our IDEA discussions last semester, and I really can’t see why you feel justified in extending that statement to the very general “evolutionary co-option hypotheses”. As I said above, I am not willing to generalize there because I haven’t any comprehensive knowledge of them.
I’ll read up on it, begining with your citations; but it may be after this week, as right now I already have more reading than I have time away from lab.
Comment by Hannah — July 17, 2006 @ 9:12 am
Thanks for your background also, Salvador..
Comment by Hannah — July 17, 2006 @ 9:20 am
The discussion of “pre-programmed” embryonic development vs. the evolution of the vertebrate heart (comments 79-84, above) clearly demonstrate the essential difference between the EB definition of a “program” (as proposed by Mayr in 1974) and the ID definition of “front-loaded” or “pre-programmed” evolution.
The EB definition of “program” (e.g. the genome of an organism) is that set of genetic instructions and developmental pathways (”devpaths”) that, when actualized, bring about the construction and operation of a living (usually multicellular) organism. That the genome/devpaths fully qualify as teleological and “pre-programmed” presents no problem for EB whatsoever. On the contrary, it explains how an organism of fearsome complexity and organization can be constructed and operated using a surprisingly small amount of initial information (i.e. the relatively small set of genes identified in the genome of most eukaryotes).
Mayr argues forcfully (and, I believe, correctly) that this kind of teleology (which he calls “teleonomy”, to distinguish it from classical “intentional purposefulness”) is fully compatible with the overall EB paradigm. What is NOT compatible with this paradigm is the idea that the genome/devpath originated by an equally teleological process (i.e. “pre-programmed” or “front-loaded” ID). Not only is there absolutely no direct or indirect postive evidence for the existence or operation of such a process, it is simply not necessary to propose that such a process exists. On the contrary (and as we will discuss in class), the EB mechanisms of variation + inheritance + fecundity can easily be shown to result in unequal, non-random reproductive success, producing the fearsomely complex and organized systems mentioned earlier. Furthermore, the theoretical demonstration that this is possible is supported by multiple lines of evidence, including the fossil record and the phylogenetic reconstruction of pathways of descent with modification from common ancestors, which even prominent ID proponents like Michael Behe assert are “strongly supported” by the available evidence.
Therefore, I believe that the following two assertions are overwhelmingly supported by the available emipirical evidence:
(1) that the “pre-programmed” embryonic development of comlex, highly organized living organisms is both teleological and not in conflict with EB theory
(2) that the origin of the aforementioned “pre-programmed” developmental programs is fully explainable using current EB theory, which asserts that such origin is, unlike the actualization of such programs, NOT teleological, and does not require (nor is there any positive evidence for) supernatural intervention or regulation
Comment by Allen MacNeill — July 17, 2006 @ 10:42 am
P.S. The analogy between “pre-programmed” embryonic development and ID evolution is yet another demonstration of the logical vacuity of arguments by analogy. Just because the two processes seem to produce the same outcome (i.e. non-living “stuff” => complex, organized living systems) is NO proof whatsoever that the two processes are actually analogous in any necessary sense.
On the contrary, the EB explanation of the origin of the programs that guide embryonic development is fully supported by inductive, deductive, abductive, and consilient logics, and are therefore both empirically supported and logically far superior to the essentially logically vacuous ID alternative.
Comment by Allen MacNeill — July 17, 2006 @ 10:46 am
In regards to Sal’s posting Behe’s Response after the Dover debacle:
Behe claims: “1) Although the opinion’s phrasing makes it seem to come from my mouth, the remark about the studies being “not good enough” was the cross-examining attorney’s, not mine.”
Here is the actual testimony:
Q. You were asked some questions about the immunity system, and Mr. Rothschild gave you some books and articles and piled some papers on top of you. Do you remember that?
A. I do remember that, yes.
Q. And you claim that you didn’t find these examples all that persuasive, correct?
A. That’s right.
Behe also claimed: “2) I was given no chance to read them, and at the time considered the dumping of a stack of papers and books on the witness stand to be just a stunt, simply bad courtroom theater. Yet the Court treats it seriously.”
THEN why did you find them unpersuasive and not good enough?
Comment by Mike Hannigan — July 17, 2006 @ 11:30 am
For the same reason that if a Lawyer dumped 500 textbooks collected from the last 100 years with Haeckel’s embryos I would have no reason to read them to determine they were unpersuasive.
Behe knew that it was all a bluff. Unfortunately, the lawyers for Behe’s side were incompetent and they should have made a huge issue of ACLU/AUSCS court room theatrics, equivocations, and Millers misrepresentations.
Salvador
PS
for the record, in order to pre-empt what some may be thinking, let me state that I thought what the Dover school board was wrong, and I do not support them. However I support Behe and Minnich who were not even defendants in this case.
Comment by Salvador T. Cordova, IDEA GMU — July 17, 2006 @ 12:27 pm
And how would you know that they contained Haeckel’s embryos? The honest answer would be “I don’t know, because I’m not familiar with these texts”. Behe’s “the research is unpersuasive even though I’m unfamiliar with it” line isn’t very impressive.
Comment by Don Baccus — July 17, 2006 @ 12:42 pm
Allen,
Thank you for engaging my arguments, and what I highlighted will be no small amount of contention for many many years to come, namely the characterization of how much complexity there really is in the first organisms.
Consider the very beautiful picture of the development of a human embryo to an adult. The embryonic cell “decompresses” into 200 trillion cells with all the incredible networks of organs and systems. Is therefore a grown adult really more complex than the embryo from an information theoretic perspective? Most IDers knowledgeable of information science would say, “NO”! The embryonic cell is more complex than the human brain or immune system, combined, and practically the sum of all the parts of a grown adult (minus a few considerations).
Part of the reason for intense argumentation is that EBers speak one language (the physical artifacts) and IDers speak another (information science). If I posed that same question to an EBer, what would they say? Is the human embryo more complex than the human brain?
About the only biologist I know who clearly saw this was Lynn Helena Caporale, author of one of the best pop evo books out there, Darwin in the Genome.
So, rather than argue, I think the idea of information measures would be worth discussing in future threads as Dembski’s work is coming up in the reading.
I think the question to provoke your thinking and that of your students is: “is the embryonic cell more complex than the human brain or immune system?” When this question is considered, Dembski’s work will be better comprehended, and it’s relevance to the evolution of complexity will be much clearer.
What I am suggesting is that the EBers characterization of “simple” may not be accurate. Is an embryo “simple” compared to the brain? Is an 1 meg Mp3 simpler than the billions of 10 meg WAV files it can create?
regards,
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 17, 2006 @ 1:03 pm
Sadly enough, Dembski’s concept of complexity is ill equipped to deal with the questions Sal presents. Let explain:
Complexity (as defined by Dembski) is the negative log(2) of the probability. In other words, if something has a probability of 1 then its complexity is zero.
Now, when it comes to probabilities, Dembski is vague and contradictory about what probability should be considered and yet the choice of probabilities has great impact.
Let’s assume that the probability reflects a chance distribution which is uniformly distributed, in that case probabilities tend to be quite small. But what if science gets to explain a particular system: it’s probability is close to one and thus its complexity is close to zero.
In other words, Dembski’s measure of complexity measures our ignorance of how a system arises and once we understand it to sufficient details, the complexity disappears…
Now, science does have some very workable definitions of complexity and given those definitions it’s trivial to show that processes such as variation and selection can increase the complexity of the genome.
From an information theoretic perspective it is extremely important to recognize the limited definition of Dembski’s concepts and avoid equivocation of these terms.
Since Salvador made the following claim, it would thus be helpful if he can further explain his statement:
Most IDers knowledgeable of information science would say, “NO”!
let’s see to what extent IDers are knowledgeable (sic) of information science.
In the mean time Erik Tellgren observed:
C11 [Erik]: The term “specified complexity” is a redundant, obfuscatory middle-man that serves no non-rhetorical purpose (it is apparently the name of the state of affairs that someone has sucessfully eliminated a set of non-ID hypotheses using the Explanatory Filter). It adds nothing to the actual argument, but it invites equivocation with other concepts with the same name (e.g. Paul Davies’s concept) and with intuitive concepts of “complexity” that lack any a priori connection to specified complexity. Dembski also seems to equivocate between specified complexity w.r.t. to a uniform probability assumption and specified complexity w.r.t. all known natural causes.
Comment by PvM — July 17, 2006 @ 1:23 pm
Indeed, and as you note, the power of evo-devo to explain the molecular basis for the past 600+ million years (and maybe much more), in simple terms, is growing quickly. Sal - for an easy to read explanation, I recommend you read Sean Carroll’s Endless Forms Most Beautiful. It’s a fascinating read, and I think should put your “contention” to rest quite easily.
Comment by Dan — July 17, 2006 @ 1:25 pm
Sal argues that Behe knew that it was all a bluff. Unfortunately, the lawyers for Behe’s side were incompetent and they should have made a huge issue of ACLU/AUSCS court room theatrics, equivocations, and Millers misrepresentations.
or perhaps Behe was really unaware of the vaste amounts of research relevant to his statement? To accuse Miller of equivocation and misrepresentation just because his side was succesful in exposing the vacuity of intelligent design, could require from some supporting evidence.
Miller destroyed Behe’s arguments in court. Ironically, Dembski posted how he was looking forward to see evolutionary science in court under oath. When ID got its time in court, it predictably did not do too well.
Perhaps the lawyers on the defense were ill prepared for the onslaught of scientific arguments, and the lack of scientific support for ID, but do not blame the messengers like Miller for exposing the major flaws and weaknesses in Intelligent Design.
Comment by PvM — July 17, 2006 @ 1:27 pm
Dan quickly returns the issues to the simple observation that embryology is increasing our understanding, and remember any time science finds a plausible explanation it ends up blocking intelligent design’s ‘explanatory filter’.
In other words, when embryology shows how the heart may have evolved, it not only blocks Sal’s assertion but it blocks ID’s hopes of inferring design. Any time ignorance is reduced, the explanatory filter is weakened.
That by itself should be significant cause for concern.
Comment by PvM — July 17, 2006 @ 1:30 pm
“Any time ignorance is reduced, the explanatory filter is weakened.”
That’s a good way of putting it - I’ll have to remember that. ;-)
Comment by Dan — July 17, 2006 @ 1:42 pm
In comment 104 Dan recommends that Sal read Sean Carroll’s Endless Forms Most Beautiful. I second that recommendation, and point out in passing that it is the final required reading for my summer evolution course. We’re diving into it next week. Having read it through twice now and discussed it with some friends in the Cornell genetics and development department, I can say with quite a bit of confidence that it does indeed show exactly what I said earlier: that the genome and the developmental pathways that it codes for can produce organisms of fearsome complexity, organization, and beauty.
But that genome itself is fearsomely complex, both in terms of the number of nucleotides of which it is composed and the developmental pathways that it sets in motion. By contrast, as one examines the genomes of organisms whose ancestors date back to earlier periods in the evolution of life on Earth, this complexity declines exponentially. In particular, the prokaryotic genome is surprisingly simple and, being unicellular, prokaryotes don’t really have any developmental pathways (only a few fairly simple regulatory pathways). What this indicates is that, rather than the “design” of complex eukaryotes being encoded somehow in the genomes and developmental pathways of their eukaryotic ancestors, they have evolved and become more complex and organized over time.
Therefore, the Deistic “front-loaded design” version of ID is entirely without empirical foundation. All that remains is yet another argument by analogy, which is losing more and more steam as the phylogenetics of eukaryotic developmental evolution is investigated.
So, rather than being representative of some super-duper “new” form of bioinformatics, ID is just the last gasp of two otherwise defunct quasi philosophical/theological doctrines: Deism/Aristotelian “formal cause” (i.e. “front-loaded” ID) and Interventionism/Aristotelian “final cause”, both of which were tossed on the rubbish heap of the history of science long ago.
As I have been hectoring my students in my evolution class, “keep your eye on the variation!” Darwin admitted in the “Origin of Species” that scientists of his time were “ignorant of the laws of variation.” That ignorance is finally yielding to empirical studies in the fields of epigenetics and evo-devo. It’s an exciting time to be an evolutionary biologist, and the future looks even brighter!
Comment by Allen MacNeill — July 17, 2006 @ 2:44 pm
I have ordered both Carrol and Kirchner’s book today. I appreciate your interest in my education on these matters.
Allen if I may plead caution in that interpretation, some are now dissenting and arguing Eukaryotes either had independent ancestry or even were ancestor of prokaryotes. This new view is consistent with ID conceptions, and a recent peer-reviewed article supports it. Please see: Genomics and the Irreducible Nature of Eukaryote Cells
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 17, 2006 @ 3:23 pm
Hannah wrote:
Hannah claims biologists criticize ID with statements like “ID is wrong because Behe/Johnson/Dembski (insert name of choice here) is an awful person”. Claiming Miller “has a tendency to misrepresent and to attack straw man arguments” sure sounds like “Evolution is wrong because Miller is an awful person.” Ok, from Josh’s original post:Taking Behe’s popular example of the cilia: is it, with any aspect removed, still functional? As a whole cilia in the manner we know it now, no it is not. However, could these cilia have been functional in another way at an intermediate point in evolution?
From “Answering the Biochemical Argument from Design” by Kenneth Miller:
Is this an example if Miller’s “tendency to misrepresent and to attack straw man arguments”?Comment by alienward — July 17, 2006 @ 3:49 pm
If indeed Evo-Devo is true (and I only believe it is partially true because I reject monophyletic origins for all creatures), it would indicate the ancestral organism would have to be extremely specified, much like an embryonic cell is tightly specified (otherwise the descendant cells would be a disaster).
This therefore leads to a catch-22 situation: if one argues evo-devo, then the ancestral organism must be highly specified, but this is bad news for explaining the path from abiogenesis to the ancestor of something like Bilaterians.
Case in point: genes involved in development and regulation are highly “conserved” (Gerhart and Kirschner’s paradox), thus this indicates a high specificity target for the ancestral organism. If this high a specificity target was missed from abiogenesis to that first ancestral form, then evo-devo falls apart. In other words, evo-devo does not negate the need for design, it may negate the need for design during subsequent evolution, but in so doing it necessitates even more design for the ancestral creatures. It only shuffles the problem to another location for someone else to solve, but the problem doesn’t go away (and in fact makes it harder for the poor OOL and early life researchers!).
Salvador
PS
going back to Josh’s questions, if IC can be evolved via evo-devo, this only increases the amount of front loaded design for the first ancestors, it does not diminish it.
Comment by Salvador T. Cordova, IDEA GMU — July 17, 2006 @ 3:53 pm
Sal,
Yes, I assumed as much when you said you were a YEC, so you reject all sorts of things (e.g. radiocarbon dating, continental drift, etc.) on theological, not scientific, skepticism.
Other comments of yours:
…it would indicate the ancestral organism would have to be extremely specified, much like an embryonic cell is tightly specified…
Specified for what?
As PvM alluded to earlier, this logic only works in the presense of ignorance.
Likewise, bad logic that relies on ignorance.
More of the same…
I dealt with this logic a while back, on my original blog:
Implying Creationist Abiogenesis
Comment by Dan — July 17, 2006 @ 5:38 pm
By specified, are you implying creationist abiogenesis?
As PvM made reference to, such ideas thrive on ignorance.
Comment by Dan — July 17, 2006 @ 6:40 pm
By contrast, as one examines the genomes of organisms whose ancestors date back to earlier periods in the evolution of life on Earth, this complexity declines exponentially.
Say what? I thought, according to the standard scientific view, all organisms have ancestors who date back to earlier periods in the evolution of life on Earth. In fact, they all have ancestors who date back to the very beginning of life on Earth! Perhaps you could take that paragraph into the shop for a bit of reworking.
Comment by ivy privy — July 17, 2006 @ 6:41 pm
(and I only believe it is partially true because I reject monophyletic origins for all creatures)
Please do justify this with some evidence. I will also note that I made comments supporting the single origin of life in a different thread and received no challenges to my statements. Specifically, I noted that horizontal gene transfer is in no way a challenge to the concept of LUCA and common ancestry in general.
Comment by ivy privy — July 17, 2006 @ 6:56 pm
I would like to thank Sal for bringing up the concept of embryology since it serves as an excellent example of how, when science explains something, it blocks the explanatory filter from inferring design. In this case, it forces Sal to move the origin to front loading and while there are several problems with this approach, Sal himself suggests why these are problems for ID
Salgoing back to Josh’s questions, if IC can be evolved via evo-devo, this only increases the amount of front loaded design for the first ancestors, it does not diminish it.
In other words, if Sal’s argument of front loading is to be taken seriously, embryology only serves to make it more unlikely.
I will address shortly Sal’s other claims, especially the ones about conserved genes which are well expected from a common descent, evolutionary perspective but since ID refuses to take any position, are left unexplained by ID. Now I am very well aware that Sal and others can invent some ad hoc explanations but these inevitably fail as they are not based on the premises of ID but most often on creationist assumptions such as the creation of kinds which leads many, especially young earth creationists like Sal, to reject for instance a monophylic origin of life and embrace the Cambrian as supporting evidence for their thesis. And while the Cambrian quickly dissolves as a relevant example supporting even the creationist claims, one cannot blame ID proponents who have been misinformed about the Cambrian explosion for continuing these flawed claims.
I will discuss the relevance of Hox Genes, regulatory genes and the Cambrian soon, needless to say, science explains and ID has to go into hiding.
Comment by PvM — July 17, 2006 @ 10:26 pm
What, like Darwin who thought, “the first life was created”.
No, by specified, I am pointing out the ancestor of something like Bilaterians would have to be very complex, at least as much as life today (with all those conserved regulatory regions and the equipment to make them function) which implies you think life can form starting from lifeless simple chemicals to bio-polymers to replicators,….complex bilaterian ancestor. But this is another “just-so” un-testable narrative, which flies in the face of 145 years of hard empirical evidence. Add to that, here are more problems characterizing the first Bilaterian:
Problems with Characterizing the Protostome-Deuterostome Ancestor.
Some in the OOL community have had enough of these simplified narratives that fly in the face of hard empiricism and serious theoretical barriers. I pointed that out here: Chance and Necessity do not explain the origin of life.
And in light of Irreducible nature of Eukaryote Cells your diagram on the way to the bacteria might not even be right.
Your diagram presumes a complex self-referencing Turing machine can evolve from a simple replicator. There is nothing in information science that would hint that is even reasonable, in fact quite the opposite. Trevors and Abel effectively pointed the quest for a scientific answer to OOL might be like the quest for square circles. Thus your abiogenesis diagram reflects more wishful thinking than what the most recent literature suggests.
Finally, from various observations we are seeing evidence of reductive (downward) evolution, not upward. See: Extreme Evolution. Who then is to say downward evolution is not possibly a general principle?
Comment by Salvador T. Cordova, IDEA GMU — July 17, 2006 @ 10:26 pm
Sal,
Nice try in obfuscating the issues. In fact, the immune system evolution example does include mutation and selection. Behe attempted to rebut Ken Miller by the absurd and naive tactic of searching the articles for the phrase “random mutation”. He didn’t find it, and in his direct testimony in court he tried to use this to debunk Miller’s argument.
But the relevant mutation is not just any old mutation. It is well-known to the evolutionary immunologists, and the specific mutation of relevance is transposition. Transposition appears throughout the immune system articles, because the hypothesis in question is the transposon hypothesis. Behe conveniently forgot about it later, but at trial Behe admitted all this under cross-examination:
As for natural selection, the relevant selection pressure is obvious: increasing the diversity of antigen recognition in the receptors, which is a ubiquitous and prevailing force in immune system evolution (and why modern immune system genes are under strong divergent selection pressures even today).
But this is all beside the point. Here’s the point: the evolutionists have a testable model, and have tested it repeatedly. The best example is the discovery of free-living transposons homologous to the immune system’s RAG genes. Apart from the transposon hypothesis, there was no reason whatsoever to even suspect that these particular transposons would exist.
The IDists, on the other hand, have squat, except for wildly innaccurate assertions about the hard work of real scientists:
Yes or no, Sal: is Behe’s claim right or wrong? This is a simple question. Can you really say with a straight face that there are no answers on the evolution of the immune system, in any of this work?
Comment by Nick (Matzke) — July 17, 2006 @ 11:38 pm
Sal once again focuses on a few papers while ignoring the vaste evidence that shows how life may have originated.
Your diagram presumes a complex self-referencing Turing machine can evolve from a simple replicator. There is nothing in information science that would hint that is even reasonable, in fact quite the opposite.
Perhaps it’s better stated that information science has shown the reasonability of origin of life scenarios and although a lot of details are lacking, Sal’s claims seem to be largely irrelevant.
Sal once faced with these simple facts resorts to claims of fact where no supporting evidence for his claims really exist.
It’s the front loading scenarios which imply a complex precursor, not the evolutionary scenarios. While Sal may object that given the age of these events (I thought that Sal was a YEC’er, does he accept the age estimates after all?) it may be hard to fully recover all the details and yet science is recovering intricate details of events that happened hundreds of millions years ago.
In the mean time, I will refrain from how ID explains it since Sal has suggested that ID is not really in the business of explaining much of anything. Something I believe we all wholeheartedly can agree with.
And yes, it seems that Sal indeed expects, like Darwin, that first life was created. Darwin however lived in a time where much details was lacking and one can understand his position. However given todays state of science, such presumptions seem far less supportable scientifically speaking at least.
But I am always willing to hear the details Sal has to offer that show that his position about the origins of life have any scientific relevance beyond ‘evolution/darwinism cannot explain it’.
Comment by PvM — July 18, 2006 @ 12:58 am
Salvador wrote:
Man, IDEA Clubbers like you and Hannah are really bent out of shape over the whooping Miller gave Behe in court. At least with you saying (about Miller) “his outright misrepresentations, strawman arguments, and falsehoods” and Hannah saying “he has a tendency to misrepresent and to attack straw man arguments”, we know Casey Luskin has his clubbers front-loaded with consistent whines about the dismantling of ID in that “landmark trial”.Comment by alienward — July 18, 2006 @ 1:12 am
Josh
In the same way that Fisher reduced natural selection to the level of alleles, Behe has reduced ID to the level of biochemical pathways.
I recall somewhere that Behe set forth his test that scientists must meet before he would be persuaded that his “theory” is worthless and he literally demanded that a “molecule by molecule” history of one of his “complex features” be proven.
That is just one of the reasons that Behe and his claims are mocked by scientists who actually do research and investigate testable scientific explanations for the diversity of life and organic molecules on earth.
As for Nick’s “yes or no” question to Sal, we know the answer even if Sal doesn’t admit it. And a Judge who was very wise and experienced in evaluating the credibility of witnesses knew what to do with Behe’s testimony.
Perhaps Sal can explain to us two or three key differences between answering questions under oath in a Federal courthouse versus answering questions here in these comment threads. Creationists and ID promoters (I make no distinction in the absence of an explanation from ID promoters as to how and when their “designs” are incorporated into living creatures) tend to do poorly in courtrooms when the merits of their scientific claims are subjected to scrutiny. Anyone care to guess why that might be? And please don’t disparage the ability of our courts to distinguish vapid scientific claims from robust claims — they do this all the time and they do it well enough.
Comment by Michael Hubl — July 18, 2006 @ 1:30 am
Hannah saying “[Miller] has a tendency to misrepresent and to attack straw man arguments”,
Oh, I’m sure it depends on what the meaning of “tendency” is. How many ID arguments did Ken Miller address? How many of those were strawmen?
And how did he get away with it? The ID promoters had their own attorneys and experts right there to keep Miller honest. What happened?
Explain please.
Comment by Michael Hubl — July 18, 2006 @ 1:34 am
Right. You’ve equivocated Behe’s sense of “answer” with your definition of “answer”. I will let Behe say it in his own words what an constitutes an answer in his mind, not your adulterated misrpresentation of his meaning of “answer”:
Calvin and Hobbes are alive and well in Darwin Land
And regarding all the literature you “cite”, I should alert Hannah, you tried to pull this same trick when you, Gishlick, and Elsberry got Nature to reference your review of Stephen Meyer’s paper. One Long Bluff: Gishlick, Matzke, Elsberry response to Stephen Meyer
I point that out because a similar modus operandi by you is at play with your discussion of the immune system.
So Nick consider the bluff called. Does your “answer” correspond to Behe’s conception of “answer”? Yes, or no. Simple question.
Comment by Salvador T. Cordova, IDEA GMU — July 18, 2006 @ 2:20 am
Denis Lamoureux, Assistant Professor of Science & Religion St. Joseph’s College, University of Alberta, wrote this on an email he received from Behe when he was reviewing a paper by Behe and had asked him for clarification about his super cell claim. Behe answered that front loading even as far back in time as the Big Bang could explain IC systems. Lamoureux quickly observes the logical fallacies
Third, note that Behe even speculates that ID could have been implemented in the Big Bang. If this is indeed the case, then he truly betrays the concept of irreducible complexity. By definition, irreducibly complex biomolecular structures cannot be put together one piece at a time through a gradual process. Irreducible complexity can only come about through “one fell swoop” acts during the course of time, and not at the very beginning of time. Behe’s shift in the direction of a full evolutionary theory not requiring interventions during the history of life is characteristic of many who have gone before him in that the gaps they once believed existed in nature are only gaps in their knowledge. Suggesting that intelligent design could have been loaded in the initial conditions of the Big Bang is evidence that the gaps are closing in Behe’s view of origins, and that he is coming to terms with biological evolution.
Lamoureux has done an excellent job at exposing such self-contradictions in the claims of ID proponents, most noticably Phil Johnson (search google for Denis Lamoureux, he has some excellent papers on this topic). As such, Lamoureux’s contributions seem to generate sometimes a strong response. I remember Salvador discussing some issues on the ARN boards with Lamoureux after Sal had called for the ex-communication of Denis for aligning himself with Darwinist leadership, arguing that Denis may call himself a liberal compromiser, a die hard Darwinists and that he has no right to call himself an evangelical.
Science can be seen as a threat to religious faith and people respond to this threat of fear with strong responses. It is thus extremely important that we understand the motivation of many ID proponents: namely the belief/fear that evolutionary science and specifically natural selection undermines religion and is atheistic and that methodological naturalism is just another form of methodological naturalism. Once various people of power in the ID movement make these claims, it is likely that such claims are believed by countless followers. This generates a certain level of fear which makes people more succeptible to authoritarian viewpoints, especially if one is already predisposed to a level of authoritarianism. As an Ex YECer I found it hard to accept that I had been misled by people I trusted when I found out that the scientific research on radiometric dating and other evolutionary aspects had been significantly misrepresented. How could these people, many of whom I trusted have placed my faith and my scientist upbringing at risk? In the end what upset me most is that despite my training in physics I had still accepted the claims about radiometric dating’s problems without any questions.
Issues of faith and science run deep and many people feel that they are intertwined. As such we have great responsibility that we carefully represent scientific knowledge
As Lamoureux observes in the same article
I have two concerns with regard to Behe’s thesis for the creation of irreducible structures in ‘one fell swoop.’ First, before Christians come to claim publicly the existence of any miraculous intervention during the course of geological time, it behooves them to be certain lest they embarrass the Church by rash and intellectually (in this case scientific) unsubstantiated claims. I am more than uncomfortable with the assertions of a single man, the biochemist Behe. Such claims should at the very least be done in a community of biochemists. I know a number of professional biochemists, including many devout Christians, and their assessment of Behe’s ‘one fell swoop’ thesis is quite negative.
After some discussion in a dedicated thread, Lamoureux and Sal parted their ways amicably.
I have found Lamoureux always quite convincing and in the book “Darwinism Defeated? The Johnson-Lamoureux Debate”, Lamoureux dismantled most of Johnson’s scientific arguments and exposed the equivocation on naturalism by Johnson when mixing the term philosophical and methodological naturalism.
Emotions and sentiments run deep when it comes to evolutionary theory. Understanding the philosophical foundations of ID and its proponents may help resolve why they so strongly object to evolutionary theory and in particular Darwinism and in particular natural selection.
It may also provide us with ways to alleviate these fears and show them how science does not need the eliminative arguments of ID to show God’s Creation in all its glory to all those willing to believe and see.
Comment by PvM — July 18, 2006 @ 3:40 am
Allen: I recall somewhere that Behe set forth his test that scientists must meet before he would be persuaded that his “theory” is worthless and he literally demanded that a “molecule by molecule” history of one of his “complex features” be proven.
I have seen Dembski make such a claim or at least one to that extent but have not found such a claim for Behe. Closest I came was a statement made by Futuyma in the Boston Review
When scientists invoke miracles, they cease to practice science. Were a geologist to cite plate tectonics, a chemist hydrogen bonds, or a physicist gravity as an instance of the miraculous, he or she would be laughed out of the profession. Moreover, they would not be doing their job, which is to seek answers by posing and testing explanatory hypotheses. Faced with the unknown, as all scientists are, the scientist who invokes a miracle in effect says “this is unknowable” and admits defeat. It is only through confidence that the unknown is knowable that physical scientists have achieved explanation, and that biologists have advanced understanding of heredity, development, and evolution to heights scarcely hoped for just a few decades ago. Yet Behe, claiming a miracle in every molecule, would urge us to admit the defeat of reason, to despair of understanding, to rest content in ignorance. Even as biology daily grows in knowledge and insight, Behe counsels us to just give up.
Ironically, the thread in which Dembski made his unreasonable demands of science also contains his now infamous statement
As for your example, I’m not going to take the bait. You’re asking me to play a game: “Provide as much detail in terms of possible causal mechanisms for your ID position as I do for my Darwinian position.” ID is not a mechanistic theory, and it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories. If ID is correct and an intelligence is responsible and indispensable for certain structures, then it makes no sense to try to ape your method of connecting the dots. True, there may be dots to be connected. But there may also be fundamental discontinuities, and with IC systems that is what ID is discovering.
William A. Dembski Organisms using GAs vs. Organisms being built by GAs thread at ISCID 18. September 2002
So here is Dembski’s requirement
Let me spell out what’s needed for a detailed Darwinian pathway to explain an IC system. The problem is similar to that of connecting two organisms in the fossil record. Given organisms X and Y, if they are related by common descent via the Darwinian mechanism, there must be a continuous chain of organisms X(0) –> X(1) –> …–> X(m) = X and Y(0) –> Y(1) –> …–> Y(n) = Y where X(0) = Y(0) is a common ancestor. In the best circumstance, each such X(i) and Y(j) must be explicitly exhibited and any arrows of causation connecting two organisms must produce small incremental changes that are highly probable on the basis of the Darwinian selection mechanism. The more intermediates that are missing from this picture and the more handwaving and just-so story-telling to describe the arrows of causation, the more problematic the evolutionary explanation.
In the case of an IC system S comprised of components {S(1), S(2), …, S(r)} and arranged in some irreducibly complex configuration C, we need a sequence of supersystems T[1] –> T[2] –> … –> T[n] where each T[i] consists of one or more functional biological systems. Thus T[i] = {T[i](1), … T[i](k)} (k depends on i and is at least 1) and each system T[i](j) consists of m components {T[i](j)(1), … T[i](j)(m)} (m depends on i and j) and is arranged in some configuration C[i](j) (not necessarily irreducibly complex). In the sequence T[1] –> T[2] –> … –> T[n], T[n] = {T[n](1)} and T[n](1) = S, the system in question. Under the assumption that S evolved by Darwinian evolution, there must be a supersystem T[1] in which the components of S are either absent or targeted in completely different systems for different functions. Such a T[1] needs to be the starting point if S is properly to be ascribed to a (macro)evolutionary process. Each arrow in this picture should represent a small incremental change that is highly probable on the basis of the Darwinian selection mechanism. In most instances it will be at the level of a single component T[i](j)(k) being slightly modified and (re)targeted to a component T[i+1](j’)(k’) of system T[i+1](j’) (thus T[i] –> T[i+1] would signify the change T[i](j)(k) –> T[i+1](j’)(k’)).
In the best circumstance, each such T[i] would be explicitly exhibited down to the T[i](j)(k) level along with all the configurations C[i](j); moreover, any arrows of causation connecting two supersystems must produce small incremental changes that are highly probable on the basis of the Darwinian selection mechanism. These changes will operate at the level of individual system components and the system functions induced by their configurations. The more intermediates that are missing from this picture (whether whole systems, components, or configurations) and the more handwaving and just-so story-telling to describe the arrows of causation, the more problematic the evolutionary explanation.
Deanne Taylor responded as follows and continued to give Dembski, and the other participants a nice lecture on the concept of scale free networks and evolution
Deanne Taylor: What you are requiring of evolutionary proponents, in the context of this reply, is that someone prove that a system or protein that currently exists as a hub (is IC) in a protein interaction network, was once, at some distant point, NOT a hub in a protein interaction network, or at least prove within a reasonable doubt that it arose from a simpler state to its current, complex state.
In other words, you wish evolutionists to contract the history of the network, back in time, run the movie backwards so to speak, and show how each of the components that make up the hubs of protein interactions became hubs in themselves.
You realize, of course, that evolutionary theory suggests that this process happens over evolutionary time, and although you demand proof for such a series of events (and I’m sure there has been proof offered), biologists will not be able to provide a series of mutations for you at this point, as this would require biological engineering capabilities we’re only working towards, right now.
Additionally, you have the ability to retort that any sequence of events proposed for a Darwinian explanation of IC is a just-so story without evidence to back it up, and you can demand hard evidence. Rightly so! Science should demand hard evidence.
If that evidence is impossible to observe, one can also look at other avenues for that evidence. If you cannot be at the crime scene directly when the murder took place, you can instead use blood, fingerprints, DNA samples and any other kind of “smoking gun” evidence to point to the murderer.
I am about to offer you some evidence, though possibly not in the form you expected when you wrote that post, yet I will await why the smoking-gun evidence is not sufficient to show how systems that appear IC appeared out of a logical sequence of events. As you probably guess, it has to do with scale invariance.
Comment by PvM — July 18, 2006 @ 4:00 am
It looks like some clarification is in order…
Sure; if I had been making that argument (Miller misrepresents, thus evolution is wrong) it would have been illogical and an ad hominem attack. As it was I was simply trying to answer my interrogators (you :) ) as to why I found some of Miller’s cooptive mechanisms “lame”.
I tried also to make clear that I had no grounds for general statements about Miller or his work, but perhaps in that sentence there was room for ambiguity.
Per 120 & 122 — I haven’t read the trial transcripts, and therefore have no opinion of how Miller performed there.
Comment by Hannah — July 18, 2006 @ 7:46 am
When I read Ken Miller’s attack on Behe’s claim of IC for the bacterium flagella, I almost fell off my seat. It was so pathetically transparent that he did not have any defense. This is from a man who should know something since he writes text books at both the high school and college level in biology.
Though, I haven’t read all of Miller’s Dover testimony, he distorts both what ID is about and he misrepresents what is in the “Of Pandas and People” text book during his testimony. These are at the beginning. He didn’t give an honest answer but one carefully designed to make the other side look bad.
When I see something like this, I ask why. If you really had strong debating points or evidence, then why not use them. The answer is that they reallly don’t have anything.
Comment by J. Cosgrove — July 18, 2006 @ 10:35 am
(and I only believe it is partially true because I reject monophyletic origins for all creatures)
Please do justify this with some evidence.
————
Challenge not met.
Moderators note: There is no requirement to justify statements of opinion.
Comment by ivy privy — July 18, 2006 @ 11:08 am
Josh and class,
Something I should note here regarding immune system evolution. The papers Nick cited frequently deal with fully functional immune systems being supposedly transformed into another functioning immune system.
To illustrate that this is not really novel IC evolution, consider that one can take a car and upgrade/downgrade it’s various different parts like but which can serve a similar function but are of possibly different construction. Here are some replaceable parts:
1. battery (many varieties would be adequate)
2. engine (many varieties and variations adequate)
3. tires (many varieties and variations adequate)
If an immune system of some sort is not already in place, likely the creature will be dead. And in fact there will be likely no chance for subsequent evolution because the entire population will be wiped out. It’s not a matter of even having much of a second attempt at this since these populations will confronted with lethal epidemic after lethal epidemic.
Perhaps one thing IDers might consider is accounting for the indirect route of a pre-existing system. Such routes don’t negate the fundamental thesis, but it anticipates and explicitly addresses the kinds of equivocations that can be leveled at the argument.
Skepticism should be welcomed by a scientific theory, but the complaint being leveled by the critics of IC is that the IDers standards of proof are too high. I don’t view it that way. How can entire populations without a functioning immune system exist in the first place for natural selection to even act upon it?
Does Nick consider the population could be non-existent without the equivalent (or reasonable facsimile) of a combinatorial antibody defense system already in place?
Behe said to discuss the available population resources — in this case it is understandable why this should be a consideration.
Salvador
PS
Combinatorial RAG systems are not the only immune strategy as evidenced by the Hagfish and Lamprey, but appealing to them as pre-cursors is disingenuous. It’s like pointing to a car which uses a rotary-engine to prove a car doesn’t need a piston-engine, and then trying to insinuate cars therefore don’t need some sort of engine. That is what is at play here with the whole issue of RAG evolution via transposition. They fail to mention this is a replacement or upgrade of pre-existing system. A more charitable reading is how the system could function without reasonable facsimiles in place!
Behe scoffed at it, and the above citations did a fabulous job of equivocating what Behe was scoffing at. The above citation theatrics were attempting to portray that Behe was dismissing the phylogeny (ancestral history) only to be proven wrong later:
But Behe was not disputing the phylogeny, he was disputing the mechanisms. Therefore the above citation theatrics were merely equivocations, IMHO.
Comment by Salvador T. Cordova, IDEA GMU — July 18, 2006 @ 12:08 pm
Sal comments:
“If an immune system of some sort is not already in place, likely the creature will be dead. And in fact there will be likely no chance for subsequent evolution because the entire population will be wiped out.”
Unless, of course, organisms evolved in an ever escalating genetic arms race, where small variances (random mutations) were subjected to copetition and environmental stresses that selectively weeded out certain types.
Hmmmm, sounds like evolution.
Comment by Mike Hannigan — July 18, 2006 @ 3:35 pm
Oh sure, by changing, in a rationalization 10 years after the fact, the words “the scientific community has no answers” into “you can’t give me every mutation that occurred over hundreds of millions of years” — a quite literally impossible demand even if we had the full genome sequence of every animal living today. This basically boils down to the ridiculous question that Ken Ham, the leader of the ministry Answers in Genesis, teaches to poor little kids who don’t know any better: “Were you there?” Basically, the creationists think that evidence should be ignored and dismissed with a wave of the hand unless an actual human being observes the whole thing first hand. Never mind if multiple independent lines of evidence all point to an explanation of past events — they won’t believe it unless their impossible demands are met.
So when ID/creationists talk in high-minded terms about the importance of testable models, peer-reviewed publications, and the like, you simply can’t believe them. They will happily deny literally piles of evidence (literal mountains of evidence, in the case of young-earthers).
To reiterate:
1. Behe said the scientific community had “no answers” on the origin of the immune system.
2. The scientific community came up with an answer, basically: rearranging antibodies arose when a transposon inserted into a preexisting, non-rearranging receptor gene.
3. The scientific community tested this hypothesis. They went out and found the predicted representatives of the receptor gene and the transposon. They published this in top journals for everyone to see.
4. Behe and Sal dismiss all of this with hand waving, and make the ludicrous demand that evolutionary biologists do something that is impossible.
5. They then accuse the scientists of “bluffing.”
Sal continues,
You know, the hilarious thing about this is that it was this exact post that confirmed for us that Behe would do exactly what he did when he was cross-examined. No amount of evidence and no amount of publications would be enough for him. He would just dismiss it all with a wave of his hand. It might make sense in his own peculiar mind, but for anyone not already committed, it would be clear that Behe simply was not engaging the actual evidence.
Sal continues,
How dare we cite published evidence to point out the problems with Meyer’s paper! How dare we point out that Meyer was unaware of results, well-known among actual biologists, that refuted his naive assertions? How dare Nature recognize serious work when they see it?
Sal, have you ever read a scientific article? Do you have any concept of how many publications are typically cited? The number is typically hundreds. Is this common practice “bluffing”? Or is it simply being well-informed?
The hilarious thing about this was that there never were any more “installments”. They did a Preface, and one installment, and we never saw the other five or six that were promised.
The scientific community answered Behe’s original, testable claim. But Behe changed his definitions to dodge criticism. He did this literally dozens of times on cross, on multiple different issues. He argued that Of Pandas and People accepts common ancestry, even when it says things like “Design proponents have a realistic and more cautious approach to the use of homologies. They regard organisms which show great structural differences, such as starfish and chimpanzees, as having no common ancestry.” Behe redefined the “core system” of the blood-clotting cascade, right there on the stand, when it was shown that two of his previous definitions contradicted each other. And he moved his goalposts for the scientific community into an alternate dimension when he dismissed the massive, published, hard work of the evolutionary immunologists.
IDists have got to understand that they can rationalize their defeats all they want, but that this only makes sense to them. Dismissing evidence is not how science is done.
J. Cosgrove
In a comment that proves he hasn’t been paying attention to the thread, J. Cosgrove writes,
First of all, all of the claims here are mere assertion with no evidence or argument backing them up.
Second, it’s “bacterial flagellum”, not “bacterium flagella”.
Third, Miller’s point was that it is not true that the flagellum had to appear “in one fell swoop”, as Behe claims, because subsets of flagellum parts are know to occur in various bacteria, and these subsets function just fine. There is nothing wrong with this argument, but Cosgrove should try and actually give us some reasons, if he disagrees with it.
Back to Sal,
Why should it work any other way? Only creationists think that evolution means that functional systems always evolve from non-functional systems.
Oh ho! Sal is now trying to tell us that the adaptive immune system is not IC!! This contradict’s Behe’s explicit statements in Darwin’s Black Box, as well as his own previous arguments!
The actual evolutionary model for the adaptive (= rearranging receptors) immune system starts with an immune system with non-rearranging receptors. Humans have many such non-rearranging receptors today — they are the first line of defense, before the rearranging receptors “learn” to recognize a new invader — and many critters, like insects, get by with nothing but the non-rearranging receptors just fine.
This is another example of a very poorly thought-out creationist objection that is derived from ignorance rather than, say, actually reading what the biologists say in their papers. No one in the scientific community thinks what Sal depicts. Immune systems evolved along with multicellularity. Heck, sponges, which only have a few different types of cells, have cells that crawl around like amoebas and eat stuff like bacteria. This, phagocytosis, is the core process in both simple eating and in immune defense. That these two processes are fundamentally not much different was recognized by Metchnikoff over 100 years ago — as mentioned in the immune system references I’ve already posted.
Why don’t you ask all of the non-vertebrate organisms how they survive without a combinatorial antibody defense system? It must be possible, because they are doing it.
Oh, wait, it looks like Sal realized this after finishing his post:
So, now you’re saying that a “combinatorial antibody defense system” is not necessary for a population’s survival, after all?
But this simpler system, called “innate immunity”, is basically what non-vertebrates have! (Lampreys and hagfish are kind of intermediate between nonadaptive and adaptive immune systems)
Adaptive immunity was added to the pre-existing system, which still existed in humans and other vertebrates. Really, you would know basic points like this if you actually read some of the science you criticize.
I am citing the scientific evidence, which answered each of the naive questions you just raised, long before you thought them up yesterday. You are ignoring the evidence, which your post demonstrates you know nothing about. I think everyone can see which of us is doing theatrics.
Comment by nmatzke — July 18, 2006 @ 4:29 pm
I think my posts are going in the spam buffer again.
Comment by nmatzke — July 18, 2006 @ 4:30 pm
Moderators note: There is no requirement to justify statements of opinion.
Note to moderator: the rules of engagement allow me to ask for justification. If someone fails to comply with my request, I see no rules violation in pointing that out.
Comment by ivy privy — July 18, 2006 @ 5:35 pm
Hannah wrote:
Miller represented science so well, the Kitzmiller decision exposes your claims about Miller misrepresenting and his lame cooptive mechanisims as completely bogus:Comment by alienward — July 18, 2006 @ 5:38 pm
Allen: I recall somewhere that Behe set forth his test that scientists must meet before he would be persuaded that his “theory” is worthless and he literally demanded that a “molecule by molecule” history of one of his “complex features” be proven.
I have seen Dembski make such a claim or at least one to that extent but have not found such a claim for Behe.
Salvador was kind enough to post this one earlier in this rather lengthy thread:
—
Calvin and Hobbes are alive and well in Darwinland
…
Professor Bottaro, perhaps sensing that the paper he cites won’t be persuasive to people who are skeptical of Darwinian claims, laments that “Behe and other ID advocates will retreat further and further into impossible demands, such as asking for mutation-by-mutation accounts of specific evolutionary pathways…” Well, yes, of course that’s exactly what I ask of Darwinian claims — a mutation-by-mutation account of critical steps (which will likely be very, very many), at the amino acid level. But that’s neither a “retreat” (In Darwin’s Black Box (page 176)I implied that many small details would be necessary for a real Darwinian explanation)nor is it unreasonable — that’s simply what’s necessary to actually explain the appearance of a complex, functional system in a Darwinian fashion, to show that it could indeed happen as Darwinists claim. Proteins change single mutation by single mutation, amino acid by amino acid, so that’s the level of explanation that is needed. What part of “numerous, successive, slight” is so hard to understand?
And not only a list of mutations, but also a detailed account of the selective pressures that would be operating, the difficulties such changes would cause for the organism, the expected time scale over which the changes would be expected to occur, the likely population sizes available in the relevant ancestral species at each step, other potential ways to solve the problem which might interfere, and much more. Alternatively, Darwinists could present a series of experiments showing that RM/NS is capable of building a system of the complexity of the adaptive immune system.
Professors Orr and Bottaro seem to think that because Darwinists’ fantastic claims are very difficult to support in a convincing fashion, then they should just be given a pass, and that everyone should agree with them without the required evidence.
…
—
Meanwhile, what evidence has Behe offered for any alternative hypothesis? Maybe he has some videotape of a new species being miraculously created.(?)
Comment by ivy privy — July 18, 2006 @ 6:32 pm
To IDists, this is EXACTLY what it looks like as well. Science conflicts with Darwinism. Enter some ‘just-so’ stories, invent some terms, and resort to ‘imagination.’ One of the two sides has got it right. Which side is it?
The putative argument here seems to be that since we can find a sort of ‘homology’ between certain biochemicals, then we are justified (and certain) in postulating intermediate steps linking one to the other. This is an assumption that needs to be demonstrated before it can be accepted. The moon travels around the earth, it shines, and it is round. The sun travels around the earth, it shines, and it is round. Therefore, there must be a way to get from ‘moons’ to the ’sun’. Is that how your argument goes? Harrumph.
Is this last statement a well-thought-out, Darwinist ‘proof’ of biological history, or is it simply an assertion? Is there ‘proof’, or is this no more than but supposition? You talk as if you’ve seen immune systems ‘evolve’ with multicellularity (which they still can’t explain very well) right before your very eyes.
The presence of an ‘immune system’ is necessary for a higher taxonomic species; an ‘adaptive immune system’ is simply better, but not necessary. It is easy to imagine that a vertebrate species could have added to itself an ‘adaptive immune system.’ However, it is unimaginable that a vertebrate species could exist without the presence of an immune system. Thus, the invocation of IC. The logic is not really hard to crank out.
Not much different? It’s hard to conceive of them being MORE different! Did they have scanning electron microscopes 100 years ago?
Is the logic this: since non-vertebrate species exist without an immune system, then vertebrate species can exist without them? But what we ‘know’ is that without them, vertebrates die. That we know. And we’ll never ‘know’ that they can live without them in nature. So why construct an argument on what is not known, rather than on what is known?
But, Nick, you don’t know that it was ‘added’. What you know is that that there are some vertebrate species which have an ‘adaptive immune system’, and some that don’t. Simply calling one a ‘pre-existing immunde system’, and the other an ‘adaptive immune system’, tells you nothing about how A went to being B. This is not some nit-picking, trivial point. Scientists should stay within the boundaries of what they actually ‘know’, and not confuse ‘assumptions’ with ‘facts’. Language is important.
Comment by Lino D'Ischia — July 18, 2006 @ 7:10 pm
Alienward:
Miller’s arugment is not cogent. And, unfortunately, Judge Jones is not a competent judge of that. And ‘exaptation’ is an invented word, completely bereft of any real significance.
Comment by Lino D\'Ischia — July 18, 2006 @ 7:17 pm
You try to represent sponge immune systems as primitive. Why? Because you think we’re dealing with poor little sponges that represent the “oldest” living phylum?
Origin of the Metazoan Immune System: Identification of the Molecules and Their Functions in Sponges
So Nick, you think a sponge can make it along without an immune system given it’s out there in yonder water with all those micro-organism floating through it? You think a vertebrate, like you, can get along without a combinatorial immune system or some reasonable facsimile? We have sadly millions of examples of immuno deficient humans to give you an idea of what happens without immune defense.
You continue to miss the point, whether the system is innate or combinatorial or whatever, without an immune system in place, a population is at risk, it doesn’t get a second chance if an epidemic breaks out. Bye-bye natural selection.
Salvador
PS
by they way, I didn’t see that article in your long literature list here:
http://www2.ncseweb.org/kvd/exhibits/immune/index.html
Is this because it’s embarrassing to find these “primitive” creatures with very sophisticated irreducibly complex immune systems already in place, possibly from the start? With sponges representing the “oldest” living phylum, that would kind of put a damper in arguments that immune systems evolved from a highly primitive state, since even the most primitive organisms have sophisticated immune systems already there. And that it further contradicts what’s written in most biology textbooks (echo Haeckel, echo Peppered Moths pasted on trees, echo racemic Urey-Miller monomers….)
You were saying, Nick?
Comment by Salvador T. Cordova, IDEA GMU — July 18, 2006 @ 7:40 pm
LOL. So Sal, are you willing to accept that article as authoritative? If you do, you and your allies here are totally sunk.
Comment by nmatzke — July 18, 2006 @ 8:04 pm
Only in as much as it supports my point, of course. :=)
Comment by Salvador T. Cordova, IDEA GMU — July 18, 2006 @ 8:15 pm
Someone has asked for evidence of my conclusion that Ken Miller has not refuted Behe’s discussion of the IC of the bacterial flagellum (thank you for the correct spelling.)
I suggest anyone who is interested in Ken Miller’s defense of the evolution of the bacterial flagellum go to his web site to evaluate for yourself how strong or weak the defense is. Here is the link
http://www.millerandlevine.com/km/evol/design2/article.html
I saw nothing that could be used as evidence other than a sub part of the flagellum may have existed by itself prior to the flagellum. His main claim is that there is another system that uses these pre-existing parts of the bacteria flagellum and that this refutes Behe’s IC claim is kind of “ ——–”. You fill in the blanks, “brilliant, rock solid, pathetic, evasive” are some possible examples.
For a critique of Miller’s testimony and Behe’s position, go to
http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=747
Essentially Miller says that if one sub part of a system has an alternative use, then this implies that the system is non IC. As I said is this the best that he could come up with.
Comment by J. Cosgrove — July 18, 2006 @ 8:26 pm
Given Behe’s definition, yes, if one subpart of a system has an alternative use, then that system is non-IC.
Why does Miller have to come up with anything better? Behe makes a claim. Claim is proven false. QED. Miller doesn’t have to beat Behe over the head with a sledgehammer with example after example after example. One counterexample is all that is needed. Then one can stop and go on to more interesting things.
Like real science.
If you claim “the square of a number can never equal itself”, and I point out that 0*0=0, are you going to demand more examples and say “harumph, one example is the best you could come up with”? You’re going to make me point out that 1*1=1, too?
Comment by Don Baccus — July 18, 2006 @ 8:43 pm
J. Cosgrove,
Behe said that IC systems had to arrive “in one fell swoop” because “any system missing a part was by definition nonfunctional.” Behe’s argument was wrong, e.g. with the flagellum, because the functional subsystems prove that, well, the system, missing parts — often many parts — remains functional. It’s a very simple point.
Again, changing your argument to “give me an infinitely detailed evolutionary model” is (1) moving the goalposts, (2) tacitly accepting that Behe’s argument against the evolution of complex systems was flawed, without being forthright and admitting it, (3) demanding the impossible from biologists, and (4) putting yourself into the same reality-proof box that Behe is in, where evidence doesn’t matter and the painstaking work of hundreds of researchers is dismissed with mere rhetoric.
Which gets us back to the immune system…
Comment by nmatzke — July 18, 2006 @ 8:53 pm
I suggest that those students interested in the IC or non IC of the flagellum should go to the links provided and make their own conclusions. They should also make some conclusions about the rhetoric that takes place on this topic.
Good night, I have to build a website.
Comment by J. Cosgrove — July 18, 2006 @ 9:31 pm
Gotcha…
Comment by Nick (Matzke) — July 18, 2006 @ 9:55 pm
I think Salvador, in Behe’s words, aptly demonstrates the anti-science nature of ID:
Now, let us compare Behe’s demand for details with Dembski’s reply when asked to propose a model for the origin of an IC system via ID.
Taken together, these pronouncements from the two leading names in the ID movement amount to the approximately following: “Until science demonstrates every last minute detail we demand to see, we are justified in rejecting any scientific conclusions we dislike, regardless of the evidence that supports these conclusions. Fortunately, there’s no need to develop scientifically viable alternatives, because, after all, the designer works in mysterious ways.” Come to think of it, this approach does have a certain appeal - it’ll make doing science infinitely easier. ;)
However, I am curious as to why most ID proponents limit ID only to the world of biology. There are plenty of scientific disciplines where our knowledge is not absolute and therefore, if we were to follow Behe and Dembski’s logic, ID should be considered as a plausible alternative. We can’t trace the trajectory of every single molecule in a large container filled with gas: why not consider Intelligent Ensemble Design as an alternative to naturalistic statistical thermodynamics? We cannot possibly trace the motion of every single air and water molecule that goes into making an irreducibly complex hurricane, so why not teach the controversy about an Intelligent Weather Maker? I see no reason why Behe would argue against this, given that his standards of proof for Darwinian evolution is as realistic as the two examples above.
Comment by Leonid Meyerguz — July 18, 2006 @ 11:12 pm
Lino Miller’s arugment is not cogent. And, unfortunately, Judge Jones is not a competent judge of that. And ‘exaptation’ is an invented word, completely bereft of any real significance.
Three unsupported claims. Not bad. Btw exaptation is a real word.
Comment by PvM — July 18, 2006 @ 11:13 pm
Well, I didn’t use the word “primitive”, because any organism living today has been evolving for as long as any other one. But we can say that sponges are a basal branch on the animal tree, and that they lack many of the features found in the supposedly “irreducible” immune system of humans. Sponges have no adaptive immunity, none of the B-cells, T-cells, etc. And they get along just fine, like many other critters. But, like I said as my original point, they do have amoeba-like cells that crawl around and eat bacteria etc., and this is fundamentally what the vertebrate immune system does also, but with a huge detection/tagging/communication network on top of it.
Here is what I said, which both you and Lino eagerly jumped on:
Sal jumped on the “primitive” interpretation, and Lino said:
Well, to see who is right, let’s look at the actual article that Sal just cited. In their historical overview of the comparative immunology of sponges, the authors write that it was Metchnikoff who started off this whole comparative study of sponges with the immune reactions of other animals:
Metchnikoff? Check. Phagocytosis? Check. Bam!
Moving on to some other recently-posted sillyness — Lino writes,
You think this because you completely ignore the huge body of technical work, some of which I have posted here, that has explicitly tested and confirmed evolutionary hypotheses. You want to see speculative, undocumented, untestable, and horribly vague “just-so stories”? Your model, “IDdidit”, is the biggest irresponsible “just-so story” ever told. It’s you ID guys that are really the ones “jumping in the magical box with Calvin and Hobbes” (as Behe puts it) to explain things. “Poof!” That’s the entirety of your “scientific explanation.” And you want scientists and educators to take you seriously? Get real.
This is the kind of ignorant no-nothingism that drives real scientists nuts. Finding homology (it does not belong in scare quotes) is not a matter of squinting and looking for vague similarities. Molecular homology is detected by looking for similarity in DNA or amino acid sequences. Genes duplicate and diverge, but they retain numerous detailed similarities in sequence, often for hundreds of millions of years. This similarity is quantified, statistically measured, and compared to null models to rule out false inferences of homology that might occur by random similarity. Every scientist who has ever worked with a gene sequence, a genome, the human genome, or bioinformatics generally — hundreds of thousands of scientists — uses these basic, routine techniques every day. The whole field of bioinformatics, and the entire massive architecture of genome databases and places like the NIH’s National Center for Biotechnology Information, which hosts PubMed, is based on homology. Massive effort has been put into methods for determining the reliability of sequence homology inferences.
In other words, you have no idea what you’re talking about, and what you are saying is the equivalent of saying that the periodic table of elements is just some random person’s loose guess at how things work, and not realizing it is the basis for the whole field of chemistry.
More silly “Were you there?” argumentation here. But getting back to the point, you guys were all initially arguing that organisms couldn’t exist without the adaptive immune system. But this is disproven by the existence of organisms that get by just fine without adaptive immune systems. This is a fact well-known to everybody who talks about immunology, except creationists, apparently.
How do we know the ancestor of vertebrates had an innate immune system? With cladistics. Key pieces of the innate immune system found in vertebrates are shared with their non-vertebrate relatives. In order of increasing distance from vertebrates, and leaving out some obscure groups, these are roughly lampreys, hagfish, cephalochordates/urochordates (which comes first is in dispute), echinoderms, “protostomes” (insects, molluscs, etc.), cnidarians, sponges, choanoflagellates (these are protozoans (!) that are sometimes colonial), fungi…I’ll stop there. Innate immunity is shared between vertebrates and all of the groups out to at least protostomes (and perhaps further, depending on how one defines things). Thus we can conclude with high statistical confidence that the common ancestor we share with protostomes also had the immune system molecules that we share. The basic facts are reviewed here: http://www.talkdesign.org/faqs/Evolving_Immunity.html …in the comparative section. The sponge paper Sal just referenced indicates that some of these molecules trace back even further.
If, as I suspect, your real problem is that you just don’t accept common ancestry at all, then this whole immune system discussion is really pointless, and you need to go read this instead.
Unfortunately for you, Behe specifically invoked the rearranging receptors of the adaptive immune system explicitly as an IC system. Changing your argument to say, “Well, maybe that system that Behe said was IC actually evolved, but you still haven’t explained the origin of this other part of the immune system” is shifting the goalposts, and tacitly admitting that Behe’s original argument has failed you. As Behe says, once we’ve explained one of his systems, then the IC argument is toast. It is utterly unconvincing to just switch to something else in the hope that your opposition won’t know enough about it to rebut you (in fact, we know plenty about the earlier evolution of the immune system before the adaptive immune system, see e.g. Matt Inlay’s section on “The origin and evolution of the complement system“).
Lampreys are vertebrates that lack the adaptive immune system shared by other vertebrates, which I guess is what you are talking about here. They get by fine. The group that includes sharks — the next most basal vertebrate group — have rearranging receptors, but I believe they are only expressed during development, and so they cannot develop an immunological memory to a vaccine like mammals can (IIRC). And I vaguely recall that various vertebrates have lost chunks of their adaptive immune system, especially if they are tiny, have high populations, and are not social (but my memory fails me here). But just with lampreys and sharks, we have proved that vertebrates very well can exist without the “textbook” adaptive immune system, and the phylogeny says they did so.
But furthermore, it is ludicrous to imply, as you do, that a vertebrate fish would absolutely require an adaptive immune system, whereas a squid or other cold-blooded, aquatic creature in a similar ecological niche would not.
It is also important to know something about a field before you brazenly declare that it is bunk and the thousands of people spending their careers in it are frauds. As I mentioned above, there is a completely standard method in evolutionary biology to figure out what arose when in a phylogeny, and that is to see which features are shared. This can be implemented quantitatively and statistically if necessary, although we have a very simple case here (innate immunity is widely shared, adaptive immunity is restricted to vertebrates minus lampreys and hagfish). One of the terms for this set of methods is “phylogenetic inference”, which you should this handy educational page on it from the U.C. Museum of Paleontology.
Nick
PS: Since I think I’ve said my piece here for the time being, let the record show that none of the creationists here have rebutted any of the literature that has been cited on the evolution of the adaptive immune, no one has explained how the scientists were able to predict the existence of these specific transposons without the transposon hypothesis, and the various attempts by the creationists to critique the transposon model consist only of (1) accusing the scientists of “bluffing” and obfuscating that the scientists have a tested model and published research, and the ID/creationists don’t, (2) changing the topic and moving the goalposts to impossible places, or (3) making poorly-thought out, incredibly poorly-researched objections that are directly contradicted by well-known facts of comparative immunology.
Keep in mind that all of this is for “the best” argument the IDists think they have, irreducible complexity.
Comment by Nick (Matzke) — July 18, 2006 @ 11:26 pm
PvM:
Not claims; educated opinions. And, as to exaptation, it is a real word with no real meaning.Comment by Lino D'Ischia — July 18, 2006 @ 11:28 pm
Arrgh. Another long post in the spam buffer.
Comment by njmatzke — July 18, 2006 @ 11:30 pm
Lino: Not claims; educated opinions. And, as to exaptation, it is a real word with no real meaning.
So you claim and yet I see no evidence of an educated opinion and thus ask you to support your claims (or we can reject them).
From Wikipedia: An exaptation is a biological adaptation where the biological function currently performed by the adaptation was not the function performed while the adaptation evolved under earlier pressures of natural selection.
From referenceDOTcom
1 entry found for exaptation.
ex·ap·ta·tion Audio pronunciation of “exaptation” ( P ) Pronunciation Key (gzp-tshn)
n. Biology
The utilization of a structure or feature for a function other than that for which it was developed through natural selection.
[ex- + (ad)aptation.]ex·apted adj.
ex·aptive adj.
Source: The American Heritage® Dictionary of the English Language, Fourth Edition Copyright © 2000 by Houghton Mifflin Company. Published by Houghton Mifflin Company. All rights reserved.
Quod Erat Demonstrandum
Hope you do better on your other two claims. Somehow, I have my doubts
Comment by PvM — July 18, 2006 @ 11:35 pm
Lino D’Ischia writes,
Therefore, most scientific terminology, which is invented to describe discoveries not known when the English language originated centuries, is bunk. Let’s toss out “DNA” and “black hole” while we’re at it.
You have no idea what you are talking about, and you can’t expect anyone to take you seriously if you just make wild, unsupported assertions.
The judge in Kitzmiller figured out the meaning of the word just fine:
So why should we listen to your absurd, unsupported claim?
Comment by njmatzke — July 18, 2006 @ 11:37 pm
I meant to say, “when the English language originated centuries ago“…
Comment by njmatzke — July 18, 2006 @ 11:38 pm
OK, last note. Back on the sponge article, I should have added this quote on the Metchnikoff/sponge point:
Comment by njmatzke — July 18, 2006 @ 11:41 pm
Because statistical mechanics does not make claims that it can create specified complexity through stochastic processes, thus statistical mechanics is consistent with ID conceptions.
Natrualistic evolution in contrast effectively argues combinations of weakly specified stochastic processes and determistic processes can create specified outcomes. This is inherently self-contradictory and the search for square circles.
It is pointless to say that given a probabilty distribution of 50/50 for each coin being heads, a stochastic process constrained by such a distribution will generate all 500 coins tails in the next trial or even once in many trials. Naturalistic evolution (particularly abiogenesis) can be shown to be making claims comparably outrageous. In contrast, a statistically mechanical description would do no such thing.
For example, I described how to relate the outcomes of such a 50/50 distribution for each coin in terms of statistical mechanics with Shannon Entropy (which is akin to Boltzman’s) here. In the case of 500 coins, the Shannon Entropy, H would equal 500 bits. With inspection of that level of entropy, expecting 500 coins to appear all tails even once in several trials would be inconsistent with that level of entropy, however, if I said something like “about 50% will appear tails”, that statement would be consistent with the entropy of the system. And that is consistent with ID conceptions.
Thus your characterization is highly inaccurate. IDers with any mathematical or physics acumen would find your suggestion non-sensical, and therefore it would be unjust of anyone to impute we might ever consider such a mis-conception. I think unjust to say IDers are anti-science for pointing out the fact it is the proponents of naturalistic evolution that are practically botching conceptions of statistical mechanics. It is they who are not only anti-science, they are anti-mathematics and anti-information science.
It’s frustrating to IDers to watch the willful refusal amongst proponents of naturalistic evolution to realize their enterprise is inherently doomed from a mathematical and information science perspective.
Comment by Salvador T. Cordova, IDEA GMU — July 19, 2006 @ 1:02 am
Sal: It’s frustrating to IDers to watch the willful refusal amongst proponents of naturalistic evolution to realize their enterprise is inherently doomed from a mathematical and information science perspective.
Again lacking in supporting logic and contradicted by empirical data and information theoretical considerations.
Proof by assertion never worked Sal. But I appreciate your attempt.
Natrualistic evolution in contrast effectively argues combinations of weakly specified stochastic processes and determistic processes can create specified outcomes. This is inherently self-contradictory and the search for square circles.
Remember that specified merely means ‘with function’. We should not be tempted by confusing the concept of ’specification’ as used by ID with ’specifies’ which suggests an a priori specification of the outcome.
Of course such a conflation of terms may lead one to suggest that it is self contradictory. Once one realizes however the differences in meaning, it is trivial to show how processes of regularity and chance can create complex specified information.
Shannon information in the genome can be shown to trivially increase under these processes.
Simple.
And yes, I can back up my claims
Comment by PvM — July 19, 2006 @ 1:28 am
Btw the information in 500 Heads is 500 bits, which is equal to the reduction in entropy from its maximum value under a uniform distribution to the minimum value when all values are Head.
Shannon information is no friend of ID
Comment by PvM — July 19, 2006 @ 1:33 am
Salvador wrote:
Perhaps once you or some other IDer can produce a definition of “specified complexity” that is mathematically rigorous, computationally feasible, biologically relevant, and amounts to more than vigorous hand-waving (ala Dembski) or painting bull’s eyes around darts that have already landed (e.g. conserved biological sequences), we can discuss whether biological evolution - which is far more complex than any stochastic process we can currently analyze or model in sufficient detail - can indeed produce this nebulous entity. Until then, you might as well point at a microstate in a thermodynamic system and marvel in awe of how improbable this microstate is, for no other reason than it being the only microstate you can observe.
But you’ve missed my point. I am not arguing that stat mech is a good analogy for evolution. I am saying that Behe’s demand for a mutation-by-mutation account of naturalistic evolution of the flagellum complete with selection coefficients for each one (which would require nearly perfect knowledge of the protein sequences and environmental conditions many hundreds of millions of years ago) is about as reasonable as demanding a particle-by-particle account of the dynamics of a highly complex thermodynamic system before he accepts “naturalistic” stat mech. (Hence, my hurricane analogy that followed.) In other words, his argument boils down to “as long as scientific knowledge isn’t absolute, we should just assume that a designer did it”. That, to me, is a profoundly anti-scientific stance.
Without a single, coherent definition of “specified”, the first sentence is not so much self-contradictory as it is word salad. Even if we had such a definition, without rigorous mathematical or computational analysis within the context of biologically realistic models, the above paragraph amounts to nothing more than a naked asserion.
It is even more pointless to try to determine the probability of getting any specific outcome of a series of coin tosses when you know nothing about the initial probability distribution at the start of the experiment, and are aware that this distribution can profoundly change both as a function of time and a function of previous coin tosses in ways that are exteremely difficult to characterize mathematically. It is even more pointless to try to compute these probabilities for a huge set of such experiments running simultaneouly, influencing each other in a myriad ways, both obvious and subtle. The outrageous claim here is that ID can derive such probabilities, when none of the ID-math even comes close to taking the complexities involved into account.
Believe it or not, there are thousands of scientists with extensive mathematical training doing biologically relevant research who do not seem to share the IDers’ frustration. We in the bioinformatics community, for instance, use evolutionary theory extensively and with considerable success in our work - yet ID has made essentially no inroads into bioinformatics, despite the field being relatively young and dealing with concepts that are supposedly ID-related. Perhaps our “inability” to realise that naturalistic evolution is “inherently doomed” stems not from our willful refusal to consider ID arguments, but from a deeper understanding of some of the actual problems involved? Just a thought.;)
Comment by Leonid Meyerguz — July 19, 2006 @ 4:16 pm
I’m afraid that misses the point. Statistical mechanics does not make claims of specific locations of molecules, but evolutionary theory does (relative to each other in a polymer or system). Thus Behe’s demand is reasonable. If a theory purports to explain the positioning of molecules, it better have, at least in principle, the power to do so. If they don’t know the exact conditions, in lieu of that, they could describe what those conditions would have to be in detail. In terms of:
1. ideal mutation rates
2. ideal population sizes
3. ideal seleciton pressures
4. ideal probablity distributions
They haven’t hardly even formulated what the ideal parameters must be much less considered real ones.
Perhaps, the most notable attempt at assuming ideal parameters, for example in mammal evolution, was Haldane’s 1957 paper The Cost of Natural Selection. It turned out even under the most ideal circumstances, certain evolutionary pathways were doomed. This has since been known as “Haldane’s Dilemma”, and it’s still unsolved….
Until the community even tries to list what the ideal parameters would be, they only project the appearance that they are content to avoid reasoned skepticism.
And there are IDer’s here with backgrounds in physics, chemistry, mathematics, computer scinece, and engineering. I don’t think we are being unduly skeptical given the skepticism we experience in our own disciplines.
Whether ID is true is a separate issue to whether the supposed mechanisms of evolutionary theory have elevated themselves to the level of other scientific disciplines.
I don’t meant to disparage the hard work of the scientists involved, but they are not yet at the level of other empirical disciplines, IMHO.
Whether ID will ever be in the future, is not my immediate concern.
Comment by Salvador T. Cordova, IDEA GMU — July 19, 2006 @ 10:25 pm
Sal, you realize Haldane’s conclusions were invalidated by later population genetics work, don’t you?
Comment by nmatzke — July 20, 2006 @ 12:08 am
Sal:
Here is an update on Halden’s Dilemma from the Talk.Origins website:
“Haldane’s “cost of natural selection” stemmed from an invalid simplifying assumption in his calculations. He divided by a fitness constant in a way that invalidated his assumption of constant population size, and his cost of selection is an artifact of the changed population size. He also assumed that two mutations would take twice as long to reach fixation as one, but because of sexual recombination, the two can be selected simultaneously and both reach fixation sooner. With corrected calculations, the cost disappears (Wallace 1991; Williams n.d.).
Haldane’s paper was published in 1957, and Haldane himself said, “I am quite aware that my conclusions will probably need drastic revision” (Haldane 1957, 523). It is irresponsible not to consider the revision that has occurred in the forty years since his paper was published.
ReMine (1993), who promotes the claim, makes several invalid assumptions. His model is contradicted by the following:
The vast majority of differences would probably be due to genetic drift, not selection.
Many genes would have been linked with genes that are selected and thus would have hitchhiked with them to fixation.
Many mutations, such as those due to unequal crossing over, affect more than one codon.
Human and ape genes both would be diverging from the common ancestor, doubling the difference.
ReMine’s computer simulation supposedly showing the negative influence of Haldane’s dilemma assumed a population size of only six (Musgrave 1999).”
So I guess you had better find a new problem to throw out there….
Comment by Mike Hannigan — July 20, 2006 @ 3:46 pm
Salvador wrote:
I think you are reaching for distinctions, Sal. You might as well say “stat mech doesn’t make any claims about human origins, but ToE does, so Behe’s demand is reasonable”. The key point is that Behe seems willing to accept naturalistic explanations of some phenomena in the absence of perfect knowledge, but demands perfect knowledge before he accepts (naturalistic) evolution.
Incidentally, evolution does not predict that specific genetic sequences must evolve anymore than stat mech predicts that specific microstates must arise in large systems. There is no evidence to suggest that the present-day evolutionary “mircrostate” - the set of genomes and proteomes comprising modern living organisms - is the only one possible, rather one of a combinatorially large number of possibilities that we simply got stuck with.
Most notable to creationists, perhaps. But oddly enough, population genetics has managed to make some progress in the last 50 years. Mike already pointed out the TO response to creationists’ touting the “dilemma”, but here’s an in-depth link explaining why there’s probably no dilemma after all.
Comment by Leonid Meyerguz — July 20, 2006 @ 5:33 pm
Wallace did not solve it. The issue is not simulatenous selection, but the cost issue (how many you have to give birth and kill to effect a fixation). Simultaneous selection of diverse traits in diverse individuals does not solve the problem. The fitness constants are also effectively superfluous to the issue of cost. Natural selection comes at a population cost, the rest of Haldane’s assumptions are relatively superflous to how many one has to kill to fixate a trait!
in contrast
Comment by Salvador T. Cordova, IDEA GMU — July 20, 2006 @ 8:00 pm
Quoth Salvador:
Haldane defines the cost of selection as the number of deaths due to selection that need to happen before fixation occurs. It has nothing to do with births. You may be thinking of genetic loads.
No, but it may render it irrelevant. If large numbers of alleles at different loci can be substituted simultaneously - and one of the nice things about sex is that it can help do exactly that - then even if the selective deaths must be spread out over a large number of generations for substitutions to occur, the average time per substitution can be decreased drastically. (e.g. Simultaneously substituting 10 mutations in 300 generations is 10 times faster than substituting them one-by-one.)
Only if the fitness constant is very small. For larger fitness constants, the simplifications Haldane makes in order to derive the cost of substitution become mathematically invalid.
One of the assumptions that isn’t superfluous is that most of the individuals killed in each generation due to selection are then resurrected in order to maintain a constant population size, which is needed by Haldane to make his calculations work. But I’m sure this assumption couldn’t possibly have any bearing on the applicability of Haldane’s model to real-world biology!
Comment by Leonid Meyerguz — July 21, 2006 @ 12:56 am
Somehow irony strikes again. When evolutionists show models like Avida, IDers object to its lack of relevance, and yet when ID shows a simplified calculation by Haldane, it somehow becomes a real problem for evolution.
Needless to say, Haldane’s Dilemma is as good as its presumptions which also limit its applicability. Not unsimilar to Behe and Snoke’s calculations…
Comment by PvM — July 21, 2006 @ 1:05 am
On “Gene Expression”, DavidB addresses the issue of Haldane’s Dilemma
n previous posts and comments I have mentioned Haldane’s Dilemma, and I thought it would be worth looking into the subject more closely.
The short answer to the question, ‘Should we worry?’, is ‘No’. But when was I ever satisfied with a short answer? The following is not intended as a casual read but (hopefully) a resource for those who are following up the subject via search engines. As usual, I claim no technical expertise in genetics, so don’t take my assertions on trust. Links and references are provided for those who want to explore the subject further.
Comment by PvM — July 21, 2006 @ 1:10 am
An example:
P. J. Darlington The Cost of Evolution and the Imprecision of Adaptation
PNAS | April 1, 1977 | vol. 74 | no. 4 | 1647-1651
Comparisons of six hypothetical cases suggest that Haldane overestimated the cost of natural selection by allele substitution. The cost is reduced if recessive alleles are advantageous, if substitutions are large and few, if selection is strong and substitutions are rapid, if substitutions are serial, and if substitutions in small demes are followed by deme-group substitutions. But costs are still so heavy that the adaptations of complex organisms in complex and changing environments are never completed. The rule probably is that most species most of the time are not fully adapted to their environments, but are just a little better than their competitors for the time being.
Comment by PvM — July 21, 2006 @ 1:27 am
Sal, instead of spending so much time and effort knocking down Darwinism why aren’t you and your fellow IDers investigating how ID explains things like the immune system? Or is it that ID is simply an argument against Darwinism and not a scientific theory in and of itself?
Comment by Dene Bebbington — August 9, 2006 @ 10:42 am