We went over the first six chapters of Dawkins’ Blind Watchmaker tonight; most of us, irrespective irregardless of our views on the evolution/design question, came to the conclusion he presented very little in the way of real arguments. The entire book reads more like a rhetorical exercise than any cogent justification of the assertions that are very freely made.
A brief summary of the major points made, as a springboard for discussion:
Chapter 1: Explaining the very improbable
This chapter sets the scene for later arguments; making the case that creationists aren’t the only ones awestruck by the beauty of nature, and staking out Dawkins’ own position. Our question: Are all biological systems really complex, and is it fair to say they have the appearance of design? Our general consensus was yes, though there was a strong dissent.
Chapter 2: Good design
The main part of this chapter is simply description of the marvelous complexity in nature, and the need for a special explanation, with the argument– natural selection is our watchmaker– limited to the last few pages. But, apparently because it is still meant to be introductory material, there is no backing for any of his statements there either.
Chapter 3: Accumulating small change
Here we look for the long-promised case for natural selection, but unfortunately Dawkins disappoints again. To show natural selection forms complex biological organisms, we have an example of artificial selection– a computer program with very little resemblance to natural selection at all– forming biomorphs that have no real resemblance to living things.
Chapter 4: Making tracks through animal space
We were grateful for some biological examples here, but the chapter would definitely be better with a bit less hand-waving.
Chapter 5: The Power and The Archive
Is Dawkins’ simplifying things to the point where it begins to loose all resemblance to the real world? On a positive note, he again brings in a small dose of actual empirical material in the end, though– again– we’re forced to imagine our own extrapolation between artificial and natural selection.
We’ll go through the rest of Blind Watchmaker during our next class, and touch on several interesting topics: origins of life, constructive evolution and and the highly questionable tree of life. And though we might not be able expect much in the way of interesting arguments from Dawkins, Prof. Provine has promised us a sound defense of evolutionary theory.
a computer program with very little resemblance to natural selection at all– forming biomorphs that have no real resemblance to living things
Professor McNeill — am I reading this right? Did you not point out to Hannah any of the ways the “biomorphs” do resemble living things?
Comment by Michael Hubl — June 29, 2006 @ 11:56 pm
Greetings Hannah,
This issue is somewhat significant. A major anti-design argument is to say, “biology does not even look designed, therefore much less can one argue it is designed.” This argument takes many forms, but most notably 2 forms:
1. “the bad design” argument.
2. “appearance is not quantifiable, thus it’s an unscientific observation” argument.
There are good answers to both. If the need arises, we can discuss it further. Please let me know.
Regarding, Chapter 3, were there students that were favorable to Dawkins argument? Even though you and I have our position, I would be curious if others found his argument convincing.
He relates his Weasel program to large-scale protein evolution, and such a claim is pre-mature, if not completely wrong. One of the fundamental flaws is that a probability of 100% is affixed to the likelihood that a selective feedback is actually available to guide the evolutionary process. That probability could be closer to 0% in the real world. The important point is that Dawkins assumes its truthfulness, he can not actually establish the probability is significantly above 0%. Dawkins, in effect (but quite subtly), appeals to the assertion he is trying to prove. His reasoning is circular in other words, but not overtly so.
Other incarnations of this Dawkin’s weasel are Adami’s Avida. Adami’s Avida has the same flaws as Dawkins weasel, but it is even more subtle! If anyone is interested, I can provide references to technical refutations of Weasel and Avida, and similar programs. We can also discuss it here if you feel it important.
Finally, I am glad you all are studying Dawkins’ book. His writings are quoted in ID literature almost as much as Darwin’s. I actually like his writing style.
Thank you for the very quick appraisal of what is transpiring in your class.
Salvador
PS
For your edification, “irrespective” I believe is the proper term, not “irregardless”
Comment by Salvador T. Cordova, IDEA GMU — June 30, 2006 @ 12:03 am
Dawkins disappoints, and it amazes me that he was taken so seriously for so many years. There are so many more thoughtful people on the evolutionary side, it is sad that Dawkins has come to be iconic for many.
I’m surprised that you dismissed the computer program so casually, as the computer simulation in the book was the one thing I thought was reasonable (much better than his other computer simulations, such as the weasel one that Sal referred to). The problem is that what it demonstrated was not anything that is really in controversy. In order for the program to work, there has to be a worked-out semantics of symbols geared toward the solution being solved. While there is truly Darwinian action occurring and accounting for the differences in the simulation, it is overwhelmed by the amount of teleology that must be imported for the program to have a reasonable expectation of working, and for the changes to be able to hit functionally interesting points.
The setting up of the search space is the much more interesting problem than the actual walking of it. To set it up so that it can “evolve” means that one must assign symbols that are of specific relevance to the situation being explored.
Comment by Jonathan Bartlett — June 30, 2006 @ 12:51 am
For your edification, “irrespective” I believe is the proper term, not “irregardless”
Especially as irregardless contains a redundancy, and is not an actual word. ‘Regardless’ would do.
Comment by avocationist — June 30, 2006 @ 1:05 am
In Chapter 3, Dawkins assumes that the initial state is functionally viable enough to start with. This scenario has its own problems.
Take the example of logins and passwords. There is no such thing as a partially working password. It’s either all or nothing. If someone is trying to hack an account by trying random passwords, they get no clue if they are “getting warm”. They have no feedback telling them they are only 1 letter off versus being 10 letters off.
Dawkins assumes that the final target is accessible through cumulative steps, that protein evolution is analogous to the Weasel illustration rather than analogous to the login/password illustration. The assumption may be false, it likely is.
Although it is true some proteins can easily be mutated by one mutation into another (nylonase evolution in our day is a good example), this tends to be the exception, and not the rule, especially for complex proteins.
If a complex protein requires simultaneously several specific amino acids, the analogy becomes more like the login/password illustration rather than Dawkins’ Weasel illustration. And early data suggests this is the case. However, to be cautious, it would be good to note both sides of the issue are throwing out probability numbers favorable to their position. But one thing is for sure, any sort of universal gradualism in protein evolution is far from being proven, and int the end it may in fact be false. We will see.
But in addition to the above considerations for just the evolution of functional proteins, it may be that evolution might not even have the chance to evolve!
For example, haemoglobin is life critical for certain organisms as it is vital to oxygen transportation. There may not be a chance for the organism to be searching for haemoglobin, because without haemoglobin the creature may be dead! This fact is true of any number of other proteins…..
Now one may argue that the above consideration therefore proves (albeit in a circular manner) that haemoglobin had to be non-life-critical at some point in the evolutionary process since it’s absence in the current organism is lethal. But this merely shifts the problem (or displaces it to uses Dembski’s words). In this scenario, the organism finds a way to re-architect itself such that a formerly non-life critical protein becomes a life-critical protein. But then, is this not possibly a more difficult problem than the one that was originally posed?….and so it goes, fixing one problem invites the creation of more.
(You may possibly recognize the arguments being made as Behe’s Irreducible Complexity argument. The fixing of one problem at the cost of creating more is Dembski’s displacement theorem at work.)
Comment by Salvador T. Cordova, IDEA GMU — June 30, 2006 @ 3:58 am
I should clarify, perhaps. Our issue was more that the program scarcely resembled natural selection, and that many (most) interesting an important aspects of living creatures were missing. I’m sure biomorphs resemble living things in some ways, but I’d classify them as extremely poor analogies.
Not really, those defending evolution were probably more vocally against it then anyone who disagreed with his premises. The one suggestion that the chapter might not be all bad was that perhaps it was only meant to show how accumalation of small change worked, and nothing further.
Regarding chapter three the book “Natural Selection in the Wild” was recommended as something actually dealing with biological N.S., but none of us have read it yet.
Thanks! I shouldn’t write when I’m too tired to think :).
Comment by Hannah — June 30, 2006 @ 7:28 am
Oh, don’t blame Allen– he had to be away, so Prof. Provine led our discussion.
But if you feel strongly about this, would you explain why I (and all of us) ought to have been more impressed?
Comment by Hannah — June 30, 2006 @ 7:38 am
Comment by PvM — June 30, 2006 @ 7:59 am
Something that often surprises me is how many people take popular science books as if they are actual technical works in science. A fair bit of the sheer confusion about the issues on the ID side (and some on the evolution side, especially from non-scientist commentators) can be attributed to this factor. You are basically criticizing Dawkins for daring to use analogies to get his point across instead of giving you a technical monograph on each issue. What did you expect from a popular science book?
If you want to learn about the evolution of protein-protein binding sites — which by the way are a quantitatively variable trait that is very easy to evolve, contra Salvador, who is basically a young-earth creationist cheerleader for the ID movement and will prove a consistently unreliable guide on the science — go study the evolution of binding sites in immune system antibodies. Highly specific binding sites evolve every day. This is how you acquire immunity to diseases in vaccines.
IMO, the real point to catch in Dawkins is how he mixes together his theological argument for atheism in with his empirical argument for natural selection. The reason he builds up “appearance of design” so much is that he wants to tear it down later, and take theism down with it.
Although you won’t know it from reading Dawkins and the ID guys, there are other ways of looking at the issue of complex adaptation in biology than the “appearance of design” view. In my view, biology has the “appearance of design” in the same way that the earth has the “appearance of being flat.” The “appearance” for each case is actually very superficial, and disappears completely once you have a significantly broad perspective.
Dawkins might agree with this if he thought about it, but he is really conducting an apologetics argument for atheism instead of just sticking to the science, and both atheist and theist apologists find it handy to take “appearance of design” as a given.
Comment by Nick (Matzke) — June 30, 2006 @ 10:08 am
On the issue of hemoglobin (4 subunits, 2 alpha, 2 beta) — Behe, of all people, says in Darwin’s Black Box that a reasonable scenario for its evolution exists, and that it is not one of the cases that cries out for a design explanation.
Just keeping you on your toes, Sal…your own side has conceded hemoglobin already.
Comment by Nick (Matzke) — June 30, 2006 @ 10:28 am
We just expected logical arguments, I guess, and didn’t find them. But certainly Dawkins’ faults don’t necessarily imply anything about the vacuity of evolutionary theory; a claim may be supported by numerous volumes of empty rhetoric and still be valid. We will– I hope– get to more interesting treatments of evolution soon.
Comment by Hannah — June 30, 2006 @ 10:29 am
Dawkins’ argument in Chapter 3 is completely bogus. I’m delighted that the class(?), or at least Hannah, picked up on that.
The whole of Chapter 3 is an effort on Dawkins’ part to overcome the need of teleology (artificial selection, if you will) in reaching a specified form. After going on for twenty pages about his Biomorph Land program, Dawkins ditches the entire thing so as to evade the limitations of the program. Having jumped directly into the probability space the program spawns, he then merely conjectures that if each ’step’ in the right ‘direction’ were ‘rewarded’, then you can ‘walk’ through this probability space and go from an insect to a fox in a small number of easy steps.
This is mere evasion. How can one take a ’step’ in 9, or 11-dimensional space? How does one ‘reward’ the correct ’step’? And if you invoke ‘direction’, you have implicitly invoked teleology–which the avoidance of was the whole point of the chapter.
Comment by Lino D\'Ischia — June 30, 2006 @ 10:37 am
Nick Matzke comments on the immune system and how antibody sites can mutate. Is Matzke sure that there is NOT an algorithm within the cell’s DNA which directly brings these kinds of mutation about? In other words, how do we know that this isn’t a case of the body directing–using a measure of randomness–the antibodies to change so as to counteract an antigen? This example, IMO, is more a demonstration that the mutations that cells themselves (not artifically induced mutations) bring about are ‘purposeful’, and, speaking of ‘appearances’, only ‘appear’ to be random–much like the sun appears to revolve around the earth.
Comment by Lino D\\\'Ischia — June 30, 2006 @ 10:55 am
“We just expected logical arguments, I guess, and didn’t find them.”
It seemed to me that you were complaining about Dawkins using analogies to explain his concepts, (and he is usually quite careful to detail the limitations of his analogies, although the IDists consistently ignore this) whereas you would apparently prefer that Dawkins write an upper-level biology textbook or a dry technical monograph.
Dawkins’s Climbing Mount Improbable (1996) focuses more on biological examples, e.g. the wasp-fig relationship, origin of flight, etc., perhaps the class should have read that, or more specifically the scientific papers by others, which he popularizes in the 1996 book.
Comment by Nick (Matzke) — June 30, 2006 @ 11:03 am
I laugh at myself then because IDers like me have spent large amounts of time trying to refute Dawkins Weasel program. There are other programs out there that are more sophisticated, like Avida, which require sophisticated refutations. I mention Avida, in case it is ever thrown out at you all.
Let me at up front say, I do not personally accept common universal ancestry, and from a scientific standpoint there is good reason to doubt it in certain areas.
However, if I may plead one area of caution, of all the arguments in BlindWatchmaker, I would regard this arguments for common ancestry as the strongest.
But first, we cannot confuse Darwin’s theory of natural selection with the “doctrine of common ancestry” (Karl Woese’s term). Though they are related, they are not the same.
The Doctrine Common Ancestry actually had acceptance before Darwin. I believe Lamark and Buffon were the early adherents. In fact the idea of Natural Selection was a creationist conception before Darwin, and was promoted by creationist Edward Blythe.
Origin of Species was written to dispute the idea all species were special creations, but descended from (a possibly created) progenitor. One sees this clearly in Chapter 14. Some quotes:
of note, Darwin seemed suggest he may have accepted the first life was created (but I leave the interpreation open, I can only provide a quoatation):
Darwin argued then that the primary (not sole) mechanism to facilitate common descent (an evolutionary idea) was natural selection (a creationist idea).
Natural selection as the sole mechanism and even primary mechanism I believe has been soundly refuted theoretically (I can hear the jeers now!). There are very sound non-ID arguments, the most readable was by Cornell Geneticists John Sanford in his book Genetic Entropy and Australian Geneticist Michael Denton in Evolution a Theory in Crisis.
But refuting Natural Selection (NS) as the mechanism for evolution does not completely remove the question of common ancestry and the “Tree of Life”.
The intelligent advocates and sympathizers are split over the issue. Those sympathetic to common ancestry would be Behe, Dembski, Denton, Davison, and others. Those who are skeptical would be Paul Nelson, Jonathan Wells, and many others. But even then, the modern day individuals who accept special creation might properly be called “Polyphyletic Hyperevolutionists” because they do accept a large degree of high-speed preprogrammed evolution for certain kinds of creatures (for example, foxes, dogs, wolves, jackals are argued to have a common ancestor).
There severe difficulties for common ancestry based on morphology (and the arguments there are very sound). But that is not necessarily the case for arguing common ancestry at the molecular level.
There are reasons for rejecting common ancestry for cellular evolution and maybe slightly beyond (Woese and Gordon), however, further down the tree of life it starts to look compelling. I would simply urge caution before rendering the hypothesis untenable.
Again, I personally do not accept common ancestry, nor human evolution, but the best minds among those who share the view that humans had independent origins, recognize there are substantial (but not insurmountable) issues regarding molecular similarities between humans and other primates.
Dispassionate and good science invites us to entertain evidence contrary to our personal inklings. I think Dr. Todd Wood (bio-informatics and student of one of our beloved GMU IDEA speakers, Dr. Gordon Wilson) does a good job of that. He shares his views (both scientific, philosophical, and theological) here:
(pdf version) The Chimpanzee Genome and the Problem of Biological Similarity
(html version) The Chimpanzee Genome and the Problem of Biological Similarity.
If one thinks independent origins of humans is more viable than evolution, I hypothesize the similarity is part of the architecture which was placed by the Designer to facilitate scientific inquiry (a theory which echoes of the thesis of Privileged Planet). This is the advanced ID topic of Steganography, and it may have serious scientific and medical potential. Ah, but let as save that discussion for another day!
Comment by Salvador T. Cordova, IDEA GMU — June 30, 2006 @ 11:07 am
Are you seriously suggesting that the mutations in antibodies in immune system cells are somehow guided by foreknowledge of what the proper binding site shape for a given virus protein will be? Unless the mysterious Intelligent Designer is intervening directly every time someone develops immunity to a virus it is hard to see how this could even work.
Suffice it to say that if the process worked as you suggest, someone would have won a Nobel Prize in Medicine for it. But what actually happens is that your body produces millions of immune system cells every day, each with different receptors, and when a new pathogen invades, by chance a few of the receptors will bind to the pathogen at moderate strength. These cells then replicate, continuing to mutate the receptor, and stronger and stronger binding evolves, until you have an antibody with very high specificity. This process of selection eventually produces high-specificity binding but billions of cells fail on the way.
Various features of the immune system increase receptor diversity and mutability but this is much different than some teleological notion of “guided” mutation.
The meaning of “random” in scientific vs. popular language is another issue worth addressing — basically in science “random” just means statistically variable, like the amount of rainfall a city will get on July 4 — whereas in popular culture it means “unpurposeful” or “meaningless” or something else. These are two totally different things, which the IDists continually confuse, but I am going on vacation…
Comment by Nick (Matzke) — June 30, 2006 @ 11:17 am
Salvador wrote
Salvador here repeats a common canard about Dawkins’ WEASEL illustration. As Dawkins himself notes in his description in The Blind Watchmaker, that illustration is not of evolution in general, but of the power of cumulative selection to amplify probability. That leaves open the question of the process of cumulative selection, which is in fact what Behe’s so-called “irreducible complexity” attempts to deny.Salvador further wrote
This is false. There is a fundamental difference between WEASEL and the Avida platform, the difference being in how the fitness function is implemented. In WEASEL there is an explicit reference to the “target” string in calculating the fitness of a member of the population — fitness is distance from the target string. Quite obviously, that’s not how evolutionary theory defines fitness. In the Avida platform there is not reference to some target in calculating a replicator’s fitness. In Avida a replicator’s fitness is dependent on performing behaviors in an environment that selectively rewards some behaviors and not others. That is the same kind of fitness function that characterizes the natural world. In the natural world, some behaviors, processes, and structures are selectively advantageous in a given environment and some are not. Dawkins’ WEASEL program and Avida are quite different in this respect.Salvdor later wrote
Yup, the discussion there is about evolution, not abiogenesis. Every evolutionary trajectory starts with a viable population, a population of (more or less) successful replicators. When one discusses theories of the viscosity of liquids one seldom imagines that one is criticizing those theories by saying that they assume the existence of liquids.RBH
Comment by Richard B. Hoppe — June 30, 2006 @ 2:06 pm
Is Matzke sure that there is NOT an algorithm within the cell’s DNA which directly brings these kinds of mutation about?
Maybe there is an algorithm in the sky that brings about rain so crops can grow. Or a consortium of “intelligent designers” who make that happen when want do. How can we be sure? And what difference does it to meteorologists whether we are sure or not?
This sort of “argument” brings us back to the first day of class and the uselessness of positing “mysterious alien beings” acting behind the scenes for unknowable purposes.
recognize antigens and we will discuss that evidence until the cows come home.
Comment by Susan Percell — June 30, 2006 @ 2:07 pm
If one thinks independent origins of humans is more viable than evolution, I hypothesize the similarity is part of the architecture which was placed by the Designer to facilitate scientific inquiry
Huh? Is this some kind of an inside joke?
Comment by Susan Percell — June 30, 2006 @ 2:11 pm
“Are you seriously suggesting that the mutations in antibodies in immune system cells are somehow guided by foreknowledge of what the proper binding site shape for a given virus protein will be?”
There is considerable evidence that immunoglobulins at the very least know _where_ in the immunoglobulin changes are likely to be beneficial (and even the fact that it needs to be on an antibody gene is direction), and I think there are even introns which specifically point the mutational mechanism to these places. In addition, there is evidence that upon recombination of the V, D, and J segments, that the cell’s system is smart enough to know what nucleotides it needs to insert at the joints in order for the immunoglobulin to function properly, and can do so by either base pair recombination or by the addition of N elements. See Sans and Capra “VK and JK gene segments of A/J Ars-A antibodies: Somatic
recombination generates the essential arginine at thejunction of the variable and joining regions”.
I don’t have specific references for the somatic hypermutation of immunoglobulin, but a pubmed search for the term should bring it up, as well as an author search for Blanden or Steele.
“The meaning of “random” in scientific vs. popular language is another issue worth addressing — basically in science “random” just means statistically variable, like the amount of rainfall a city will get on July 4 — whereas in popular culture it means “unpurposeful” or “meaningless” or something else. These are two totally different things, which the IDists continually confuse”
This is incorrect. In standard evolutionary theory, randomness refers to the idea that whether or not a mutation occurs is not related to whether or not it is likely to be beneficial. Here’s what Berkeley’s evolution site has to say:
“In this respect, mutations are random—whether a particular mutation happens or not is generally unrelated to how useful that mutation would be.”
I have not finished reading this one yet, but a good paper on the subject is Eble’s “On the Dual Nature of Chance in Evolutionary Biology and Paleobiology”.
Comment by Jonathan Bartlett — June 30, 2006 @ 2:29 pm
I’m sure biomorphs resemble living things in some ways, but I’d classify them as extremely poor analogies.
Thanks for the clarification, Hannah. I think “extremely poor” is rather harsh. Do you think the papers should not have been published in Nature or Science? My impression is that the papers were rather well-received by most professional scientists in the field. They have not been retracted. Are Cornell’s evolutionary biologists disappointed with the quality of the papers?
By the way, I addressed your strange statement about scientists not “proving” things in the other thread. You may want to consider “clarifying” that statement as well.
Comment by Susan Percell — June 30, 2006 @ 2:31 pm
Susan —
I think you should read up on some of the more recent literature which shows algorithms in a cell’s DNA which brings beneficial mutations about. See for instance Barbara Wright’s “A Biochemical Mechanism for Nonrandom Mutations and Evolution”. In many cases the secondary structures formed by single-stranded DNA points the cell to the best potential locations to make changes.
Comment by Jonathan Bartlett — June 30, 2006 @ 2:33 pm
I’m trying to stay out of the way and let the class participants dominate, but as an observer, I have a question: What do you mean by beneficial mutation algorithms? Is that something like “Directed mutagenesis?” … either way, the way I understand what you’ve said, it sounds very Lamarckian.
Comment by Dan — June 30, 2006 @ 2:56 pm
Greetings Nick,
(Though we are on opposite sides of the issue, my regards to you. Good to see you….)
I have the Darwin’s Black Box (1996), and looked in the index for Hemoglobin. I returned paged 11, 174, 206-207, 225. I did not see any reference to him conceding anything about Hemoglobin. I point out Behe is sympathetic to Front Loaded Evolution (over special creation). That implies the intelligent design was loaded into the first organism (or organisms) and that evolution proceeded, independent of natural selection. So “evolution” in his case does not necessarily mean “no ID anywhere”.
I point out Behe submitted a Peer Reviewed Paper with Dave Snoke in 2004 in Protein Science that talked about complications with hemoglobin evolution in far more detail than I did.
Selectively neutral means it is not visible to Natural Selection (just like the password illustration), thus potentially invalidating Dawkins analogy. Behe and Snoke outline other routes that should be explored beyond their initial paper, but the preliminary conclusion is not favorable to Dawkins Weasel. We will see, they leave the issue open for future investigation.
There has been a LOT of back and forth over this paper. I think there has been a lot of mischaracterizations and uncharitable renderings of Behe’s paper and his comments in the aftermath. I simply invite the reader to hear the arguments. The issue is not over, and is far from settled.
So in conclusion, I think it was premature to claim Behe conceded hemoglobin.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — June 30, 2006 @ 2:59 pm
The immune system example Nick cits is an inappropriate illustration for neo-Darwinian evolution. Here is a link to an essay discussing why:
Finally Nick says something about me:
No one should cite me as a guide or authority, and I do not claim to be one. And if I’m spreading bad information, Nick and friends are invited counter my arguments rather than discussing my affiliations, motivations, and supposed un-reliability.
But if Nick is trying to warn the readers that I promote subversive and heretical ideas, I don’t deny that. :=)
Comment by Salvador T. Cordova, IDEA GMU — June 30, 2006 @ 3:53 pm
In many cases the secondary structures formed by single-stranded DNA points the cell to the best potential locations to make changes.
In bacteria, the chromosome is in the form of supercoiled double-stranded DNA. Where the helix is broken and single-stranded regions are exposed, the DNA needs to be repaired (so both strands can be replicated according the semi-conservative mechanism of replication first postulated by Watson/Crick and proved, as anyone will tell you, by Frank Stahl).
The cellular proteins which “repair” DNA are relatively mutagenic, i.e., they do perfectly repair the damage and on occasion the cell’s genome is changed. Is this the “algorithm” you are referring to?
Claiming that the site of damage “points the cell” to repair the damage is like claiming that a cut “points our bodies” to cause our blood to clot there. That is a rather confused way of talking about biology, especially in a thread which purports to point out allegedly deep flaws in papers by people who are taken very seriously by the world’s professional scientists.
Comment by Susan Percell — June 30, 2006 @ 3:57 pm
And if I’m spreading bad information, Nick and friends are invited counter my arguments rather than discussing my affiliations, motivations, and supposed un-reliability.
Were you joking in your earlier thread when you said that “the designer” made certain life forms in a particular way in order to give scientists something to study?
If it was a joke, I didn’t think it was very funny. I really don’t get it.
If it wasn’t a joke, I am curious to know what you think that comment added to the discussion about the science biology.
Also, motivations are important to understanding the form that particular arguments take and why certain things are stated in certain ways. We’ve seen that here already in the past two days (e.g., the idea that scientists don’t “prove” things, etc.). With respect to Professor Behe, he admitted under oath that he already knows who the “intelligent designer” is: it’s his deity.
Given that information and given the well-known regard people have for their deities, it is difficult to take Behe or his disciples seriously when they claim that the identity of the designer is irrelevant to their claims.
You’ll need to forgive us “intelligent design” skeptics for not forgetting that fact.
Comment by Susan Percell — June 30, 2006 @ 4:07 pm
Salvador writes:
Stenography, contrary to Salvador’s assertion, is not an “advanced ID topic”. It has existed as a sub-topic of cryptography long before the emergence of the ID movement, and the emergence of ID has had virtually no influence on the field.
I am assuming that by ID-stenography, Salvador is referring to Bill Dembski’s recent suggestion that DNA sequences - especially the non-coding regions - might contain stenographically coded messages placed there by the designer(s). Well, the research area is so advanced that, to my knowledge, it doesn’t actually exist yet. Even if we were all to agree that genomes were “designed”, I would still think that the idea has very little merit. Regardless of one’s view on evolution, we all agree (I hope) that genomes tend to mutate, and mutations would be likely to obliterate any carefully coded messages in DNA, especially if the said DNA does not have any other function. The idea that stenographic messages could be hidden within the genome seems to stem primarily from a lack of understanding - or perhaps an unwillingness to accept - that evolution happens.
Comment by Leonid Meyerguz — June 30, 2006 @ 4:19 pm
Salvador wrote
This is a red herring. In fact, Behe & Snope (available here) is pretty much irrelevant to Dawkins’ WEASEL program. Dawkins’ program is a demonstration of cumulative selection; B&S specifically disallowed selection for intermediates, and hence disallowed cumulative selection.RBH
Comment by Richard B. Hoppe — June 30, 2006 @ 4:32 pm
Oops. Make that “Behe & Snoke” above.
Comment by Richard B. Hoppe — June 30, 2006 @ 4:32 pm
Susan —
What happens is that semipalindromic sequences form stem-loop structures during transcription. The loops are the sites where mutagenesis often occurs. Also, I believe that nicking is often a tool used by the cell to induce mutagenesis on itself. If you have doubts as to the efficacy of this mode of evolution, you should read Hall’s “Adaptive mutagenesis: a process that generates almost exclusively beneficial mutations”. He was writing before Wright’s hypothesis, so he doesn’t include it. However, that essay gives an idea as to the beneficial nature of these types of changes.
I suggest you read Wright’s article. It’s available for free online. Just google for it.
And Wright’s information is not the only one. In fact, in 1999 a whole book of these was published by the New York Academy of Sciences, called “Molecular Strategies for Biological Evolution” (or something similar).
Comment by Jonathan Bartlett — June 30, 2006 @ 4:54 pm
If it takes ‘billions of cells to fail on the way’, then we’re dealing with a ‘random’ process. The more important question is what triggered all of this. Why don’t other human cells–having the same genome as the immunce system cells–mutate their proteins? Either something is ‘triggering’ the mutation of the ISCs (immune system cells), or something is preventing such mutations in the other human cell types, or both. All of this is suggestive of some kind of algorithm.
Let’s also note that the mutations process in ISCs is ‘goal oriented’; namely, the blocking of the receptor site for the targeted pathogen. Again, suggestive of an algorithm.
Comment by Lino D'Ischia — June 30, 2006 @ 5:32 pm
Your post is a highly uncharitable rendering of what I said.
Any one sufficiently familiar with ID conceptions would know the phrase “the advanced ID topic of Steganography” could not possibly imply any claim that Steganography originated with ID, rather it refers to Steganography being applied within the exploration of ID.
You apparently understood that was context as evidenced by your second paragraph. Nevertheless, through Equivocation, you decided to attribute assertions to me which I do not make nor intend to make.
For the readers sake, here is a statement of Steganography:
Thus in the ID conception, the sense that Steganography is an advanced ID topic, is only in that Steganography’s application is an area of reasearch that is at the extreme edge of ID exploration.
Leopold’s uncharitable interpretation of my phrase “the advanced ID topic of Steganography” had nothing to do with claims that ID somehow spawned the field of Steganography. If the context of discussion was ID, invoking the word Steganogrphy is reasonably interpreted “Steganography within, or as applied to ID exploration”.
Comment by Salvador T. Cordova, IDEA GMU — June 30, 2006 @ 5:43 pm
I don’t know if he does in Darwin’s Black Box, but he did under cross-examination in Dover
Comment by Don Baccus — June 30, 2006 @ 5:47 pm
Who really cares about meaningless speculation about something for which absolutely no physical evidence exists?
Comment by Don Baccus — June 30, 2006 @ 5:51 pm
Thank you for your comment ( albeit an opposing view).
I think the proper portrayal is that Behe and Snoke’s paper show why Dawkins Weasel and cumulative selection are irrelevant to the evolution of certain complex features, features requiring simulatenously appearing well-matched parts.
Dawkins references haemoglobin, and simply assumes selectable intermediates along the way which will facilitate evolution toward a target. That may not be the case simply because functionally selectable intermediates simply may not exist, or at the very least are rare.
For a protein made of a hundred or so amino acids, several (not necessarily all) of the amino acids have to be where they are simultaneously, or no protein. That is a simple fact. It is very much like a password.
For the readers benefit, to give an idea of the difficulties, Dawkins describes the 146 amino acids in one part of the Haemoglobin. Behe and Snoke focus on a mere 8 amino acids or less!
Comment by Salvador T. Cordova, IDEA GMU — June 30, 2006 @ 9:41 pm
In that case one should consider: Understand Evolution (at Berkeley’s website)
Indeed, motivations explain this statement at Berkeley perfectly. :-)
Comment by Salvador T. Cordova, IDEA GMU — June 30, 2006 @ 9:52 pm
First, may I congratulate Susan Percell for some very cogent arguments, supported by evidence and all presented without stooping to ad hominem attacks or obfuscation. Brava!
Now, to business: Much as I tremble at this admission, I must say that I agree that Dawkins’ arguments, both in this book and in most of his other publications for the “popular” (i.e. non-scientist) market, are very long on speculation and abstract models and short on real evidence. Furthermore, I find Dawkins’ constant hectoring on the subject of the inevitability of atheism in evolutionary biology to be both distracting (at best) and counterproductive, if not deliberately inflammatory (at worst).
Be that as it may, however, the point of The Blind Watchmaker, and especially of the “Biomorph” and “Weasel” programs is not to “prove” that natural selection can or can’t produce something that looks designed, but rather to do something like what might be called “proof of concept”: that is, to show how such a program might be constructed.
Moreover, since this book was published, much more sophisticated computer models of natural selection have been constructed and tested, and have indeed accomplished a “proof of concept” equal to most such tests (and certainly more successfully, and with fewer serious limitations, than the Behe and Snoke “test of concept.” One may be found at: http://nar.oxfordjournals.org/cgi/content/full/28/14/2794 , and there are many others.
Furthermore, evolutionary biologists (unlike ID theorists) actually carry out field and laboratory research testing the hypotheses and models they formulate concerning evolution, something that ID “theorists” have to date not even attempted (maybe this is why they’re usually referred to as ID “theorists” and not ID “scientists”).
True, there may be topics in evolutionary biology that are resistant to emipirical verification or falsification, such as the biochemical origin of the genetic code and translation apparatus (I refer the reader to my comments on the previous post to this website). However, despite such difficulties, biochemists, physiologists, ecologists, and other empirical scientists continue to produce hundreds of thousands of pages of research reports on field and laboratory tests of evolutionary hypotheses every year. Until the ID “theorists” begin to participate in this kind of research, their public relations efforts will remain just that: public relations, not science.
Comment by Allen MacNeill — June 30, 2006 @ 9:57 pm
Salvadore Cordova wrote:
“…we cannot confuse Darwin’s theory of natural selection with the “doctrine of common ancestry” (Karl Woese’s term). Though they are related, they are not the same.”
Indeed: as I have already pointed out in my introductory Evolution course (it’s on Monday and Wednesday evenings, same time, same building, different room), Darwin’s “long argument” in the Origin of Species actually has two parts:
1) that the diversity of life on Earth is the result of “descent with modification” from a small number of (or perhaps just one) common ancestor(s), and
2) that the process by which such “descent with modification” (Darwin’s term for “evolution”) has taken place is “natural selection.”
However, contrary to Salvador’s assertion, these two parts of Darwin’s argument are inextricably linked all the way through the Origin. Indeed, as some of my students pointed out in section on Wednesday night, the two arguments are both mutually reinforcing and logically coherent in a way that Lamark’s was not (at least not as much). Leclerc/Buffon didn’t even make an argument for a mechanism for evolution at all, but simply speculated (without evidence) that it had occurred, and proposed an essentially untestable process by which it might have come about.
Which brings us, of course, to the state of evolutionary biology in 1859, not 2006. ID theorists and other creationists are fond of attacking “Darwinism,” by which they often mean Darwin’s original theory a la 1859, ignoring (for their own purposes) that evolutionary theory has had a century and a half to mature, and for immense amounts of empirical evidence to be gathered in its support. Attacking Darwin’s version of the theory today is somewhat like attacking Newton’s theory of gravitation, while ignoring the fact that Einstein, Wheeler, and Hawking (among many others) have broadened and deepened the theory of gravitation to the point that its original version is almost unrecognizable in the current one.
And so, if you want to be taken seriously by anyone in the field of evolutionary biology, start reading and trying to understand where the field is now, and make your arguments on that basis. Unless, of course, your real program is one of political obfuscation and deliberate misleading of public opinion. As the Kitzmiller v. Dover trial and decision showed, in the long run such a strategy will only render your arguments counterproductive and nugatory.
Comment by Allen MacNeill — June 30, 2006 @ 10:12 pm
I fear Salvador is misrepresenting Behe & Snoke. Salvador wrote
Behe and Snoke did not test whether the several point mutations required to reach a selective state had to appear simultaneously, and they don’t. Behe & Snoke modeled neutral mutations occurring at any time. They all had to be present for selection to kick in, but did not have to appear simultaneously.Salvador wrote
Salvador’s juxtaposition of the Behe & Snoke model with the 146 amino acids in one part of haemoglobin is simply misleading, because the “8″ in Behe & Snoke’s model is the number of point changes, not the total length of a protein as though it all had to appear de novo. Salvador is here slipping from one argument (number of changes and whether they’re selectable) to a different argument (de novo occurrence of the whole protein). It’s only creationism that imagines that the latter occurred.The Behe & Snoke paper (1) employed only point mutations, (2) disallowed selective advantage for intermediate steps, (3) ignored processes like scaffolding, cooption, and redundancy reduction, and (4) showed that at least some of the phenomena they modeled should occur on a microsecond time grain in realistic biological populations, say of bacteria. See here for a detailed critique of Behe & Snoke’s claims with some reference to biologically realistic populations and time scales. See also here for a discussion of a recent Science paper on the evolution of hormone-receptor binding that directly invalidates Behe & Snoke’s model. The latter also has some interesting remarks on the ability of ID proponents to move goalposts when in danger of refutation, even when moving them constitutes a contradiction of Behe’s own sworn testimony.
RBH
Comment by Richard B. Hoppe — June 30, 2006 @ 11:19 pm
While reading through this thread, I found a lot of irrelevant remarks and some disingenuous remarks but the most egregious one was by Allen MacNeill when he said that “ID theorists and other creationists are fond of attacking “Darwinism,” by which they often mean Darwin’s original theory a la 1859, ignoring (for their own purposes) that evolutionary theory has had a century and a half to mature”
This is absolute nonsense. The ID people are well aware that there has been several revisions to the original Darwin theory based on mutations, genetics and other processes that affect the makeup of a genome. It is constantly discussed on ID websites and in books they have written.
Why would such a statement be made here with the additional expressed statement that ID proponents essentially don’t know anything about modern evolutionary biology. It sounds like the obfuscation is not by the ID people but from people who make statements like Allen MacNeill did.
Comment by J. Cosgrove — June 30, 2006 @ 11:30 pm
I shall retract my statement if you can show me that ID theorists do the following:
1) Show me that ID theorists do not regularly attack “Darwinism” (and do not use that term to characterize a body of theory and supporting empirical research which bears only a generative reference to Darwin’s original concepts of descent with modification and natural selection;
2) Discuss the Fisher/Haldane/Wright formalisms describing the proposed genetic mechanisms for allele frequency change, and showing both logically and with empirical evidence that such formalisms are fundamentally misguided and presenting a revised formalism that both includes and extends this foundational work (bringing us up to somewhere in the 1930s);
3) Discuss Dobzhanski and Mayr’s “biological species concept” and its implications for phylogeny, and showing how ID theory both empirically and logically contradicts this conceptual framework (bringing us up to the 1950s);
4) Discuss the Jukes/Crow/Kimura/Ohta theories of neutral and nearly neutral evolution, providing both a logically compelling and empirically supported alternative theory that explains why over 90% of the DNA of a typical eukaryote is entirely lacking in promoter sequences, and therefore quite literally non-coding (not to mention much of it being highly parasitic), thereby bringing us up to the 1960s;
5) Discuss the Eldrege/Gould theory of punctuated equilibrium, embedding it in the context of Mayr’s theory of peripatric speciation and Simpson’s descriptions of tempo and mode in macroevolution, and providing both logical arguments and empirical evidence that ID theory is superior, based on the known contents of the fossil record;
6) Discuss the implications of Margulis’ theories of endosymbiosis and cooperation for the theory of macroevolution, and show how ID theory both logically and empirically falsifies this theoretical framework and presents a more productive paradigm for further empirical research;
7) Discuss the innovations in selection theory proposed by Hamilton, Trivers, Price, E. O. Wilson, Sober, and D. S. Wilson and the massive amounts of empirical data supporting such innovations, showing how ID theory proposes a logically compelling and empirically supported alternative explanation of such phenomena as eusociality, reciprocal altruism, and the evolution of cooperation as the result of multilevel selection (bring us up to the 1970s and 80s);
8) Discuss the massive amounts of information being gathered by investigators into the genomes of humans, chimpanzees, dogs, various plants, bacteria, and a myriad of other organisms, virtually all of it supporting the mainstream theory of evolution (and virtually none of it produced by ID theorists), bring us up to the end of the 20th century; and
9) discuss the contributions of Sean Carroll and Mary Jane West-Eberhard (among many others) to our understanding of the relationships between evolutionary theory and developmental biology, and show how ID theory presents a logically compelling and empirically supported alternative to the current state of knowledge and understanding of the field of evo-devo, thereby bring us up to the present.
And while you’re at it, show us all how ID does this without being utterly (and egregiously) parasitic on the work of generations of evolutionary biologists, field ecologists, laboratory geneticists and developmental biologists, and an army of other researchers who, unlike every ID theorist of my acquantance, has actually done field and/or laboratory research supporting their hypotheses, the results of which have been published in peer-reviewed mainstream scientific journals.
We’re waiting…
Comment by Allen MacNeill — June 30, 2006 @ 11:55 pm
An argument isn’t ad hominem if, in fact, it is factual. What I stated regarding Dawkin’s failed attempt at, what you term, a ‘proof of concept’ stands on its merits. How can you justify Dawkins’ spending 15-20 pages promoting, developing, and describing his ‘Biomorph’ program–the whole time the reader is presuming that in the end Dawkins will have demonstrated his ‘concept’–only to have him, on the last page of a 37 page chapter abandon–for no stated purpose or reason–this program, then attacking ‘punctuated equilibrium’ and then simply making assertions? This is an edited book. Either you throw out the argument entirely, or you admit failure. As it stands, it’s no more than an intellectual sleight of hand. As I stated, let’s ask the questions: WHAT is a ’step’ in 9-dimensional space (no one can even imagine such a space)? WHO ‘rewards’ this step? WHAT is the ‘reward’? WHAT does he mean by ‘direction’? Unless Dawkins satisfactorily answers those questions, I see no reason to take either him, or his ‘proof of concept’, seriously.
I’m in my middle fifties. I’ve read lots of books. There have only been 3 books that have come flying out of my hand in disgust: Origin of Species, The Blind Watchmaker, and What is Evolution? (Mayr)–all due to their outrageously fallacious arguments. Three strikes, and you’re out!
Comment by Lino D'Ischia — July 1, 2006 @ 12:12 am
“Show me that ID theorists do not regularly attack “Darwinism” (and do not use that term to characterize a body of theory and supporting empirical research which bears only a generative reference to Darwin’s original concepts of descent with modification and natural selection”
Ummmm… the problem here is that the term Darwinism is still used in the technical literature. It refers quite specifically to natural selection operating on random mutations (with respect to fitness). This is specifically what ID’ers disagree with. ID’ers use the term Darwinism to be specific about what they disagree with. If current evolutionary theory is not at odds with ID, then what is the problem? If ID is only against an 1850s view of evolution, why does the NCSE work against it, rather than working with it to remove the 1850s conception from the public mind?
“explains why over 90% of the DNA of a typical eukaryote is entirely lacking in promoter sequences, and therefore quite literally non-coding (not to mention much of it being highly parasitic)”
What about Sternberg’s “On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic-Epigenetic System”? Or the papers by Sternberg and Shapiro in the last few years?
“Discuss the massive amounts of information being gathered by investigators into the genomes of humans, chimpanzees, dogs, various plants, bacteria, and a myriad of other organisms, virtually all of it supporting the mainstream theory of evolution”
In what way does it support the mainstream theory of evolution? How do we know that all of the in-between organisms leading from one organism to the other are all viable organisms, much less more fit? Is there enough reproductive excess for all of the changes to occur and become fixed in the population without some sort of guiding mechanism moving the changes?
“how ID does this without being utterly (and egregiously) parasitic”
I think that’s uncalled for. Is not _any_ new theory necessarily “parasitic” off of all of the work that has gone before it? Is not the purpose of science to put experimental evidence in the purview of anyone who wishes to check and verify that the conclusions follow the evidence? How is actually performing this task “parasitic”? This is the entire point of science as a unique enterprise — that there is not some special “class” that gets to interpret the data. The data is there for all to see and determine if the conclusions logically follow.
The fact is that the small amount of empirical work done by ID’ers is that there are very few ID’ers, and almost no funding available for ID research. But there has been some interesting work done by Axe, Minnich, Schwartz, and others nonetheless.
Comment by Jonathan Bartlett — July 1, 2006 @ 12:28 am
Salvador wrote:
Leopold, may I point out, did not write anything. Leonid, however, did. :)
One may argue that your response is an uncharitable characterization of what I wrote. As you point out, those familiar with ID may recognize that you were referring to the above cited ideas of Dembski. I suspected as much, and in my previous post I discuss why such ideas are, to be charitable, highly implausible. However, this course and this forum is for the benefit of participants who may not be very familiar with the ideas behind ID (and some who may not be familiar with stenography), so it would pay to be clear about what you mean. Since you provided very little context for your phrase “advanced ID topic of Stenography”, I wanted to set the record and point out that stenography is a field that is independent and currently entirely separate from ID.
Further, those of us familiar with ID conceptions know that ID proponents do occasionally, to once again be charitable, overestimate the importance of ID as it pertains to scientific endeavors - be that archeology or SETI research. (Here is what Steve Shostak, senior astronomer at SETI has to say about these claims.) Given this history, and your ambiguous choice of words, I honestly could not be sure whether or not you meant that ID encompasses stenography: after all, one may argue, what is the act of looking for hidden messages in text but an attempt to detect intelligent design? To characterize my reply as equivocation is unfair; I was honestly not certain of what you meant, and attempted to cover all bases in my reply.
I am glad you did not intend to make the above assertion about stenography, and now that you’ve clarified your meaning, I don’t think there is a need to press the point further. However, given the lack of clarity in your original post, I believe my reply to you was entirely reasonable, not at all unkind, and equivocation-free. Now, I suggest we wrap up this particular disagreement, before it devolves (de-designs?) into volleys of finger pointing and squabbles about semantics. I am sure we’ll have much more interesting things to disagree about.
Comment by Leonid Meyerguz — July 1, 2006 @ 2:27 am
If current evolutionary theory is not at odds with ID, then what is the problem?
Nothing scientific is truly at odds with “intelligent design” because “intelligent design” is not a scientific theory. It’s shorthand for “I don’t believe in evolution therefore mysterious alien beings did it for a purpose that I can not tell you.”
It’s amusing to see ID proponents so proudly criticizing Dawkins’ book. Uh … who cares? If Dawkins dies tomorrow, is that a problem for biologists? I guarantee you that most biologists have not read Dawkins book or the Origin of Species. Why would most of them bother doing so? It’s not necessary to do so in order to grasp the basic concepts of evolution which are not seriously disputed by any professional biologists. It’s 2006.
If you have a serious objection to the idea that life on earth evolved without the intervention of mysterious alien beings, show scientists evidence for these mysterious alien beings — evidence that exists outside of the objects you claim are made by these beings.
The fact is that the small amount of empirical work done by ID’ers is that there are very few ID’ers, and almost no funding available for ID research.
How do you do empirical research to test the hypothesis that mysterious alien beings designed every life form that ever lived on earth?
If someone in the ID promoting movement could articulate an experiment that would yield data that only the existence of “mysterious alien beings who act for unknowable reasons” could explain, they might get some funding to do it.
Is that going to happen in the next, say, century? What do the experts think? Not the UFO experts. The ID “experts.”
Comment by Michael Hubl — July 1, 2006 @ 2:39 am
My apologies for the formatting in the previous comment. The last three paragraphs should not be italicized.
Comment by Michael Hubl — July 1, 2006 @ 2:42 am
In fact, the Behe and Snoke paper does nothing of the sort. They arbitairly assume that all amino acid changes in the formation of the beta haemoglobin 2,3-diphosphoglycerate (DPG) binding site were neutral (ie non-selectable) up until , when they are all, bar one, selectable (see this article for a review of the Behe and Snoke paper and also Lynch M, 2005. While neutral mutation can and does occur, it does not invalidate natural selection. Indeed, the DPG binding site example only reenforces the importance of cumulative selection in the development of complex biochemical sturctures.
This is a rather incoherent statement. I think you are trying to say, “for a given function, you need several amino acids in position simultaneously or a protein will not have that function”. For may cases this is not true, and selectable function can occur with several “out of place” amino acids. In other cases, while you may need all amino acids (typically between 3-6) in place, you can get there from simple single amino acid mutations in other functional enzymes (eg single mutations can turn epimerases into aldolases, aminotransferases into nitrile hydrolases, reductases to dehydrogenases and so on. see this review for some examples, but there are numerous other examples in the literature).
Simple stepwise cumulative selection of new functional entites for pre-existing proteisn is seen often in booth the wild and the laboratroy, we even have laboratory examples where random proteins have evolved into functional proteins.
Salvador’s assertions to the contrary, we have abundant experiemntal and observational evience for the efficacy of cumulative selection.
Comment by Ian Musgrave — July 1, 2006 @ 2:43 am
Except none of it has anything to do with ID. Axes work is completely irrelevant to ID (where he shows that proteins can be extraordinarily resistant to mutational damage, for example, he shows you can completely scramble the core amino acids of barnases with no effect), and Axe has said so himself. Minnich has some interesting work on understanding control mechanisims for assembling genes products, but this is irrelevant to ID. Schwartz has revived some ideas of macromutation, but nothing that supports ID.
Comment by Ian Musgrave — July 1, 2006 @ 2:54 am
Salvador keeps mentioning the 2004 Behe and Snoke paper, and I thought I would offer a few counterpoints. The paper indeed purports to show the difficulty of evolving proteins requiring multiple amino acid residues to function, but Behe and Snoke’s critics have accused them - correctly, in my view - of using a highly restrictive and simplistic model of evolution that had little to do with biological reality. In particular, a follow-up paper by Michael Lynch, published in Protein Science in 2005, directly challenges Behe’s and Snoke’s claims, and argues that evolution of complex proteins is considerably easier than those authors suggest.
(Abstract follows: the paper itself may be accessed here)
For the sake of completeness I would like to add that Behe and Snoke have published a brief response to Lynch in the same issue of Protein Science. For anyone with access to the full text of the Protein Science journal, the response can be accessed though this page. For those interested, the journal issue is Protein Science (2005), 14:2217-2225.
Comment by Leonid Meyerguz — July 1, 2006 @ 3:02 am
Hmm, you somehow missed this passage (bolds added):
Comment by Nick (Matzke) — July 1, 2006 @ 3:42 am
Having weighed in here with two comments (and thus being as guilty as the rest), I’d like to remined the other, non-student contributors that this is meant to be for the participants of BioEE 467. It’s nice to have outside commentary, but this has completely drowned out the student voices. As I know from my own classes, it is often hard for students to speak up in any forum, and the volume of non-student comment (especially the uninformed comment) can hardly make the students feel comfortable. So please, let the students have a chance.
Comment by Ian Musgrave — July 1, 2006 @ 7:52 am
Nick Matzke says
This is ad hominem and as such is against the ground rules. Moderator, please do your duty.
Comment by David Springer — July 1, 2006 @ 8:11 am
Prof. MacNeill writes:
Citations of published papers and data are not restricted to only those who are in agreement with the author or investigator of the cited work. Denigrating those who interpret existing data in a different way is reprehensible.
Comment by David Springer — July 1, 2006 @ 8:43 am
Salvador wrote:
“What about Sternberg’s “On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic-Epigenetic System”? Or the papers by Sternberg and Shapiro in the last few years?”
Precisely my point: none of these papers reports original empirical research of any kind. On the contrary, they use existing information and theoretical models to argue for an hypothesis for which they provide no new empirical data whatsoever.
Again: until ID theorists begin to formulate positive hypotheses (i.e. hypotheses that do not depend entirely on data obtained through the blood, sweat, and tears of other people who, unlike ID theorists, seem willing to go into the field or the laboratory and actually study something) and then use generalizations formulated on the basis of such hypotheses to make predictions that can then be tested by additional empirical research, and then analyze the results obtained from such research using standard statistical analytic techniques, they will not be taken seriously by anyone in the community of scientists, they will not get published in peer reviewed scientific journals, and their “research” will continue to consist of the spinning of airy speculation entirely unsupported by any palpable connection to physical reality.
Comment by Allen MacNeill — July 1, 2006 @ 9:09 am
Sorry, that was Jonathan who wrote “What about Sternberg’s “On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic-Epigenetic System”? Or the papers by Sternberg and Shapiro in the last few years?”, not Salvadore.
Stepping back just a bit, I disagree with the criticism of this forum that it doesn’t allow student participants in the seminar course to contribute. On the contrary, it is in fora like this (i.e. entirely unmoderated commentary threads, in which anyone is free to post under almost any moniker, so long as they do not represent themselves as someone else for nefarious purposes) that people who feel inhibited in the oral rough and tumble of a seminar like ours can let fly. Having attended two of the seminar sessions, I can vouch for the loquacity of our student participants and their ability to defend themselves and make cogent arguments. It is, after all, the weekend and they are living in Ithaca in June (i.e. in the closest one can get to paradise on Earth), and they have actual lives, unlike some of the denizens of these boards (myself included) who sit hunched over their keyboards while the gorgeous days of summer slip slowly away…
Ergo, I will not be posting for the rest of the weekend. See you all next week.
Comment by Allen MacNeill — July 1, 2006 @ 9:17 am
Not so fast. Thankfully Behe and Snoke’s paper is now available online for free because at the time the “refutatation” at PT was written, only paying individuals had access to the paper.
Because the article is available for free here, comparisons can now be made between the original paper and Musgrave and Lynch’s respective critiques.
These critiques follows a general propensity to characterize and frame ID literature in a manner highly inconsistent with ID authors actual thesis and claims.
A very good exercise for the readers, independent of which side they ultimately tend to favor, is to comprare Behe and Snoke’s paper and ask themselves, did Musgrave or Lynch accurately and fairly represent the arguments? The general assessment will be clearly, NO! We call such rhertorical maneuvers Straw Men.
Let us start with Distinguished Professor Michael Lynch. He made comments which on the surface seems devastating to Behe and Snoke’s thesis (and nicely window dressed with peer-reviewed papers):
But on closer inspection, Lynch made an egregious misrepresentation of Behe and Snoke’s position! He attributes to them, conclusions and assumptions which they never made. Lynch offers a classic Straw Man argument. Such tactics are unbecoming of a scientist of his stature.
Here is Michael Behe’s response:
It may be lost upon the readers in the many pages written by both sides on the issue, that much of the flaws in the critiques of Behe and Snoke can be refuted by the two simple statements I bolded by Behe: “We imply no such thing.” and “We made no such assumption.“.
I can say the same about the critique Musgrave offered as well has similar flaws. For example, Musgrave claims,
Wait as second, this is a highly uncharitable framing of what Behe and Snoke are doing.
They are considering highly specific circumstance, and in no way are they conveying this is expected to be a general rule. The assumption is NOT to be taken as a generally true for all proteins, but to circumstances where the protein needs several well matched parts. That is the specific circumstance in question.
One, upon reading Musgrave’s comments (and for that matter Lynch’s comments) comes away with the impression, Behe and Snoke assume this for all proteins. That is not the case, it something they don’t imply, nor something they assume.
An fictional illustration for the readers might be helpful as it might clarify the StrawMan arguments being employed.
Behe and Snoke: “Our model will FOCUS on males weighing who weith 160 pounds and up…On the assumption that the subject of study is a male weighing 160 pounds or more…”
ID-Critics: “It is an unwarranted assumption that males weigh 160 pounds and up, we have numerous examples where this isn’t true. This is gross miscahracterization of the well established scientific literature. Here is a dauntling list of peer-reviewed papers demonstrating that their assumptions that males weith 160 pound or more is totally unwaranted…”
I hope this helps clarify the kinds of rhetorical devices being employed to attack Behe and Snokes paper. This fictional example is highly analogous to the way Behe and Snoke’s paper are critiqued. I invite the reader to look carefully! This exercise will be a revealing lesson in rhetoric, and it’s all the more amazing as such devices would not be expected to be at the root of some highly technical critiques!
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 1, 2006 @ 11:25 am
I don’t understand the dislike of the weasel program as an example of, as mentioned above, cumalative selection. The probabliities, whilst seeming very low, don’t seem like a limiting factor.
For example::
Assumptions
Take one bacteria, that divides once every 20 minutes. (fairly standard)
The bacteria’s ‘genome’ for simplicities sake is xxxxxxxxxxxxxxxxxxxxxxxxxxxx (the same length as ‘Methinks it is like a weasel’).
To make the odds even lower, we choose a path to watch, that being each mutation must follow one letter at a time (ie, m, me, met, meth etc till the mutation is complete).
We set a mutation probability of 1% for one mutation occuring within the bacteria upon copying from the prvious bacteria.
We can even set a 25% survival probablilty for each new mutatant strain that is created.
So, onto the maths::
1% chance of mutation, 3.5% that it will occur on the right gene, 4% chance it will be the right mutation, 25% chance it will survive.
That sums up to about a 3.5x10^-6 chance that a single mutation will happen and the bacteria survives, or, for every 285714 bacteria we have, one of them should be a mutation for the first part of the weasel genome. There is a miniscule 1.7136E-153 chance that the original xxx genome will change into the Weasel genome on a mutation.
However, we know that the bacteria doubles in number every 20 minutes. in one hour, there will be 8 bacteria, in two hours there will be 64 bacteria. In 6 hours there will be 262144 bacteria. As there should be the first successful mutation by 285714 bacteria, The first mutation we are looking for should happen within 6-7 hours.
After this mutation, we start off the process again with the one mutatant bacteria. In another 6 hours there should be another beneficial mutation leading towards the Weasel ending. So, theorectially, we whould have a complete change from the xxxx genome to Weasel (28 characters long) in 168 hours. (A .01% chance of mutation will extend each period out to around 10-11 hours)
This is, of course simplifing the issue, as it does not take into account death, competition, food resources, etc, but as an exercise in numbers, a probability as low as 1.7136E-153 can be resolved in a number of days.
From what I’ve read, in about a square centimetre of your hand around 100,000 bacteria can be found. In a teaspoon of soil, around 1 billion bacteria can be found. What I don’t get is why there aren’t more mutants…
Comment by Geoff Lee — July 1, 2006 @ 12:13 pm
I looked at the abstract you linked to in the italicized part. It’s not a very impressive experiment. Bacteria mutate all the time; that’s their raison d’etre. What the experiment showed is an increase of a little more than two orders of magnitude in a bacteria that was originally six orders of magnitude lower in its infectivity. And the process appears to have employed a kind of ‘artificial selection’ in that the cultures that developed the highest infectivity in one growth cycle were used to grow the next batch of cultures. Had this process enabled the bacteria to restore itself to its orginal infectivity, then, despite the tinkering, this would be somewhat impressive. But we’re dealing with an ‘improvement’ in infectivity of 0.025%—-a little more than a hundredth of a percent increase. What if they hadn’t tinkered, would it have been a thousandeth of a percent increase in infectivity? Like I say, it’s not impressive.
Comment by Lino D'Ischia — July 1, 2006 @ 1:43 pm
Regarding Geoff Lee’s post above:
Geoff, is it humanly possible to isolate ‘one’ bacteria amidst 285714? How would you ‘know’ that its genome had changed in the proper way? Wouldn’t you have to ‘kill it’ so as to examine its genome?
But, for argument’s sake, haven’t you’ve just proved that bacteria, left alone, could never achieve this sequence alone since the chance of doing it randomly is so enormously large; that is, 1.7136E-153. (There are 10^90 particles in the universe) Hence, if we discovered a bacteria with this precise sequence in its genome, then we would be completely justified in asserting that the only way this sequence came about was through some scientis purposively bringing this about in his laboratory—that is, INTELLIGENT DESIGN! You’ve just demonstrated how the ‘design inference’ operates. Thanks.
Comment by Lino D'Ischia — July 1, 2006 @ 2:02 pm
The start of the second paragraph in my last post should read:
But, for argument’s sake, let’s assume you’re able to do all of this. Then haven’t you….. Sorry.
Comment by Lino D'Ischia — July 1, 2006 @ 2:04 pm
I find it fascinating how Sal seems to suggest that the critics of Behe and Snoke somehow made a strawman of the position of ID.
First of all, ID activists are quick to make these claims but seldomly succeed in pointing out a relevant case. Behe is notorious for being’misunderstood’ for instance, mostly because of the flawed nature of his Irreducible Complexity claim and partially because of the amount of equivocation and partial or even contradicting arguments presented.
Pandasthumb showed many real problems with Behe and Snoke’s paper and the critique by itself was devastating for the ‘argument’. The later work by Lynch was icing on the cake. Like Dembski, Behe seems to be mostly interesting in looking at the worst case scenarios. However, for IC or the explanatory filter to stand a chance they have to show that the best case instances are still too unlikely. The problem for ID is that they cannot exclude best case scenarios and thus we have a range of possibilities ranging from the total impossible to the plausible and since ID is based on elimination, the ID inference is effectively blocked.
Remember that there is no competing ID hypothesis to compete with science.
Comment by Pvm — July 1, 2006 @ 2:39 pm
Lino D’Ischia wrote:
“But, for argument’s sake, haven’t you’ve just proved that bacteria, left alone, could never achieve this sequence alone since the chance of doing it randomly is so enormously large; that is, 1.7136E-153. (There are 10^90 particles in the universe) Hence, if we discovered a bacteria with this precise sequence in its genome, then we would be completely justified in asserting that the only way this sequence came about was through some scientis purposively bringing this about in his laboratory—that is, INTELLIGENT DESIGN! You’ve just demonstrated how the ‘design inference’ operates.”
According to this logic, therefore, virtually every nucleotide sequence in every living organism must be created de novo every generation, otherwise the combinatorial possibilities are so enormous that they can’t possibly exist. This is essentially the same logic as asserting that the odds against winning the lottery are so astronomically large that no one could every win it. However, somebody wins it about once every three weeks. Daniel Dennett attacks this logic in chapter 5 of Darwin’s Dangerous Idea “The Library of Mendel.”.
And besides, of what practical use is the assertion that virtually every nucleotide sequence that has ever existed is “impossible” without divine intervention? What kinds of empirically testable hypotheses would such a conclusion stimulate? None that I know of, and for the same reason that Deism is both scientifically and theologically sterile: it suggests no testable hypotheses of any kind, and strongly suggests that any further research into the origin or evolution of nucleotide sequences would be utterly futile (a conlusion that Michael Behe apparently endorses, as he has suggested that ID and IC should be used by scientists as a guide to what kinds of research shouldn’t be performed - a “science stopper” by definition.” I am thankful that every scientist that I know pays absolutely no attention to such nonsense, but continues to investigate the currently unknown details of genome evolution.
Comment by Allen MacNeill — July 1, 2006 @ 2:44 pm
Sal’s comments about rethoric miss the point as it takes attention away from the major shortcomings of the work by Behe and Snoke.
To a reader, it should become quickly self evident that the work provides little support to ID and that it describes what most would consider a strawman version of evolution.
The lesson for today? Intelligent Design is still lacking in much of any scientific relevance. This lack of scientific content is caused by the appeal to ignorance or eliminative nature of the Design Inference. In many ways, the argument is not dissimilar from the Young Earth Creationist arguments about probabilities.
It’s easy to make a worst case scenario, it requires real hard work, and lots of science to come up with more realistic scenarios for evolutionary events. Realize that ID offers no scientifically relevant explanation of ANY of the claimed designed systems. What is ID’s explanation for the flagella? Poof…
ID is scientifically vacuous. Remember this whenever ID proponents make claims in this area, ask them to show how their predictions etc follow directly from ID. ID is quick to claim that the junk DNA (or finding function amongst Junk DNA) and the Cambrian explosion are relevant ID predictions but it should be clear by now that ID provides no guidance here. In fact, the only guidance for these ideas come from religious foundations.
Comment by Pvm — July 1, 2006 @ 2:51 pm
Dr. MacNeill criticized my comment about his comments on the nature ID.
My comment - This is absolute nonsense. The ID people are well aware that there has been several revisions to the original Darwin theory based on mutations, genetics and other processes that affect the makeup of a genome. It is constantly discussed on ID websites and in books they have written. (I do not know how to use the formatting so this will have to do till I figure it out - my comment was 11:30 PM last night)
Also in my original comment I said there were many irrelevant remarks in the discussion and Dr. MacNeill’s response appeared after my comment and it is another one of these irrelevant remarks. He should show in the readings assigned where ID criticizes each one of the areas he brings up since I have not seen them do so. For all I know someone, somewhere might do exactly what he says but it hardly paints a picture of what ID is about. I have read a lot of their literature and these topics are not part of the discussion.
But it is not necessary for him to show me where ID supposedly made these criticisms of evolution theory because is irrelevant to do so based on what I present below. The evolution issue is framed the wrong way which is why I believe Dr. MacNeill’s series of comment are irrelevant.
Evolution is not in dispute by ID in the sense that over the past 3.5 billion years life appeared and has changed dramatically and these changes indicate a trend to a generally more complex form of life. What is in dispute is how the first cell formed and the mechanism for subsequent changes that have taken place since this first cell appeared 3.5 billion years ago. Evolution is not the same as Neo Darwinism which is just one of many theories for the mechanisms of evolutionary change. There are basically 4 tiers of evolution, each with its own specific problems and theories.
The first tier is the origin of life itself, or how did the first cell appear. The first cell seemed to appear roughly at the same time water was forming on earth. In other words it happened very quickly in geological time. There is no scientific theory to explain how something as complex as the cell could have arisen other than wild speculation. While lots of effort is directed at this problem there is little if any progress. In fact some origin of life researchers think the problem has gotten larger, not smaller. Few who do research on this problem ever describe the immensity of the problem.
The second tier is the origin of multi-celled organisms and this also includes the formation of complicated body systems such as eyes, appendages, nervous systems, digestive systems etc. Very small multi celled organisms first appeared about 700 million years ago or almost 3 billion years after the first cell. In a relatively short time there was what is known as the Cambrian explosion which when most of the modern day phyla appeared in a geologically short period of time, 10-20 million years. These phyla were diverse, that is they represented completely different body plans and there is zero evidence that they were descended from any common ancestor. This represents the complete opposite of Neo Darwinian evolution which would predict a bottom up sequence of development of the gradual diversity of species with the phyla forming after substantial diversity took place. The Cambrian explosion appears as a top down evolutionary event (little diversity but great disparity). There is no known mechanism for this event.
The third tier of evolution is what is known as macro-evolution or how did species with substantially different body parts or functions develop. In this tier there are a wide spectrum of issues. For example, how did species with very distinct body parts such as wings (bats and birds), lungs for land animals, different heart types, warm vs. cold blooded, methods of birthing (eggs, mammals etc.) develop? Then there is the more modest problems such as different types of mammals, birds, land to sea transitions take place. Again lots of speculation but almost no hard evidence. The fossil record is often used here to try to discern patterns but unfortunately it always falls short. People frequently make the statement that there is no sequence in the fossil record of one animal type transforming into another. When this discussion takes place it generally leads to the same few sequences of 1 or 2 fossils and maybe occasionally one with 6-8 when there should be millions of transitions. Neo Darwinism as you know predicts gradual transitions so as a mechanism for change it comes up short in the fossil record with no good examples. Thus, Neo Darwinism has zero evidence backing it in tiers 1 and 2 and very little if any in 3. It depends upon how narrowly you want to define species change in tier 3 before you could claim an example of Neo Darwinism working.
Tier 4. This is micro-evolution or small changes that take place within a population with changes in allele frequency or maybe some mutations in the DNA or some other events which modify the genome slightly. This is what Darwin witnessed on the Beagle and what is most frequently presented as evidence for evolution. Here there is very little to no debate with the ID people because they all accept this. But it is all the Neo Darwinists have and they make believe it is everything. How much of your very technical reply refers to tier 4 alone. How much that isn’t in tier 4, just speculation such as punctuated equilibrium. The discussion of immune systems above no matter how important or interesting could be classified as a tier 4 discussion and is not relevant for the ID/Neo Darwinism debate. A lot of very interesting and useful biological research takes place in tier 4 and ID has no problem with most of it.
This is a brief outline the areas of evolution. ID is mostly concerned with tiers 1 and 2 which is where irreducible complexity is most apparent while Neo Darwinism is mostly concerned with tier 4. In tier 3 ID has many issues with the origin of complexity such as wings, the oxygen system of birds and human consciousness but it is literature is mainly focused in tiers 1 and 2 where the sudden origins of extremely complex cell elements and organism body parts take place. ID has no issue with tier 4 so while I do not understand all the theories that you presented, if they were discussed in lay terms, I would probably agree that those with hard evidence have relevance to tier 4.
I don’t speak for ID and am not necessarily promoting it as a science in itself but have found the writings of their people extremely logical and relevant to the basic issue of evolution.
Thank you for letting me comment.
Comment by J. Cosgrove — July 1, 2006 @ 3:03 pm
Lino wrote:
Not necessarily. If we knew that a particular genotype (or set of genotypes) was the only way to achieve a particular effect, and we were to observe this effect (e.g. bacteria achieve a certain level of infectivity, or are able to digest a chemical compound that they previously could not, or start glowing a certain color), then we would be justified in concluding that some bacteria have evolved the genotype in question. But sequencing the genome is certainly a possibility if we wait a bit: after all, if some bacterium evolves the selectively advantageous genotype, it will improve its chances of reproductive success, and there will likely be a large number of its descendants in the near future.
You’ve missed Geoff’s point. The probability of the “right” genotype existing originally in the bacterial genome is indeed exteremely low, as you point out above. However, as long as there is a selectable pathway - e.g. a series of mutations, where each mutation gives better odds of reproductive success over pre-existing genomes - the bacterial colony will have no problem following this pathway, one step at a time. (To answer your questions upthread, a “step” in multi-dimensional genome space is essentially any small change from one genome sequence to another, or simply a mutation; a “direction” is simply a series of consecutive steps, and “rewards” are provided by the organisms’ common environment, where some mutants flourish and others languish.) So, even though the odds of starting with the “right” genotype at random are extremely low, the fact that mutants who are closer to this genotype have increased reproductive success would allow evolutionary processes to quickly “home in” on this genotype without examining a myriad of useless possibilities in the process. Or, to put it more succinctly, mutation is random, selection is not.
Of course, the main counterargument by ID proponents is that in real life, selection is not so cut-and-dry, and there may exist biological systems to which no clear selectable pathways exists. While it is obvious that in the real world both mutation and selection are far more complex than Dawkins’ “Weasel” example, aside from arguments from incredulity, ID advocates have offerred little evidence as to why the standard mechanisms of mutation and selection should be so limited.
At the risk of being cheeky, may I suggest that it is you who just demonstrated how the “design inference” operates? Specifically, you misunderstood Geoff’s argument for evolution, and wound up using the most common design inference there is: “I don’t understand how it evolved, so it must have been designed.” :)
Comment by Leonid Meyerguz — July 1, 2006 @ 3:22 pm
Not surprised to see Nick attack Sal with an ad hominem. I guess this course is going to be precisely what I said it to be- completely unbalanced, as even Nick and Allen himself cannot follow the rules set forth in the guidelines.
This quote from the professor makes it obvious he can NOT be fair and balanced with this issue:
Again: until ID theorists begin to formulate positive hypotheses (i.e. hypotheses that do not depend entirely on data obtained through the blood, sweat, and tears of other people who, unlike ID theorists, seem willing to go into the field or the laboratory and actually study something) and then use generalizations formulated on the basis of such hypotheses to make predictions that can then be tested by additional empirical research, and then analyze the results obtained from such research using standard statistical analytic techniques, they will not be taken seriously by anyone in the community of scientists, they will not get published in peer reviewed scientific journals, and their “research” will continue to consist of the spinning of airy speculation entirely unsupported by any palpable connection to physical reality.
Does ANYONE honestly believe the professor is one bit fair here? In his world ID-supporting scientists don’t do actual research, nor do they do any real science. This guy’s mind is made up from the word ‘go,’ and nothing will change his mind.
Not only is he showing his absurd bias, he’s lying. Behehas done ID-related lab work, as has Wells…same thing for Minnich. Dean Kenyon has done the lab work associated with the ideas as well.
If the professor himself can tell lies about ID, it’s proponents, and mock them at every turn, why does anyone think this course is anything bus his platform to do just that- be dishonest and unfairly mock.
I should note- the MRI was invented by a young earth creationist. Nick said no one should take any YEC seriously basically- thus, I want Nick to proclaim he will never get an MRI, as if you can’t trust the “science” of a YEC, no way you can trust their inventions.
Sorry, but someone has to say it- Nick and Allen are acting like children. No one else has acted like a kid, besides the professor himself and a talking head who loves to go on cable news and attack ID with dishonesty. See a pattern yet,klids?
Comment by Ben Katz — July 1, 2006 @ 6:47 pm
In his world? Try the real world.
Quick, now, convince us all that you’re right by naming the ID supporters who are doing real scientific research into ID.
Comment by Don Baccus — July 1, 2006 @ 7:32 pm
Ben Katz wrote:
Actually, thus far, out of all the posts to this blog, yours wins hands down in the ad hom content. While Nick’s characterization of Sal as a “YEC cheerleader for ID” may have been unkind - albeit accurate, given the ID movement’s recent public efforts to distance themselves from young earth creationism - it was a one-time occurrance. Your post, however, is laced with multiple overt insults and personal attacks, calling Nick and Allen childish, repeatedly accusing them of lying, and referring to Nick as “a talking head who loves to go on cable news and attack ID with dishonesty.” Personally, I’d rather be called an “evo-cheerleader” (and have been, in a different forum).
Aside from their emotionally charged nature, I’m sad to say none of your accusations holds any water. You wrote:
You are, of course, completely misinterpreting what Allen wrote. A very small percentage of scientists have indeed openly voiced their support for ID, and undoubtedly a great many of them do good research in their own fields. However, what Allen said is that there currently appear to be no positive, “only ID and nothing else could explain this”, hypotheses out there, and ID ideas are entirely parasitical on the ideas formulated and data collected by other researchers. (Parasitical in the sense that ID, just like such organisms in nature, attempts to thrive by tearing down the ideas and labor of mainstream biologists on which it is dependent for its very existence, without contributing anything of its own.) While one can argue that there are now ID-only ideas out there - such as Wells’ guess about centrioles, or Dembski’s suggestions about stenography - these ideas are considered highly implausible in the scientific community, and, more importantly, no actual serious research has been conducted and published in these areas. If that ever changes, it will be most welcome news for ID.
Accusing someone of lying is a very serious charge in scientific circles, and should be backed up by convincing evidence, which you utterly failed to provide. Would you care to point us to peer-reviewed publications of Wells and Minnich where they postulate and develop positive ID hypotheses and back them with original evidence from their own research? Care to enumerate any follow-up work that this research has generated, or any contributions to their respective fields flowing from their ID-only hypotheses? Simply throwing out a few names isn’t going to cut it.
As for Behe, to say that he has done ID-related labwork is inaccurate. His one and only ID-relevant scientific publication is a mathematical analysis of the difficulty of using a highly limited and biologically unrealistic model of an evolutionary process (duplication and divergence) to generate novel protein functions: one does not need to ever set foot in a lab or in the field in order to conduct such research. While I do not mean to denigrate the vast improtance of mathematical and computational modeling for biology in general and protein evolution specifically - my own research is in a related area as well - it is generally considered important in such line work to make sure that your models correspond as much as possible to the underlying biological reality. More importantly, Behe and Snoke’s work in no way invalidates Allen’s observation: there are no ID-only ideas in the entire work, and the whole paper can be seen as an exercise in attacking a crippled model of biological evolution rather than presenting any positive evidence for intelligent design.
In short, your accusations of “absurd bias” and “lying” on behalf of Professor McNeill are entirely bogus. Perhaps, before accusing others of childish behavior, a little introspection might be in order.
Comment by Leonid Meyerguz — July 1, 2006 @ 9:00 pm
In response to Lino D’Ischi
Most of this has been addressed above already, but…
::Geoff, is it humanly possible to isolate ‘one’ bacteria amidst 285714? How would you ‘know’ that its genome had changed in the proper way? Wouldn’t you have to ‘kill it’ so as to examine its genome?::
We do not have to isolate it. Do we bother trying to find a lotto winner by sending one person out to check each ticket? That would take forever. I ‘isolated’ it mathematically so we could look at how long it takes that single mutatant to develop into a serious population. Just because we do not isolate it physically, does not mean it doesn’t exist or replicate. As stated above, as we are watching a particular path, we will be able to observe and watch for particular characteristics of the bacteria as it mutates. A change in colour, a reaction to UV light, a sudden burst of growth, a particular shape, etc.
::But, for argument’s sake, haven’t you’ve just proved that bacteria, left alone, could never achieve this sequence alone since the chance of doing it randomly is so enormously large; that is, 1.7136E-153.::
But we reach that number in just 510 iterations of doubling, starting from 1 bacteria. It is merely 28 groups of 285714 bacteria. Of course this is theoritical, because as I said it does not take into account resources, death, predators, etc. But it does also not take into account the beneficial mutations that the bacteria collects each step of the way - the mutation ‘METHINK’, for instance, may allow the bacteria acceess to a type of food source that the other bacteria cannot digest. The mutation ‘IT IS LIKE’ may provide a rudementary propulsion/secretionary system which allows the bacteria to access new locations previously uninhabited by other bacteria. Or a mutation may change reproduction rates, life spans, cell membrane toughness, size, etc.
By the way, once we reach the 285714 of bacteria, 99% of the bacteria will be the xxxx bacteria, while in that 1% there should be one of each other mutation. As there are more mutations, the xxxx bacteria will become obsolete, and potentially another food source for other, more agressive bacteria. So instead of seeing 99% of the bacteria being xxxx, this proportion will slowly receed to a much lower %, maybe even becoming extinct. By the time we see a ‘methinks it is like a Weasel’, there will be potentially any and all possible combinations of mutatant genomes out there that we have not followed, up to 4.22775E+37 variations for a 28 letter long genome (28^26). So if we aren’t looking specifically for “methinks” but merely a mutatant that differs from the xxxx gene, it would be vary easy to notice many significant mutations.
::(There are 10^90 particles in the universe)::
So we have counted all matter in space and time now, have we? Seems like a bold assertation.
::Hence, if we discovered a bacteria with this precise sequence in its genome, then we would be completely justified in asserting that the only way this sequence came about was through some scientis purposively bringing this about in his laboratory—that is, INTELLIGENT DESIGN! You’ve just demonstrated how the ‘design inference’ operates. Thanks.::
Well, i guess if we found a bacteria with “methinks it is like a weasel” as its genome, we could almost certainly infer a designer. One with a wicked sense of humor :)
Comment by Geoff Lee — July 1, 2006 @ 11:51 pm
Professor Allen wrote:
According to my logic, the last part of your sentence is true. I have no idea at all how the first part of the sentence follows from what I said. As to the first part, “everything comes from an egg”. I’ll let you figure out the rest.
No, it’s the same logic that says that if a single individual wins the lottery 2,000 weeks in a row, then something is definitely up.
It’s very practical. It will keep all kinds of minds, and all kinds of money from being wasted on an attempt to ‘prove’ that protein sequences can arise all by their little selves.
It would strongly suggest that the genome operates like a software program, and, along those lines, would also suggest that there is an algorithm responsible for what “appears” (you know, just like biological systems “appear” to be designed) to be raw random mutations, which might prove very helpful in coming up with powerful antibiotics.
Maybe you need to spend more time at the beach and relax. I suggest you read the introduction to the Skeptical Environmentalism to see that knowing where to spend your time and money, and where not to, is, indeed, a valuable endeavor.
Comment by Lino D'Ischia — July 2, 2006 @ 12:21 am
So many errors. In fact the evidence shows a nice nested hierarchy all the way into the pre-cambrian. The top-down versus bottom-up again is a fallacy. A nested hierarchy by logical necessity starts with a phylum since the first ’species’ is also the phylum, family, order etc.
Anyone familiar with Valentine would be aware that he considers Darwinian theory quite adequate for explaining the Cambrian. In the past, ID proponents have often ‘quote mined’ Valentine and it is interesting that they fail to mention his latest conclusions.
Why is it that once again, ID’s claims are mostly based on ignorance.
As far as Nick’s comments being an ad hominem, I fail to see exactly why this is the case as it quite accurately describes Salvador.I do hope that the participants of this class understand the meaning of the term argument ad hominem.
The professor is quite fair in pointing out that ID remains without any clothes so to speak. That the reality may come as somewhat of a shock to ID activists is mostly because ID has oversold it’s scientific relevance and focused on socio-political activism rather than scientific research to further their claims.
And before we accuse the professor of a strawmen let’s distinguish between IDers being able to do science and IDers being unable to do science relevant to Intelligent Design.
Of course creationists can do excellent science but the scientific foundation of their claims remains fully absent. And the evidence, or rather lack thereof, is there for all to see.
Denial is the first step to recovery my dear friend and I understand that the realization that ID has no clothes may have come as quite a shock and as a Christian I apologize for the poor science and poor theology presented by overzealous Christians. As many have come to conclude, ID has failed to make itself
scientifically relevant.
If anyone disagrees then please show how ID has contributed in a non-trivial manner to scientific knowledge and that this is directly related to the foundational claims of ID.
I argue that since ID is an argument from ignorance based on elimination, it cannot make much of any relevant claims beyond ‘x’cannot be explained by science.
Comment by Pvm — July 2, 2006 @ 12:45 am
Your answer completely misses the mark. How can you distinguish a bacteria that is ONE nucleotide different than the bacteria next to it? You’re assuming that this one nucleotide difference is going to result in notable phenotypic effects. What’s the basis for that assumption? If all we’re going to do is play make believe, what’s the point?
It’s make-believe time again. Show me this pathway. Show me where in nature you can see this happening. If all you’re doing is “assuming” all of this, then, like I say, we’re playing “make-believe”. Why don’t we leave “make-believe” to the kids?
But we’re not talking about ‘genome space’, we’re talking about “Biomorph Land”. Let’s not mix our analogies.
Right out of the Darwinist’s ‘bible’. You see, I’m not a ‘believer’. I’m from Missouri. You gotta show me.
And they are completely justified in their arguments.
Charles Darwin would have been proud of this last sentence. However, I’m afraid that intellectual ’sleights of hand’ don’t work on me.
At the risk of sounding ‘cheeky’, according to Geoff’s argument it wouldn’t take bacteria more than a few weeks to ‘evolve’ a human arm. But we haven’t seen that happen in our laboratories, have we? I ‘don’t understand how it evolved’ because you have failed to present anything close to a sensible scenario for how anything of this might come about.
Comment by Lino D'Ischia — July 2, 2006 @ 1:14 am
In response to Geoff Lee’s latest post:
Geoff, if you really believed what you are saying, you would go out and perform the experiment. You would be hailed everywhere as the greatest evolutionary scientist of all time. You would receive 10 Nobel Prizes. The world would be yours.
But, instead, you’re here writing posts. You say you ‘mathematically’ isolated the ‘one’ bacteria with the correct genome. But the real world doesn’t operate like the ‘ideal’ world of mathematics. You, and Leonid, are living in a world of make-believe. It’s almost like you’ve been brain-washed. I’m beginning to think that Darwinism is not only a religion, but a cult-religion at that. I’ve begun reading Behe and Snoke’s paper. They take a very realistic approach to the questions we’re interested in. It’s their kind of approach that I find intellecutally compelling—-because it’s realistic.
Comment by Lino D\'Ischia — July 2, 2006 @ 1:44 am
Obviously real bacteria are more complex, and take a lot longer to mutate than a 28 string phrase. Again, this is not the definative evolution calulator, it merely demonstrates how cumulative selection works. :S
As for the science, it’s already being done every day - how do you think bacteria become immune to antibiotics? Sometimes within the mutatant population of that bacteria there will be a mutation that makes it resistant to that particular antibiotic. Those mutant bacteria survive, and then multiply from there. From then on that mutated strain of bacteria will be more resistant against that antibiotic.
This has been tested in labs. It has been known for years. It is realsitic.
And be sure to read the rebuttals to the Behe & Snoke paper too :P
Comment by Geoff Lee — July 2, 2006 @ 2:15 am
ie
http://www.accessexcellence.org/RC/AB/BC/Bacterial_Mutations.html
Although potentially I was being a little too generous with the 1% mutation rate. Maybe even .01%. However, this article only deals with mutations for antibiotic resistance, not all mutations.
Comment by Geoff Lee — July 2, 2006 @ 3:09 am
One step at a time, Lino. You completely misunderstood Geoff’s original post, and stated that he was making a “design inference” and proving that a bacterial colony under the effects of cumulative positive selection “could never achieve this sequence alone since the chance of doing it randomly is so enormously large” (I assume you meant “infinitesimally small”). I tried to clear up your confusion, and explain to you that in this toy example, the bacteria could achieve the genotype in question through the effects of random mutation and non-random selection alone, and that no “design inferences” are necessary. Now, before we proceed, do you agree?
The point of point of playing “make believe”, as you call it, is to simplify a subject in attempt to clear any conceptual hurdles that may impede one’s understanding. Sometimes, such simplifications do not depart too far from reality. The realism behind Dawkin’s example may well be questionable, but it is a very effective illustartion of how random mutation in the context of selection can produce some seemingly very improbable results.
Sure. Start by reading the paper Ian cited, about evolution of functional proteins from random sequences. You dismissed that paper out of hand, but it is actually a very convincing demonstration of how easy it is to develop and refine a previously non-existent function in the context of incremental positive selection. The point of the experiment was not to revert to the original level of virulence in bacteria: but rather to see whether they could evolve and improve virulence from random starting points, in the context of positive selection. The “artificial” component you talk about is a red herring: bacteria that achieve greater infectivity would be more successful in nature, so natural selection would apply just as well (albeit possibly somewhat slower).
And of course there is always an example of rapid evolution of immune system proteins, as Nick Matzke points out. Here is a good introductory link. The section on clonal selection should be of particular interest.
Actually, we are talking about ‘genome space’ in both cases. Just like the bacterial genome encodes the bacterial phenotype, so do the 9 “genes” in the biomorph encode its phenotype. The notions of steps, directions, and mutational pathways are identical in both cases.
I can try, but we’ve gotta establish some criteria first. You seem to believe that mutations are pre-programmed into living organisms - this position, in my view, is inherently unfalsifiable. But if you disagree, what would it take to convince you that mutations are indeed statistically random events with respect to an organism’s needs?
And while we’re at this, why not provide some positive evidence for your belief that mutations constitute a part of a “software program”? Or is it OK to play “make-belief” as long as you are the one who gets to make stuff up?
Comment by Leonid Meyerguz — July 2, 2006 @ 3:31 am
Lino wrote:
Methinks it’s like someone just violated forum ground rules 1 and 4 in the same post. Let us keep this discussion civil, shall we? You have Uncommon Descent to voice your opinion of me, and I have the Panda’s Thumb to voice my equally flattering opinion of you. And if you really want to take the rhetorical gloves off, there’s always talk.origins.
Comment by Leonid Meyerguz — July 2, 2006 @ 4:03 am
This will be my last post, as unanticipated family and work issues will take me away from my computer for some time. All the best to you students.
Comment by Ian Musgrave — July 2, 2006 @ 7:48 am
I respect your position Allen, though I disagree on some points. There is no need retract your statement, nor do I make any request in that regard.
I thank you for your hospitality in hosting this discussion, and giving ID a hearing in the biology classroom. That is far more than what most universities offer. Whaterver your feelings may be, I sense you have made an effort to set them aside (even if it may bubble to surface occasionally), and for that you have my respect and support.
Regarding Fisher, Haldane, Crow, Kimura, Jukes, Ohta, Crow, Gould, Eldredge — these names are revered and respected in ID circles.
The other name, most notably Margulis — well she frequently quoted by IDers, but her theory of endosymbiosis may be in for a crisis.
In any case Allen, I thank you for hosting this discussion. I take no offense to any of your words.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 2, 2006 @ 12:39 pm
This is such nonsense. Remember that the Templeton foundation invited ID to submit grant proposals for scientific research. None were submitted.The workby Axe,while interesting has no relevance to ID (he stated so himself in the past). Similarly the work by Minnich has no relevance to the concept of ID.
In over 10 years, ID has virtually NOTHING to show other than some poorly developed mathematical concepts and as Allen said, a parasitic dependency on scientific research, claiming it to be ID relevant when in fact it couldn’t be because any time science explains something, ID has to retreat.
ID is scientifically vacuous because it fails to present any scientifically relevant hypotheses which follow directly from ID’s foundational assumptions. Let’s take the design inference which is based on elimination and as such basically established our ignorance. ID has no positive hypotheses to put forward other than the unproven assumption that intelligence creates CSI. But in all known cases, the probabilities approach 1 and thus the information (another poorly chosen name for the log of probability) approaches zero. Poof goes the CSI….
And when ID is asked to present detailed pathways, it responds that
William A. Dembski Organisms using GAs vs. Organisms being built by GAs thread at ISCID 18. September 2002
How more vacuous can one get?
Comment by Pvm — July 2, 2006 @ 12:57 pm
That is not quite true and I will show why, and I will also show why I don’t think Behe would say, “it is not one of the cases that cries out for a design”.
What Behe actually said in 1996 (and I will add my commentary afterward):
On the surface this seems to support Nicks assertion, but on closer inspection of the context of discussion, Nick’s assertion becomes less sustainable.
The design being considered in the context of Behe’s remarks was hemoglobin’s ability to interact (bind) with oxygen. Behe and Snoke’s paper dealt with hemoglobin’s (or some other protein’s) ability to interact (bind) with other molecules (ligands) such as DPG (2,3-diphosphoglycerate). Oxygen is not the same as DPG. And the ability of hemoglobin to process both is important to hemoglobin’s evolutionary history.
(For the reader’s benefit here is an article: Why Receptor Ligand Binding is Important to learn more about protein binding of ligands.)
Behe was discussing oxygen binding by hemoglobin in 1996, but hemoglobin binds to other things like DPG in addition to oxygen. So Behe’s 1996 reference was in the context of the evolution of oxygen binding capability, not the evolution of all features of hemoglobin (including DPG ) binding. Behe was indicating the case for design is weak (on the assumption of myoglobin’s pre-existence) with respect to oxygen binding, not the total evolution of hemoglobin itself.
I think Nick’s interpretation, was a little fast and loose with what Behe was intending to communicate. This is on par with saying we see bacteria evolve antibiotic resistance via natural selection, thus there is no need to invoke ID in the evolution of bacteria. Such statements are an example of Fallacy of Equivocation.
Behe’s statement in no way is saying all the other features of hemoglobin need no design, or that the totality hemoglobin’s features are accounted for independent of design. This is all the more reinforced by Behe’s investigation of hemoglobin in 2004.
Furthermore, it would be no small task to account for the scenario where ancestral myoglobin becomes hemoglobin. We may have “phylogenetic reconstruction’s” (sequence similarity comparisons) which attempt to outline a path, but that is a circularly reasoned appeal in which one assumes the thing one wishes to prove. But even on the assumption there is common ancestral pathway “proven” by phylogenetic reconstruction (albeit a circular proof), there is no requirement that natural selection is the mechanism which brought it about.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 2, 2006 @ 1:37 pm
I think that Sal has shown us that Behe is really saying much of nothing and little of anything.
As far as Sal’s understanding of phylogenetic reconstruction, it underlines his lack of understanding of these tools. Sequence similarity is one of the many examples showing the importance of common ancestry, following from the simple mechanisms of inheritance, replication, variation and selection. To call this circular reasoning ignores the logical arguments involved.
I have to agree with Nick, that limited knowledge can be quite dangerous tool.
Sal’s unwarranted assertion of circularity seems a good example here. And that despite the fact that many people have tried to inform him of his flawed assertions. That’s too bad.
Comment by Pvm — July 2, 2006 @ 4:51 pm
Circularity is a common ‘argument’ against evolution. From the claims that natural selection is a tautology (it can be but need not be) to claims that fossils arguments are circular. While these claims may seem to be superficially correct, on closer scrutiny they quickly fall apart, most of the time because those who are making these claims are unfamiliar with the details of the arguments involved.
So let’s look at how science has established the fact of common descent.
In http://www.talkorigins.org/faqs/comdesc/ Douglas Theobald describes the many evidences in support of this simple concept that life leads back to, as Darwin suggested, one or more ancestors.
He shows how from different data, the evidence strongly supports the fact of common descent. It’s quite an interesting read.
Douglas explains why the ‘argument’ of circularity fails
And that’s how science typically works, it makes assumptions, derives predictions or post-dictions, tests these predictions and if supported is strengthened in its relevance.
Note that on the other hand, ID cannot and has not made any relevant predictions in this sense beyond “evolution or Darwinian evolution cannot explain ‘X’”. When asked for details as to how ID explains ‘X’, the response invariably seems to be similar to Dembski’s
William A. Dembski Organisms using GAs vs. Organisms being built by GAs thread at ISCID 18. September 2002
Which is why people like Nichols conclude that
R. Nichols, Scientific content, testability, and the vacuity of Intelligent Design theory The American Catholic philosophical quarterly , 2003 , vol. 77 , no 4 , pp. 591 - 611
Note that so far ID has failed to present any scientifically relevant hypothesis relevant to ID and which follows logically from its premises. Statements about the Cambrian and “junk DNA” are invariably inspired by theology and not by science. The Cambrian by the insistance that God created ‘Kinds’ in an abrupt manner and “Junk DNA” because God created functional DNA. Of course neither ‘prediction’ has much of any scientific value because there is no way to determine the motivations or capabilities of the designer, as any ID proponent would quickly admit.
Think about it: If ID cannot constrain its ‘designers’ then it cannot make any predictions, and cannot be refuted. An example: God created DNA to be perfect, hence no Junk DNA. Alternatively, after the fall, the genome became victim of the 2nd law of thermodynamics, causing it to degrade.
ID is so self contradicting that it should become quickly self evident that it cannot play any relevant roles in science until it resolves these major shortcomings.
Comment by Pvm — July 2, 2006 @ 5:08 pm
Sal, you seem to miss the point. Allen is willing to retract his statements. All that is needed for ID to show a few simple things. The reason why ID seems quick to respond that Allen need not retract his statements seems to strengthen Allen’s statements and indicate that ID really has no answers for his well reasoned questions.
Until ID can stand up and address these and many other questions, ID will stand no chance to become scientifically relevance.
Why should ID go into hiding anytime the veil of our ignorance is lifted? Think about it, is that what one would expect ’science’ to do when confronted with questions?
Comment by Pvm — July 2, 2006 @ 5:11 pm
Now I’m envious of MacNeill’s students, for not only having a fair-minded teacher who loves to teach, but for living in Edenic Ithaca.
Comment by Bilbo — July 2, 2006 @ 5:31 pm
If I understand it, the objection to the Weasel analogy, is that the entire message: “METHINKSITISWEASEL”, must be achieved before it is selectable. Such a case puts it beyond the bounds of probability. If each change, from “x” to one of the letters of the message were selectable, then there wouldn’t be a problem.
Likewise, if I understood the point of the Behe and Snokes paper, they were addressing one of the common answers to how an irreducibly complex system can originate: by neutral mutations from a another system. Their point is that after a few neutral mutations (was it 3?), such a scenario becomes too improbable. This does not prove that a supposedly irreducibly complex system couldn’t be achieved by some other Darwinian pathway, or by a combination of them. Just that it probably couldn’t happen by neutral mutations alone. Whether or not they succeeded in showing that, I leave for others to determine.
Comment by Bilbo — July 2, 2006 @ 5:40 pm
Maybe PVM should give us specifics to his comments on the Cambrian Explosion and James Valentine.
Comment 1 “So many errors. In fact the evidence shows a nice nested hierarchy all the way into the pre- Cambrian. The top-down versus bottom-up again is a fallacy. A nested hierarchy by logical necessity starts with a phylum since the first ’species’ is also the phylum, family, order etc.”
What is the basis for this claim? Please be specific and in particular if you could quote from James Valentine latest book “The Origin of the Phyla” it would be useful. I do not have the book but just ordered it from Amazon so maybe we can compare your interpretation with what is in the book.
Comment 2 ” Anyone familiar with Valentine would be aware that he considers Darwinian theory quite adequate for explaining the Cambrian.”
What is the basis for this claim? Does Valentine endorse Darwinism as the mechanism that caused the Cambrian Explosion? If so, then where because I have a quote from him that says Darwinism is inadequate to explain it.
Here is the question to Valentine - “Does the fossil record confirm or contradict the bottom to top pattern?”
Here is Valentine’s answer “Darwin had a lot of trouble with the fossil record because if you look at the record of phyla in the rocks as fossils why when they first appear we already see them all. The phyla are fully formed. It’s as if the phyla were created first and they were modified into classes and we see that the number of classes peak later than the number of phyla and the number of orders peak later than that. So it’s kind of a top down succession, you start with this basic body plans, the phyla, and you diversify them into classes, the major sub-divisions of the phyla, and these into orders and so on. So the fossil record is kind of backwards from what you would expect from in that sense from what you would expect from Darwin’s ideas. Although once we get into the fossil record where we got a complete fossil record we can see the gradual changes within lineages as Darwin predicted.”
Now Valentine is a believer in a naturalistic approach to evolution so I would assume that the above quote is not biased and thus supports the comments I made about the Cambrian Explosion from the world’s pre-eminent invertebrate paleontologist.
I have other quotes which express the same sentiment but for the time being this will do. From what I understand his book also is consistent with a non Darwinian explanation for the Cambrian Explosion. For example, one of the chapter sub-headings is “In Sum, the Cambrian Fossils Imply an Explosion of Bodyplans, but the Underlying Causes Remain Uncertain”
Readers of this comment should go to a review of Valentine’s book, ‘The Origin of the Phyla’ in the American Scientist by Briggs in the May-June 2005 issue. The url is
http://www.americanscientist.org/template/BookReviewTypeDetail/assetid/42353
I am sorry that I do not know how to use the formatting options yet on this forum so as to embed the link.
Comment by J. Cosgrove — July 2, 2006 @ 6:13 pm
Bilbo: Likewise, if I understood the point of the Behe and Snokes paper, they were addressing one of the common answers to how an irreducibly complex system can originate: by neutral mutations from a another system. Their point is that after a few neutral mutations (was it 3?), such a scenario becomes too improbable. This does not prove that a supposedly irreducibly complex system couldn’t be achieved by some other Darwinian pathway, or by a combination of them. Just that it probably couldn’t happen by neutral mutations alone. Whether or not they succeeded in showing that, I leave for others to determine.
The idea that evolution proceeds through neutral mutations alone is as flawed as the idea that evolution proceeds through selection alone. Nevertheless, neutral mutations are essential for the success of evolution as has been shown by for instance Toussaint.
The reasons are simple; Neutrality confers both robustness as well as evolvability to the genome. Sounds contradictory doesn’t it? How can something which is robust also enhance evolution?
Since Behe seems to have isolated IC from pathways which include change of function, he may have successfully created a strawman. In addition, the assertion that intermediate steps are exclusively neutral also serve to increase the improbability of such pathways but serve little to show that other pathways do not exist. In other words, rather than focusing on worst case scenarios, ID should focus on best case scenarios and show that evolutionary pathways are still impossible or at least improbable. But there lies the problem, the best case scenarios show that evolution is quite plausible and as such it prohibits much of any design inference from being triggered.
Which is why Lynch concluded
In fact, Behe and Snoke suggested that most/all intermediate mutations were detrimental rather than neutral.Lynch shows that this assumption significantly reduced the probabilities and goes against the data and evidence.
As Richard Azevedo concludes comparing the work by Lynch and Behe/Snoke’s response
And Lynch’s paper is just one of several showing how the assumptions of Behe and Snoke were flawed. See for instance Bridgham JT, Carroll SM, Thornton JW. Evolution of hormone-receptor complexity by molecular exploitation. Science. 2006 Apr 7;312(5770):97-101, also discussed at Pandasthumb in the thread titled Evolution of IC: Evolution of Hormone-Receptor Complexity
What is even more funny is that Behe and Snoke’s pathways were quite non-Darwinian and if the intent was to show the inadequacy of Darwinian pathways, then the paper did nothing to resolve this.
Lynch’s assumption about neutrality seems well supported as Ian Musgrave on PT points out
This simply isn’t true. Lynch quotes several experimental studies (eg Guo et al. (2004)) that show that the majority (~70%) of substitutions are neutral, even the papers quoted by Behe & Snoke in their original paper show that the majority of substiutions are neutral
Another interesting paper contradicting Behe and Snoke seems to be Missense meanderings in sequence space: a biophysical view of protein evolution Mark A. DePristo, Daniel M. Weinreich and Daniel L. Hartl in Nature Genetics
Comment by Pvm — July 2, 2006 @ 6:17 pm
And just when you think things could not get any worse for Behe and Snoke we read the following
In summary, not only is cryptic genetic variation not significantly eroded by the accumulation of deleterious mutations, but instead it is positively enriched for potential adaptations. The minimum condition for enrichment is that selection on hidden lethals is appreciable, and the optimal condition is when selection on unhidden potentially adaptive alleles is highly effective. Enrichment is weak with respect to potential adaptations resulting from a single mutation, but is dramatic for potential adaptations based on a combination of mutations. This provides a powerful mechanism for achieving an adaptation involving multiple mutations when each mutation, taken by itself, is deleterious. This gives a rigorous basis to previous speculations that adaptive combinations of mutations may appear more readily when variation is subject to weakened selection (KOCH 1972; TRUE and LINDQUIST 2000; HARRISON and GERSTEIN 2002). Recent models of the rate of obtaining an adaptive combination of mutations (BEHE and SNOKE 2004; LYNCH 2005) are therefore substantial underestimates, since they do not take this enrichment into account.
Joanna Masel Cryptic Genetic Variation Is Enriched for Potential Adaptations, Genetics, Vol. 172, 1985-1991, March 2006,
Comment by Pvm — July 2, 2006 @ 6:22 pm
Sorry, PvM, but obviously Lynch, you and others have misunderstood the intent of Behe and Snokes paper. Numerous attempts to show how IC systems could have come about by Darwinian pathways depended upon several consecutive neutral mutations taking place. Behe and Snokes were only trying to show that such scenarios are too improbable to be taken seriously. If you had been involved in the earlier discussions at ARN, when Nick was trying to convince us all (or Ken Miller in his papers and books), that neutral mutations could account for the bloodclotting cascade, you would understand why Behe and Snokes had to address the question. Instead, you and others make up strawmen of your own, and attack Behe and Snokes for things they never claimed. Go read their paper again.
Comment by Bilbo — July 2, 2006 @ 6:50 pm
Bilbo
Are you sure you understand what BS argued? They argued that most intermediate mutations were ‘detrimental’ not neutral. Lynch showed that when this was corrected for, neutral mutations indeed can explain evolution quite adequately.
Could you point out the specifics? If they were intent on neutral mutations how come their model seems to have modeled something ’slightly’ different?
Neutral mutations hardly seem to be the problem and BS may have chosen the wrong approach here. Nothing wrong with that, after all science is quick to correct such flaws as we have seen in this case.
While some examples given for pathways to IC systems may have included neutral mutations, you may want to show that BS’s scenario is relevant to these instances.
Comment by Pvm — July 2, 2006 @ 7:07 pm
PvM wrote:
Funny, it’s Lynch they cite, when explaining that most non-neutral mutations to duplicate genes result in a null allele:
Although the great majority of nonneutral mutations to duplicated genes are expected to result in a null allele (Walsh 1995; Lynch and Walsh 1998), that is, a gene that no longer codes for a functional protein,occasionally one might confer a novel function on the incipient paralog.
Comment by Bilbo — July 2, 2006 @ 9:12 pm
Your point being? You do understand what the term non-neutral means? Please explain what you are trying to say here.
Why do you not quote directly from Lynch ?
From Walsh and Lynch
A recently duplicated gene can either fix a null allele (becoming a pseudogene) or fix an (advantageous) allele giving a slightly different function, starting it on the road to evolving a new function. Here we examine the relative probabilities of these two events under a simple model. Null alleles are assumed to be neutral; linkage effects are ignored, as are unequal crossing over and gene conversion. These assumptions likely make our results underestimates for the probability that an advantageous allele is fixed first. When new advantageous mutations are additive with selection coefficient s and the ratio of advantageous to null mutations is {rho}, the probability an advantageous allele is fixed first is ([1 - e(-S)]/[{rho}S] + 1)(-1), where S = 4N(e)s with N(e) the effective population size. The probability that a duplicate locus becomes a pseudogene, as opposed to evolving a new gene function, is high unless {rho}S {complex} 1. However, even if advantageous mutations are very rare relative to null mutations, for sufficiently large populations {rho}S{complex} 1 and new gene function, rather than pseudogene formation, is the expected fate of most duplicated genes.
Genetics, Vol 139, 421-428, 1995
Comment by Pvm — July 2, 2006 @ 11:03 pm
Also check out
Evolutionary Potential of a Duplicated
Repressor-Operator Pair: Simulating Pathways
Using Mutation DataPLoS Computational Biology May 2006 Volume 2 Issue 5
… over 99% of all optima in the landscape are in fact below our divergence criterion. Such
local optima represent traps in which the system gets permanently stuck once it encounters one. However, the results show that the system is still guided in the right direction to (near) global optima, which indicates that the fitness landscape contains funnel-like features. Moreover, the optimal paths contain negligible detours (Figure 3A) and lead to the nearest optimum (Figure 3B), showing that the funneling is efficient and not constrained by ruggedness. A funnel-like organization of the landscape is also supported by the monotonous fitness increases of the probabilistic pathways (Figure S2C), as well as by the smooth fitness decrease when stepping away from a global optimum (Figure 3C).
Again, the evidence strongly contradicts the ideas of B&S
Comment by Pvm — July 2, 2006 @ 11:11 pm
If this is what you think I said, then you have misunderstood me. The people in charge of lotteries ‘use’ a random-number-generator. Their ‘goal’ is an array of random numbers. But there is purpose behind this generation. And even the generator itself is the by-product of design. I hope this makes it easier to understand.
Comment by Lino D'Ischia — July 3, 2006 @ 12:29 am
The problem with front-loading is that unless one provides evidence that design was involved, all one can establish is that design is an ‘option’. It’s up to science to establish how such design can be explained. Occam’s razor surely seems to quickly resolve the requirement for intelligent designers here. As Dembski explains
Comment by Pvm — July 3, 2006 @ 12:33 pm
Ben Katz says:
Let me see if I can’t defuse some of the bitter undercurrents that frequently tend to arise in these debates. Let me quote from Allen Mac Neill’s post at another site discussing his approach to this course in general:
http://telicthoughts.com/?p=634
What else would I have him say? Nothing. I think Allen pretty eloquently summed up an intellectually defensible approach to exploring a controversial issue. That is a sufficient set of principles for me to feel comfortable challenging him on some of the issues where we disagree.
There is no need, nor is there any value, in you labeling him as a l*ar. If he is indeed so overcome by bias that he either can’t see reality, or is being intentionally d*shonest, then he isn’t doing anything “to” ID or its proponents. He is instead undercutting his OWN arguments. That is the beauty of logic. In that case, you need to get a big smile on your face, and genially feed him slowly all the rope he needs to hang himself, which he is likely to do if what you claim is true.
And if you can do that, it will be much more impressive than any bit of name calling you can think up.
I’m not sure why so few people today understand this today. Logic seems to be in short supply. People are highly educated, but apparently not so smart. And I was rather surprised to see that a good portion of those “not so smart” folks claim to be defenders of science, logic and rationality.
Go figure.
Comment by Roger Rabbitt — July 3, 2006 @ 2:25 pm
Lino wrote:
It would appear so. My apologies, then. However, now I’m really at a loss for what you meant. I wrote the tried and true cliche:
To which you replied:
Since I don’t have this “Darwinist’s bible” anywhere on my bookshelf - the closest I’ve got is the Newtonist’s Necronomicon - I am really not sure what it is that I have to show you. Which part of the above statement do you disagree with?
Further, you write:
It does, thank you. However, this doesn’t really help us in any way. Essentially, what you are saying, if I am understanding you correctly: “Living organisms rely, in part, on random changes to adapt to their environment. Intelligent entities occasionally use randomness for their own purposes.” What sort of conclusions can we draw from those premises? Certainly not “Intelligent entities must have designed living organisms”. That would be a non-sequitur.
Further, mutations are not like random lottery numbers. A better analogy would be errors in transmission of electronic messages. They are not really random in the sense that they just happen all of a sudden for no reason at all: quite the opposite, their occurrance is a necessary consequence of the underlying physical reality. However, the time, location, and frequency of occurrance of these errors is, by and large, independent of the needs of the organism in whose genome they occur. Thus, from the perspective of living organisms, and the scientists studying those organisms, mutations can be seen as events following a random statistical distribution, rather than a necessary but unpredictable consequence of the work of DNA replication mechanisms. In that sense, mutations are random. You are correct that in principle that mechanism *could* have been built by some designer(s) for some nebulous purpose - it’s just that this proposition is inherently unfalsifiable, and has no scientific value. (You of course, are welcome to argue otherwise.)
If you want a better example than lottery numbers of humans making use of evolution-like techniques, I suggest you look into evolutionary algorithms, if you still have not. But once again, the fact that humans use evolutionary algorithms tells us nothing about the existence or non-existence of intelligent designers of living things - aside from demonstrating the ability of variaton and selection to solve problems that we, (supposedly) intelligent humans, can’t solve otherwise.
Comment by Leonid Meyerguz — July 3, 2006 @ 2:39 pm
Allen says:
No ad hominem attack? Then how do you label this:
Probably not an “ad hominem attack” if you think of that as “vicious insult”. But likely an ad hominem, as in the logical fallacy sense. For example, in the category of ad hominem fallacies of relevance, we have:
http://www.philosophicalsociety.com/Logical%20Fallacies.htm#genetic
And that’s putting aside the little “spin” on what Behe actually said under oath. His comments were reasonable and nuanced. The “spin” seems to lose that.
Comment by Roger Rabbitt — July 3, 2006 @ 3:21 pm
The Behe/Snokes paper was examined in the Dover vs Kitzmiller case. Behe was on the stand and I thought the transcript was great reading. It puts the study in a bit of perspective. Check out Mr. Rothschild grilling of Behe in the cross examination at http://www.talkorigins.org/faqs/dover/day12am.html
Comment by Mike Hannigan — July 3, 2006 @ 3:55 pm
I think that some may have misunderstood Susan’s statement. It is the claim by ID proponents that the identity of the designer is of no relevance while on the other hand arguing that the designer is clearly God.
Much of the claims by ID follow directly from the assumption of the Designer being God. For instance that the Cambrian shows evidence of ‘creation of kinds’ or that “Junk DNA should have function”. There are straight out of the creationists’ playbook and have no foundation in the strictest foundation of Intelligent Design and rather follow from side-assumptions about the designer.
It’s this going back and forth between making assumptions about the designer, often carefully shrouded, and claims that ID says nothing about the designer. In fact, the claim that ID says nothing about the designer makes ID scientifically irrelevant as ID cannot constrain its designer and thus ID can explain anything and thus really nothing.
This is not a trivial observation, but rather is the fundamental foundation of ID’s thesis and thus one has but one choice and reject ID’s thesis as scientifically relevant.
Susan is right, motivations are important as they help understand many of the claims and arguments made.
Such as for instance
Dembski, Touchstone Magazine. Volume 12, Issue 4 July/August, 1999This leads Dembski to conclude that Christ is indispensable to any scientific theory.
But if Christ is indispensable to any scientific theory then how come that ID will not identify its designer? And if it will not or cannot, then it seems that it has failed in a major contribution to science.
To me, ID is full of internal inconsistencies, caused by a variety of reasons, including its religious foundations, its attempts to avoid dealing with the issue of the ‘designers’, its reliance on ‘information theory’ as a substitute for old creationist canards such as the improbability arguments and the unavoidable links with religion.
Which is why Judge Jones ruled that
Comment by Pvm — July 3, 2006 @ 5:05 pm
I haven’t given up on our discussion of Behe and Snoke, PvM. I’m just too burned out after reading cross-examination of Behe at Kitzmiller that Mike Hannigan was kind enough to provide; and then posting at the other class notes. No libraries open tomorrow. I’ll try to be back here Wednesday night.
Comment by Bilbo — July 3, 2006 @ 8:39 pm
How is this anything other than pure opinion, and a slam of ID. It’s really marvelous that you know exactly what how ID defenders think and what they feel. Here’s my suggestion: listen to what they have to say instead?
Comment by Lino D'Ischia — July 3, 2006 @ 9:52 pm
Leonid wrote:
I don’t so much ‘disagree’ with the statement as I don’t ‘believe’ the statement. You write it, and recite it, as though it’s as firmly demonstrated as Coulomb’s Law; and, yet, it’s almost entirely supposition. My grandfather used to say that the way you build a house is by building four walls and a roof. In other words, verbally, it’s very easy to solve difficult problems.
This is typical of the kind of interpretations those defending ID can expect from the Darwinists. Sal Cordova has already expressed some frustration along these lines. If you want to be a real scientist, then you should make a sincere effort at understanding someone else’s position/conjecture.
How about this conclusion: random mutation might not, in fact, be entirely random in its origin.
It seems it would be very easy to falsify this view: you simply demonstrate that there exists no genomic algorithmic program for such mutations. But, we already know that something like this already exists. It’s not a big stretch at all to infer that the emergency correction system that bacteria use operates this way.
I’ve looked at a number of ‘evolutionary algorithms’. My experience is that they all have to sneak in teleological information (target information) to make it work. Behe and Snoke’s algorithm seems the most realistic; I’d recommend it to you.
Comment by Lino D'Ischia — July 3, 2006 @ 10:42 pm
Leonid wrote:
I don’t so much ‘disagree’ with the statement as I don’t ‘believe’ the statement. You write it, and recite it, as though it’s as firmly demonstrated as Coulomb’s Law; and, yet, it’s almost entirely supposition. My grandfather used to say that the way you build a house is by building four walls and a roof. In other words, verbally, it’s very easy to solve difficult problems.
This is typical of the kind of interpretations those defending ID can expect from the Darwinists. Sal Cordova has already expressed some frustration along these lines. If you want to be a real scientist, then you should make a sincere effort at understanding someone else’s position/conjecture.
How about this conclusion: random mutation might not, in fact, be entirely random in its origin.
It seems it would be very easy to falsify this view: you simply demonstrate that there exists no genomic algorithmic program for such mutations. But, we already know that something like this already exists. It’s not a big stretch at all to infer that the emergency correction system that bacteria use operates this way.
I’ve looked at a number of ‘evolutionary algorithms’. My experience is that they all have to sneak in teleological information (target information) to make it work. Behe and Snoke’s algorithm seems the most realistic; I’d recommend it to you.
Comment by Lino D\'Ischia — July 3, 2006 @ 11:05 pm
From my reading of both the Dover trial and Behe and Snokes article as posted above, my initial impressions are…
First, look at figure 6 in Behe’s article.
I’ll provide some excerpts from the case (behe being cross examined):
Q. And yesterday, you explained about bacteria, that 10,000 generations would take about two years in the laboratory, correct?
A. Yes.
10,000 generations is 10^4
Q. In that first paragraph, he says, There are more than 10 to the 16 prokaryotes in a ton of soil. Is that correct, in that first paragraph?
A. Yes, that’s right.
If you look at Figure 6 in the Behe & Snokes article, the 10^16 population line begins already past the 2 point mutation line during the 2 years (10^4) worth of mutations.
Within one ton of dirt there will be 2 point mutations happening within 2 years. Within 20,000 years 5 point mutations are expected to happen. All within one ton of dirt.
And this is from someone who is sceptical about evolution, so one can only assume that the figures would be very conservative.
Am I looking at this the right way? It doesn’t seem to imply that evolution wouldn’t happen to me…
Comment by Geoff Lee — July 4, 2006 @ 11:06 am
This presupposes that the designer, rather than working in mysterious ways, works exactly as you imagine a human software engineer does. But of course a designer might build something that looks as though it could’ve evolved naturally, and it is this that makes it unfalsifiable.
You also seem to have forgotten one of the basic tenets of ID. Not only can’t ID tell us anything about who the designer is, but ID can’t tell us anything about how the operates.
Also, of course, you falsely argue that the existence of a “genomic algorithmic program” proves evolution wrong. That’s just more or less a handwaving assertion.
Comment by Don Baccus — July 4, 2006 @ 11:50 am
Bilbo,
Here is the plantiff’s finding of fact that Judge Jones agreed with in his decision regarding the Behe/Snokes paper:
118. Similarly, there are no peer-reviewed articles supporting Professor Behe’s argument that certain complex molecular structures are “irreducibly complex.” 21:62, 22:124-25. The one article referenced by Professors Behe and Minnich, as supporting intelligent design, Behe and Snoke, “Simulating evolution by gene duplication of protein features that require multiple amino acid residues” Protein Science, P721, does not mention either irreducible complexity or intelligent design. Professor Behe also admitted that this study did not rule out many known evolutionary mechanisms and that the research actually might support evolutionary pathways if a biologically realistic population size were used. 22:41-55; P756.
Comment by Mike Hannigan — July 4, 2006 @ 1:48 pm
Comment by PvM — July 4, 2006 @ 2:10 pm
The topic of randomness is a tricky one and is easily confused to mean something it does not. On PT I am working on a posting to address the concept of randomness, which merely states that variation is not uniquely beneficial with respect to its effect in a given environment. In fact, Darwin went much further and speculated how the environment could affect the kind of variation that would arise.
Recent research has suggested that variation is not random in various aspects such as location, mechanisms, time. So how does science explain this? In fact, one may also ask the question “how does ID explain this?”
It should be clear by now that all ID can do is throw up its hands and hope that science cannot explain it and that if science explains it (and in this case it has), it will have to move ‘design’ backwards in time, hiding in the shadows of our ignorance.
Thus we arrive at the concept of evolutionary algorithm. Again a non-trivial concept which may confuse many to conclude that EA’s are inherently ‘teleological’. But remember that evolution itself is inherently teleological due to the concept of selection. So in other words, that EA is teleological seems to be a requirement for it to accurately model evolution. And that’s where Behe and Snoke fail: rather than model the most likely scenarios and show that evolution is still impossible, they chose the least likely scenario and then conclude that “look evolution could not have taken this pathway”… Lynch and others quickly showed how irrelevant their ‘conclusions’ really were.
Back to biased mutations. As Caporale has so eloquently argued: If variation mechanisms arise whose variation is more likely to have been successful in the past, selection will in fact preferentially select them. In other words, mechanisms of variation themselves can be under selection. This is known as ‘evolvability’. No miracles needed…
So remind us again: How does ID explain this? And help us understand the means, motives, mechanisms etc involved that allow us to formulate an actual hypothesis? Or is ID not interested in what Dembski so clearly called a ‘pathetic’ request?
Comment by PvM — July 4, 2006 @ 2:21 pm
PvM wrote:
If an Arab, born in Kuwait, who has abandoned the religion of Islam, argues that the Cambrian Explosion (recently validated as a real phenomena) along with the improbability of random mutation and selection accounting for biological complexity, you would call him a ‘creationist’. Instead of my explaining why the arguments are similar (afterall, logic is logic), why don’t you explain why you would call this non-believing Arab a ‘creationist’?
This seems like an empty statement. Maybe you can help me understand what you mean. As it stands, it sounds like this: Nature is brought about by selection. Selection is brought about by Nature. There’s an article by George Gilder posted in UncommonDescent.com. In the article, Gilder quotes Max Delbruck: Nobel-laureate biologist Max Delbrück (who was trained as a physicist) described the contradiction in an amusing epigram when he said that the neuroscientist’s effort to explain the brain as mere meat or matter ‘reminds me of nothing so much as Baron Munchausen’s attempt to extract himself from a swamp by pulling on his own hair.’” Your scenario sounds very much like ‘nature’ pulling itself out of the swamp by pulling on its hair.
Well, this seems exactly what Sal and you have been arguing about. I’ve read the introductory parts of the paper where they explain their stochastic model. The set-up they’re using seems entirely reasonable, and very realistic. The necessary MR point mutations have to appear before the genome becomes dysfunctional through a harmful mutation (which includes a neutral mutation in a very critical functional part of the protein). You say they chose the least likely pathway. Well, that’s arguably wrong. But even if it is true, the obvious reason they chose the pathway they did was because it was the most straightforward way of modeling evolution, meaning it was the least difficult to handle mathematically. Why fault them for that? You have to start somewhere don’t you? Why move on to the greater mathematical difficulty of including ‘recombination’ in the model when you haven’t yet ruled out the possibility that evolution can be modeled without using it?
The obvious difficulty with this assertion is that the bacterial emergency repair mechanism is irreducibly complex. If all the parts (and algorithms must have parts) are present, then the bacteria die. If you want to invoke the ‘miracle of all miracles’, that is, ‘neutral evolution’, then there’s this problem: Behe and Snoke have ruled out that possibility. An ‘algorithm’ would likely require hundreds of nucleotides coming together in just the right location. You can invoke all the huge bacterial populations you want, but it isn’t going to be big enough to account for hundreds of said nucleotide substitutions needed for the formation of an algorithm.
Comment by Lino D\'Ischia — July 4, 2006 @ 7:12 pm
What is “cumulative selection”
What is “the efficacy of cumulative selection?”
Comment by Scott — July 4, 2006 @ 7:55 pm
Duh. Read the book. It’s in there somewhere.
“We went over the first six chapters of Dawkins’ Blind Watchmaker tonight”
Its kinda what the treads about.
Or go google it if you really can’t be bothered.
Comment by Geoff Lee — July 5, 2006 @ 4:50 am
Lino:Instead of my explaining why the arguments are similar (afterall, logic is logic), why don’t you explain why you would call this non-believing Arab a ‘creationist’?
I am sure that some non-believers accept ID’s arguments which do nothing for the simple fact that ID’s claim about the Cambrian are based on creationist foundations. Or perhaps you could explain to us how, based on ID’s foundations, you have reached your conclusion about the Cambrian?
Lino responding to my statement that evolution is teleological This seems like an empty statement. Maybe you can help me understand what you mean. As it stands, it sounds like this: Nature is brought about by selection. Selection is brought about by Nature
Why is it an empty statement? Check out the various people who have commented on this such as Nagel, Ruse, Ayala. Selection selects for function, function is teleological. Let me know if you need more pointers (Google: ayala teleology evolution)
Lino: But even if it is true, the obvious reason they chose the pathway they did was because it was the most straightforward way of modeling evolution, meaning it was the least difficult to handle mathematically. Why fault them for that? You have to start somewhere don’t you? Why move on to the greater mathematical difficulty of including ‘recombination’ in the model when you haven’t yet ruled out the possibility that evolution can be modeled without using it?
Of course you have to start somewhere but if you start with an example which has little relevance to reality then why spend the time and effort to show that something which does not match reality could not have happened? If ID wants to be relevant it has to address real pathways not imaginary ones.
Lino: The set-up they’re using seems entirely reasonable, and very realistic.
Could you share your findings with us in more detail. What do you find reasonable and realistic?
Lino: The obvious difficulty with this assertion is that the bacterial emergency repair mechanism is irreducibly complex. If all the parts (and algorithms must have parts) are present, then the bacteria die. If you want to invoke the ‘miracle of all miracles’, that is, ‘neutral evolution’, then there’s this problem: Behe and Snoke have ruled out that possibility.
You must have misunderstood Behe and Snoke’s argument because they have not ruled out neutral mutations. I thought you said you had read the paper, or was it just the introduction?
So let’s explore this biased mutations again. IDists, including you?, seem to argue that biased mutations are evidence of design. I would agree to the extent that the designer is ’selection’. In other words, variation and selection can at least in principle help explain how evolvability evolves. As I explained before, the first step towards evolvability is the degeneracy of the genetic code which means neutrality and neutrality means robustness and evolvability (Toussaint, Wagner, Stadler, Fontana).
Or to put it in more simplistic terms: the genome can learn from its past how to deal best with future challenges. Of course how well it can do this depends on how accurately the past models the future.
For instance hypermutations. When in stress bacteria can enter a state of hypermutations, allowing the to search for ’solutions’. Such a response can be very well understood in terms of evolution and I would be interested how ID explains this.
While I agree that the concept of neutral evolution may sound like a miracle to some, the fact is simple: neutrality is an essential part to evolution, increasing the ability to evolve (aka evolvability) and providing robustness. I would love to dive deeper into this concept since much research has been done to show how this is the case. In other words, theoretical and empirical foundations that show how neutrality not only is selectable but how it is important to evolvability as well as robustness.
Let me know if you are interested. Perhaps a new posting to discuss neutrality and evolution would be helpful.
And no, Behe and Snoke did not provide any evidence against neutrality. What they showed is that probabilities of neutrality only evolution goes down when one requires more multiple neutral mutations.
Comment by Pimothy-(PVM) — July 5, 2006 @ 1:39 pm
Pimothy-(PVM)
Function is NOT teleological! Function is….function. Seeing is seeing, and no more; hearing is hearing, and no more; urine production is urine producation, and no more.
It is design alone that is teleological. A designer must CHOOSE/SELECT various functions and meld them into a greater whole. That’s what intelligent agents do. In the field of biology we call it artificial selection.
I said I was reading it. And I didn’t say that they ruled out ‘neutral mutations’ in their experiment; I said that their experiment rules out the possibility of invoking ‘neutral mutation’ as an explanation of the presence of an algortihm.
Why? Because if you look at Figure 6, you will see that for lambda=10, a population of 10^30 is needed to bring the MR to fixation. What do 10 nucleotide bases represent in terms of information? I’m just guessing, but I bet it doesn’t represent more than 30 bits of information. That’s not even enough for one ‘byte’ of information in 32-bit computer programs. Behe and Snoke are modeling a “disulfide bond”–this is hardly an information rich reality.
Here’s a Behe quote from the Kitzmiller trial:
So, using Figure 6, and extrapolating both the top and bottom, a population of 10^40 would likely correspond to lambda=8 to 10 (remember the lines are slanted from bottom to top). So, using the most prolific non-viral reproducer on earth, over the entire span of biotic life here on earth, point mutations will generate only about two ‘bytes’ of information. Excuse me if I think that is a little less information than is needed to ‘evolve’ an algorithm.
It’s a very simple explanation. It’s a ‘defense mechanism’. If you were designing a bacteria to defend itself (keep itself alive) in various emerging environments, you would do well to equip it with a ‘defense mechanism.’ You see, hypermutation is really very suggestive of an ID premise.
And they’re not ’searching for a solution’, they’re generating enough different combinations to finally overcome the extremely low probabilities involved in reaching the ‘goal’ using the limitations of random generation. And it’s not ‘nature’ that selects the ‘goal’; it’s the bacteria. And they’re able to make this selection because they contain all the information necessary to make that choice.
The problem is much more serious than that. See my response above.
Comment by Lino D'Ischia — July 5, 2006 @ 8:01 pm
You think so? Please tell us where? Does Dawkins actually define what is meant by the term cumulative selection, or does he merely provide an example and claim that this is cumulative selection?
And even if the term is defined and the efficacy described in the book, does it necessarily follow that when someone claims “we have abundant experiemntal and observational evience for the efficacy of cumulative selection,” that what they claim as experimental and observational evidence for the efficacy of cumulative selection is actually the same as what is in the book? No, it does not, and thus the question is both valid and reasonable.
What does that “Duh” stand for? Is that a way of calling someone an ignorant creationist moron?
Comment by Scott — July 5, 2006 @ 8:25 pm
Where? What page?
On what page of the book does Dawkins define the term cumulative selection?
I know he says cumulative selection is more powerful than single-step selection, but that doesn’t mean much if he doesn’t define cumulative selection.
What does that “Duh” stand for? Is that a way of calling someone an ignorant creationist moron?
Comment by Scott — July 5, 2006 @ 8:36 pm
PVM.
Explain the false claim you are making that “the simple fact that ID’s claim about the Cambrian are based on creationist foundations.”
Have you read James Valentine’s “The Origin of the Phyla?” James Valentine is certainly not a creationist nor a supporter of ID and he voids Darwinism as mechanism for the Cambrian explosion.
Have you read Stephen Meyer’s article “Intelligent Design: The Origin of Biological Information and the Higher Taxonomic Categories” in the Proceedings of the Biological Society of Washington (volume 117, no. 2, pp. 213-239). This has nothing to do with creationism.
How can you make such outrageous claims? Don’t you think people will call you on it?
Comment by J. Cosgrove — July 5, 2006 @ 9:49 pm
It’s not a false claim, it’s a historical fact.
The fact that other people might independently state the same thing doesn’t change the historical fact that ID grew from Creationism. In the beginning, at least, IDers (such as Philip Johnson) made no effort to hide this fact.
Hopefully the course will include a section on the history of the ID movement, and this will clear things up for you?
Comment by Don Baccus — July 5, 2006 @ 10:03 pm
Don Baccus,
Your comment is irrelevant. We are talking about the Cambrian Explosion, James Valentine and Stephen Meyer. I am a supporter of ID and certainly not a creationist. It is not the issue here.
Address the fact that the all the phyla appeared fully formed and preceded all the diversity within the phyla. In other words a top down event. Don’t reply with some creationist/ID irrelevant nonsense that has nothing to do with this finding.
Comment by J. Cosgrove — July 5, 2006 @ 10:51 pm
Cosgrove: Explain the false claim you are making that “the simple fact that ID’s claim about the Cambrian are based on creationist foundations.”
Clear observable fact (see also the Dover trial)
Have you read James Valentine’s “The Origin of the Phyla?” James Valentine is certainly not a creationist nor a supporter of ID and he voids Darwinism as mechanism for the Cambrian explosion.
Yes I spent lots of money on this book and guess what, he states the following
Seems you have not read the book too carefully or have been misled by creationist sources. I am quite familiar how Valentine’s statements have been abused over time by creationists. However yours seems to be topping them all..
Have you read Stephen Meyer’s article “Intelligent Design: The Origin of Biological Information and the Higher Taxonomic Categories” in the Proceedings of the Biological Society of Washington (volume 117, no. 2, pp. 213-239). This has nothing to do with creationism.
Yes I have, a poorly written review with countless
problems. And Meyer’s creationist sources for many of his claims can be quite well documented.
How can you make such outrageous claims? Don’t you think people will call you on it?
I hope that people call me on what they believe to be outrageous claims and I will happily support them.
Comment by Pimothy-/-(PVM) — July 6, 2006 @ 12:33 am
Cosgrove What is the basis for this claim? Does Valentine endorse Darwinism as the mechanism that caused the Cambrian Explosion? If so, then where because I have a quote from him that says Darwinism is inadequate to explain it.
In “On the origin of Phyla”
I am quite aware that Valentine has been abused by creationists to support their position. Valentine, one of the foremost researchers of the Cambrian however seems to be quite clear.
As far as Meyer, his paper is pretty substandard and seems to recycle many creationist canards. Details surely will follow if requested.
Always willing (and able) to support my statements when called upon :-)
Comment by Pimothy+(PVM) — July 6, 2006 @ 12:38 am
Function is extremely teleological, heck Dembski even uses it as his ’specification’ in biology. Teleology and function have historically been seen as quite related concepts. Did I not give you some names to search for?
LinoI said that their experiment rules out the possibility of invoking ‘neutral mutation’ as an explanation of the presence of an algortihm.
Huh? This does not make much sense. Presence of an algorithm? We are trying to exlain the success of evolution in its ability to increase the information in the genome.
A bit ad hoc. Why would one propose a designer when natural processes can be sufficient in explaining hypermutations?
Of course, a designer can do almost anything so how do we know he is interested in providing bacteria with their ability to fester diseases :-)
Seems the designer has some interesting fascination with diseased…
Lino And it’s not ‘nature’ that selects the ‘goal’; it’s the bacteria. And they’re able to make this selection because they contain all the information necessary to make that choice.
Many more unsupported assertions. The bacteria during starvation enters in a stage of ’stress’ or ‘hypermutations’. The chemistry involved is quite well understood. Do the bacteria do the selecting? How?… Could you show how they contain the infromation to make that choice? Do you mean that the bacteria come prepared for all situations of stress and have a built in answer or is it that hypermutation generates sufficient variation for the bacteria to ‘find a solution’? If bacteria know the solution, why the wasteful response?
Science has answers, ID merely claims which remain unsupported and do not even follow from the basic premises of ID.
Comment by Pimothy+(PVM) — July 6, 2006 @ 12:46 am
PvMComment 1 “So many errors. In fact the evidence shows a nice nested hierarchy all the way into the pre- Cambrian. The top-down versus bottom-up again is a fallacy. A nested hierarchy by logical necessity starts with a phylum since the first ’species’ is also the phylum, family, order etc.”
Cosgrove What is the basis for this claim? Please be specific and in particular if you could quote from James Valentine latest book “The Origin of the Phyla” it would be useful. I do not have the book but just ordered it from Amazon so maybe we can compare your interpretation with what is in the book.
I am more than happy to oblige
Common objections to the Cambrian explosion and the tree of life include the ‘top-down/bottom-up’ fallacy which is based on equivocation of two different kind of trees.
TOP-DOWN OR BOTTOM-UP
Some critics of evolution make much of the “top-down” versus the “bottom-up” pattern of appearance of higher taxa. That is, phylum-level diversity reaches its peak in the fossil record before class-level diversity, and the class-level diversity before that of orders, etc. These critics interpret this apparent “top-down” pattern as contrary to expectations from evolutionary theory. However, this pattern is generated by the way in which species are assigned to higher taxa. The classification system is hierarchical with species being grouped into ever larger and more inclusive categories. When this classification hierarchy is applied to a diversifying evolutionary tree, a “top down” pattern will automatically result. Consider species belonging to a single evolving line of descent given genus-level status. This genus is then grouped with other closely related lines of descent into a family. The common ancestors of these genera are by definition included within that family. Those ancestors must logically be older than any of the other species within the family. Thus the family level taxon would appear in the fossil record before most of the genera included within it. The “top down” pattern of taxa appearance is therefore entirely consistent with a branching tree of life.
(Keith Miller on Wells)
and
Continuing to move the shells, Wells invokes a semantic sleight of hand in resurrecting a “top-down” explanation for the diversity of the Cambrian faunas, implying that phyla appear first in the fossil record, before lower categories. However, his argument is an artifact of taxonomic practice, not real morphology. In traditional taxonomy, the recognition of a species implies a phylum. This is due to the rules of the taxonomy, which state that if you find a new organism, you have to assign it to all the necessary taxonomic ranks. Thus when a new organism is found, either it has to be placed into an existing phylum or a new one has to be erected for it. Cambrian organisms are either assigned to existing “phyla” or new ones are erected for them, thereby creating the effect of a “top-down” emergence of taxa.
(Gishlick ICONS OF EVOLUTION? Why much of what Jonathan Wells writes about evolution is wrong)
Dawkins:
Suppose you have a great oak tree with huge limbs at the base and smaller and smaller branches toward the outer layers where finally there are just lots and lots of little twigs. Obviously the little tiny twigs appeared most recently. The larger boughs appeared a long time ago and when they did appear, they were little twigs. What would you think if a gardener said, “Isn’t it funny that no major boughs have appeared on this tree in recent years, only small twigs?” You’d say he is stupid.
(Richard DawkinsTHE “ALABAMA INSERT”: A STUDY IN IGNORANCE AND DISHONESTY)
Richard Dawkins, THE “ALABAMA INSERT”: A STUDY IN IGNORANCE AND
All are referenced in Icons of ID: Darwinian predictions and the Cambrian
See how Wells quoted Valentine (Wells part is in BOLD)
In general, for those taxonomic levels for which fossil data seems adequate, higher levels reached their peak diversities earlier, and successively lower levels progressively later, in geologic time (Valentine, 1969). This pattern creates the impression that metazoan evolution has by and large proceeded from the “top down,” that the body plans of the phyla originated presumably as adaptations that permitted the occupation of major adaptive zones, and then, according to the potentials and constraints provided and imposed by the body plans, they in turn branched to produce the major modifications that are ranked as classes, and so on to the ordinal [order] level and below….
Hope this helps clarifiy this issue. Does it surprise you?
Comment by Pimothy+-+(PVM) — July 6, 2006 @ 12:56 am
Comment by Owen Phelps — July 6, 2006 @ 6:21 am
Meyer’s “The origin of biological information and the higher taxonomic categories” was shredded by numerous individual and scientific organizations. A great example of this shredding can be accessed at the National Center for Science Education website at http://www.ncseweb.org/resources/news/2004/ZZ/463_id_in_the_spotlight_8_27_2004.asp. What I found interesting is that Meyer’s presents no new research. He simply rehashes other peoples work. Unfortunately, many of the sources he cites raised the ire of the actual authors whom he cites. Some of these authors were ticked off when Meyer misrepresented their work. Isn’t it getting obvious . . . those in the ID camp never present actual research, especially Meyer!
Comment by Mike Hannigan — July 6, 2006 @ 9:59 am
Sal claims the following about Dawkins
Remember that according to the definition of ID, complex specified information (CSI) disappears when science finds an explanation for the system. In other words, CSI is a circular argument that states that natural processes cannot explain CSI. Of course not, CSI disappears once you explain it.
But there lies the achilles heel of ID, namely that when ID gets to explain the system, CSI similarly disappears since the probability of the system approaches 1 and the information/complexity measure, which is the logarithm of the probability, goes to zero,
In other words
1. ID defines CSI in such a way that natural processes cannot explain it since CSI disappears once the process is explained.
2. ID avoids the logical conclusion that if CSI disappears when science explains it, that CSI should disappear as well if ID explains it.
Neat trick eh…
Comment by PvM — July 6, 2006 @ 12:30 pm
Mike Hanigan: Meyer’s “The origin of biological information and the higher taxonomic categories” was shredded by numerous individual and scientific organizations.
Yes, PandasThumb was one of the many, and early ones, which provided a thorough rebuttal of this paper.
A great example of this shredding can be accessed at the National Center for Science Education website at http://www.ncseweb.org/resources/news/2004/ZZ/463_id_in_the_spotlight_8_27_2004.asp. What I found interesting is that Meyer’s presents no new research. He simply rehashes other peoples work.
That’s but one of the problems of ID in that it seems to be unable to perform any novel research themselves.
Unfortunately, many of the sources he cites raised the ire of the actual authors whom he cites. Some of these authors were ticked off when Meyer misrepresented their work. Isn’t it getting obvious . . . those in the ID camp never present actual research, especially Meyer!
There lies the problem namely that Meyer was shown to be selective in his evidence and making various unsupported assertions.
I have documented some relevant examples on PT
Meyer when discussing [1] the Cambrian period states the following
[3]
The full reference reads: Valentine, I. W. 1995. Late Precambrian bilaterians: grades and clades. Pp. 87—107 in W M. Fitch and FJ. Ayala, eds., Tempo and mode in evolution: genetics and paleontology 50 years after Simpson. National Academy Press, Washington, D.C..
The paper also appeared in PNAS as: Valentine, J.W. 1994. Late Precambrian bilaterians: grades and clades. Proc Natl Acad Sci U.S.A. July 19; 91 (15): 6751-6757.
Notice my surprise when I thus read
But perhaps the measure used by Valentine would give some support to Meyer’s arguments?
So why would Meyer quote Valentine as supportive of Meyer’s claim that
When the actual paper does not lend much support to such a thesis?
References
[1] Stephen C. Meyer, The origin of biological information and the higher taxonomic categories, PROCEEDINGS OF THE BIOLOGICAL SOCIETY OF WASHINGTON 117(2):213-239. 2004
[2] As others already have shown, Meyer makes no attempt to show that his concept of CSI has any relevance to a similarly named concept found in the works of William Dembski.
[3]As is typical (see (Pennock [4]) with Meyer, this is a verbatim quote of an earlier paper by Meyer, Ross and Chien “The Cambrian Explosion: Biology’s Big Bang”.
[4] See Pennock DNA by Design?: Stephen Meyer and the Return of the God Hypothesis.
In Ruse, Michael and William Dembski (eds) Debating Design. New York: Cambridge University Press for more examples of how Meyer recycles his claims.)
Comment by PvM — July 6, 2006 @ 12:37 pm
J. Cosgrove
Your comment is irrelevant. We are talking about the Cambrian Explosion, James Valentine and Stephen Meyer. I am a supporter of ID and certainly not a creationist.
That’s funny. So what are your “mysterious alien beings” doing when they do their mysterious things to life forms on earth if they are not “creating”?
Seriously.
Comment by Susan Percell — July 6, 2006 @ 2:33 pm
Lino
It’s a ‘defense mechanism’. If you were designing a bacteria to defend itself (keep itself alive) in various emerging environments, you would do well to equip it with a ‘defense mechanism.’
Would I do well to equip it with a “defense mechanism” that doesn’t work very well? Because a whole hell of a lot of the bacteria die during the SOS response. But I guess you’re going to tell me that I’ve already designed bacteria to reproduce rapidly so I don’t need a very robust system to keep the species alive. But remind me: why didn’t I put little wings on all them so they can fly to a better environment? And why did I make some bacteria really deadly to humans? Maybe I was bored and needed excitement. Or I wanted to give scientists something to study. Yeah, that’s it.
This ID research is sorta fun, actually. When do I get my Ph.D. in ID research?
Comment by Susan Percell — July 6, 2006 @ 2:43 pm
Lino
And it’s not ‘nature’ that selects the ‘goal’; it’s the bacteria. And they’re able to make this selection because they contain all the information necessary to make that choice.
And the fact that most of the bacteria die? Is that because they’re stupid?
Comment by Susan Percell — July 6, 2006 @ 2:46 pm
This is wonderful, Throw out enough irrelevant information and people will be unable to know what is going on. The fact is that the phyla came out of nowhere. There was nothing preceding all these various body plans. A full blown ecology popped right into existence in an incredibly short geological time period.
What caused the different body plans to appear? There is no answer. There haven’t been any new phyla since. Why? Yes some did show us a little later but Valentine believes they were around during the Cambrian explosion but not yet discovered.
Here is Valentine’s quote again in case you missed it,
“Darwin had a lot of trouble with the fossil record because if you look at the record of phyla in the rocks as fossils why when they first appear we already see them all. The phyla are fully formed. It’s as if the phyla were created first and they were modified into classes and we see that the number of classes peak later than the number of phyla and the number of orders peak later than that. So it’s kind of a top down succession, you start with this basic body plans, the phyla, and you diversify them into classes, the major sub-divisions of the phyla, and these into orders and so on. So the fossil record is kind of backwards from what you would expect from in that sense from what you would expect from Darwin’s ideas. Although once we get into the fossil record where we got a complete fossil record we can see the gradual changes within lineages as Darwin predicted.”
In case you do not understand what Valentine just said. He said the process was a top down phenomena. He said it was the opposite of Darwin’s theory. So once the phyla come into existence the process then proceeds in a somewhat Darwinian manner. So you still have to deal with where did the phyla come from. And here Valentine speculates but it is not Darwinian and it is just speculation.
Another comment – Every time someone tries to tie ID to creationism you are just indicating the weakness of your arguments. Deal with the claims made and do not try to bring religion into the discussion. It is another irrelevant rhetorical technique and is used to play to the stereotypes people have.
The comment by Susan Purcell is sophmorphic. It is arrogant and indicates a lack of seriousness. Deal with the evidence.
Comment by J. Cosgrove — July 6, 2006 @ 3:03 pm
PvM said:
That is indeed the achilles heel of ID. Of course, you committed the cardinal sin of bringing up the probability of a designed event, which means that your comment will be filtered out by ID proponents’ browsers.
If “necessity” means that an event occurs with a probability of 1, and “chance” means that it occurs with a probability of less than 1, and designed events are not a product of necessity or chance, then the probability of a designed event is neither 1 nor less than 1. In other words, it’s a mathematical impossibility, which makes it a huge taboo elephant in the ID living room.
Comment by secondclass — July 6, 2006 @ 3:07 pm
J. Cosgrove
The comment by Susan Purcell is sophmorphic.
You’re dissembling. Answer the question.
It is arrogant and indicates a lack of seriousness.
You’re dissembling. Answer the question.
Deal with the evidence.
I am. More importantly, I’m dealing with the fact that you have zilcho evidence for the existence of “mysterious alien beings” who act in “mysterious ways” using “mysterious forces” for “unknowable reasons.”
You said you were an ID supporter but not a creationists. Now, answer the question: what are your “mysterious alien beings” doing to alter the appearance of every form of living organism that ever lived on earth if those mysterious alien beings are not “creating”?
Just answer the question. Either that or admit that the difference between “ID supporting” and “creationism” is a politically contrived difference hopelessly intended to distance ID *legally* from creationism.
And while you’re at it, remind Lino that biologists do not usually refer to each other as “Darwinists” but creationists very often call professional biologists “Darwinists”. As do ID supporters. Interesting, isn’t it?
Comment by Susan Percell — July 6, 2006 @ 3:27 pm
J. Cosgrove
So you still have to deal with where did the phyla come from.
Dude, a phylum is an artificial (i.e., human-made) grouping of organisms according to shared characteristics. The creatures in those phyla “came from” creatures who looked similar — but not exactly identical — to them. The farther back in time you go, the less similar the creatures look to their descendents (generally speaking). Do you have some new evidence which casts serious doubt on the way in which organisms reproduce and share their genetic material? Do you think that back in the Cambrian organisms reproduced in fundamentally different ways? Any evidence to support this fundamentally different mode of reproduction?
Is this where your “mysterious alien beings” come in? Did they fly in on saucers or did they use some sort of magical ray to cause animals in the Cambrian to evolve rapidly?
Oh, I forgot: we aren’t allowed to ask you that! Very serious business, this creationism/ID theory stuff.
Comment by Susan Percell — July 6, 2006 @ 3:51 pm
Okay– I know after 136 comments it’s perhaps unavoidable that we all have rather low opinions of each other, but we’re going to need a stronger attempt to be civil. Please go and re-read the ground rules before posting your next comment.
If you are completely exasperated by your fellow commentators and feel they don’t deserve that civil answer, you may need to take a break from the thread for a while.
As a side note: it makes your posts much more interesting to read– at least for us here at Cornell– if you can stick to the topic at hand. If you’ve got a favorite notion, such as “mysterious alien beings”, “vacuity”, or some such thing, we’d pay far more attention if you can manage to save it for when it has more than an incidental relevance to the topic.
I suppose part of the problem there is that the “topic at hand” has been pretty much exhausted over our long July 4th vacation. We have class both tonight and tomorrow night, so there should be more material to cover soon.
Comment by Hannah — July 6, 2006 @ 3:55 pm
Susan Percell,
James Valentine defined phyla in his book and in other places. He uses the phrase “body plans” often. There are people who quibble with this definition as well as other taxonomic terms but he wrote the book and is considered the world’s expert on the Cambrian Explosion.
If you want to challenge Valentine’s definitions, findings, conclusions or approach, go right ahead but provide us with the rationale for your challenges. Right now I will use him as a source and he is definitely not a supporter of ID.
Comment by J. Cosgrove — July 6, 2006 @ 9:35 pm
If you want to challenge Valentine’s definitions, findings, conclusions or approach, go right ahead
Why would I want to challenge Valentine? Does he believe that mysterious alien beings must have been involved in effecting the observed organisms whose fossils we find in the Cambrian? He seems to be an evolutionary biologist, not a creationist. Why would I challenge him?
Right now I will use him as a source
a source for supporting an argument that the creatures in the Cambrian did not evolve without the help of mysterious alien beings? I wonder what Valenite would think about that. Shall we ask him?
If you’ve got a favorite notion, such as “mysterious alien beings”, “vacuity”, or some such thing, we’d pay far more attention if you can manage to save it for when it has more than an incidental relevance to the topic.
Hannah, mysterious alien beings lie at the core of every design argument. They are relevant to any discussion about evolution in which “gaps” in historical evidence (i.e., the necessarily incomplete fossil record) are presented as “evidence” that the evolutionary theory for explaining the diversity of the earth’s life forms is “flawed.” If “intelligent design theory” no longer includes a resort to the actions of mysterious alien beings, then that’s big news. Headline news, really. Are we going to break the story here?
Comment by Susan Percell — July 6, 2006 @ 10:25 pm
Susan Percell,
It is a shame Carl Sagan is still not alive. He was a very popular Cornell professor who might have been able to answer your concerns about mysterious aliens. Maybe ask the SETI people. They may be able to help you.
Unfortunately, I cannot. I prefer to stick with the evidence of what has been found. My main concern here is that the Darwinian process cannot explain the Cambrian Explosion, something I agree on with James Valentine.
Maybe there will be new findings in the future that will change that conclusion but current data supports a non-Darwinian explanation, whatever it might be.
Comment by J. Cosgrove — July 7, 2006 @ 10:10 am
Casgrave:
Despite me showing that Valentine disagrees with this conclusion, Casgrave continues to misrepresent Valentine’s position. A flawed understanding of the Cambrian explosion which extends (deep) into the precambrian, a confusion about top-down/bottom up and how it applies to evolutionary theory all lead IDers to a flawed conclusion. Meyer’s poor paper on this topic has caused more harm than done good. I will spend some time in the next few days to explore how science looks at the Cambrian explosion and how said event can be explained in evolutionary terms, including Darwinian evolution.
Even the quote of Valentine, shows no support for Casgrave’s position. The quote describes how in Darwin’s times the Cambrian was seen as enigmatic and yet when additional information became available, its evolutionary mechanisms have become more clear. It’s once again that ID relies on science’s ignorance to further its claims about the Cambrian. May I also point out that the Cambrian ‘arguments’ once again have their roots in creationisms which relies on independent origins. Casgrave insists that phyla arose with no precursors and yet the available evidence shows the contrary.
Comment by Pimothy-PvM — July 7, 2006 @ 12:49 pm
J Cosgrove
Maybe there will be new findings in the future that will change that conclusion but current data supports a non-Darwinian explanation, whatever it might be.
If this is true, then why can’t you show us, say, a dozen papers by evolutionary biologists in peer reviewed journals which make that claim, unreserverdly, point blank? This would seem trivial to do if what you were saying is, in fact, the opinion of professional biologists based on the evidence as opposed to just hand waving by an “ID supporter”.
And I’m still waiting to here when and where “ID theory” stopped including mysterious alien beings. This is a big revelation, JC. If “ID supporters” no longer believe that mysterious alien beings are tweaking life on earth, then I have no idea what an “ID supporter” is. You claim to be one so maybe you can help explain this conundrum to us.
Comment by Susan Percell — July 7, 2006 @ 2:19 pm
Pimothy:
You say, “Function is extremely teleological.” This is no more than a patent assertion. You have a harddrive in your computer. It performs a certain function. Now, take the harddrive out of your computer. Now put that harddrive into a Tivo box. It’s still performs the same function, but has an entirely different ‘end’. Function is not explicitly teleological. It becomes teleological only when it is integrated into some greater role.
As to Dembski, if you had understood him properly, you would have understood that in studying an object that performs particular functions, that those functions help ’specify’ that particular object; any ‘teleology’ present comes from the INTEGRATION of these various functions into an operating whole; just like your computer uses your hard drive to help you surf the net.
You have perhaps forgotten that this topic came up as a result of Leonid’s assertion that ID is unfalsifiable. I said that if an algorithm for the bacteria’s SOS response could not be found, this would invalidate ID. Point out what’s wrong with my argument—–or accept what logically follows from it.
But you see, Pimothy, there’s this unsettling fact that Behe and Snoke’s paper mathematically demonstrates what common sense indicates: random mutations plus selection won’t produce anything whatsoever–it gets nowhere. That rules out Darwinism. Now, since Darwinism is ruled out, what does the amazing complexity of the eukaryotic cell imply? The presence of Grand Intelligence. That’s why ID is making headway. Because it conforms to common sense and to what we’re discovering every day about nature.
Am I to understand that we are now having a discussion of theology? Since you’ve begun this theological debate, then let me give you a theological answer: Maybe the Good Lord made the world the way it is so that all of us might yearn for a better world (’a new heavens, and new earth’), and so that people who have a difficulty believing in God might have reason to pray, and thus be saved. But let it be noted, it was the Darwinists who first started asking questions about theology.
Assertions? It doesn’t take a lot of thought to see that this ‘response’ is a pre-programmed response. And, as I said above, “they’re not ’searching for a solution’, they’re generating enough different combinations to finally overcome the extremely low probabilities involved in reaching the ‘goal’ using the limitations of random generation. Once a ‘mutation’ is brought about that is able to counteract the ’stress’, then the bacteria goes back to normal functioning. ‘Nature’ doesn’t select this ‘beneficial mutation’, the bacteria does, depending on the circumstances. Most likely there is some kind of feedback loop that ’signals’ to the bacteria that the ’stressor’ has been counteracted.
The bacteria don’t ‘know’ the proper solution, they ‘discover’ it. Let me give you an analogy to what’s going on here. The French say: “If you give a man a fish, you feed him for a day. If you give him a fishing pole, you feed him for life.” It makes more sense to have a “one-size fits all” mechanism to handle all such ’stressors’, than to have a ‘built-in’ solution for every ‘possible’ ’stressor’. THAT would be wasteful.
Yes, the kind that Behe and Snoke provide. But apparently you don’t like their answer. (Oh, but it isn’t in a peer-reviewed journal! Oops, but in fact it is)
Comment by Lino D'Ischia — July 10, 2006 @ 1:13 pm
Stenography, contrary to Salvador’s assertion, is not an “advanced ID topic”. It has existed as a sub-topic of cryptography long before the emergence of the ID movement
You’re thinking of steganography. Stenography is the practice of writing in shorthand.
Comment by arensb — July 10, 2006 @ 6:00 pm