The Altenberg Sixteen

_{Paul Nelson

March 4, 2008

Intelligent Design}

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HT to Larry Moran’s Sandwalk for the link to this fascinating long piece by journalist Suzan Mazur about an upcoming (July 2008) evolution meeting at the Konrad Lorenz Institute in Altenberg, Austria.

“The Altenberg 16” is Mazur’s playful term for the sixteeen biologists and theoreticians invited by organizer Massimo Pigliucci. Most are on record as being, to greater and lesser degrees, dissatisfied with the current textbook theory of evolution. Surveying the group, I note that I’ve interacted with several of the people over the years, as have other ID theorists and assorted Bad Guys. This should be an exciting meeting, with the papers to be published in 2009 by MIT Press.

Mazur’s article is worth your attention. Evolutionary theory is in — and has been, for a long time — a period of great upheaval. Much of this upheaval is masked by the noise and smoke of the ID debate, and by the steady public rhetoric of major science organizations, concerned to tamp down ID-connected dissent. You know the lines: “Darwinian evolutionary theory is the foundation of biology,” et cetera.

But the upheaval is there, and increasing in amplitude and frequency.

[Note to Kevin Padian: journalists don’t like it when you do this to them. Mazur writes:

Curiously, when I called Kevin Padian, president of NCSE’s board of directors and a witness at the 2005 Kitzmiller v. Dover trial on Intelligent Design, to ask him about the evolution debate among scientists –- he said, “On some things there is not a debate.” He then hung up.

That hanging-up part…not so wise. If you’re going to say there’s no debate, explain why.]

Comments

Allen_MacNeill Welcome back. Appreciate you willingness to take up these issues. On Sanford, you say:
"all lineages of organisms should eventually degenerate and disappear because their genomes “decay”. However, that would only be the case if their genomes: 1) had no built-in error correction mechanisms (which all do, and which use “sex” – that is, exchange of genetic material — as part of the mechanism); and 2) depended completely on the genome for assembling and operating the organism."
(without access to Sanford's Genomic Entropy) I don't think 1) applies. I believe the population models that Sanford reviews result in an accumulating load of near neutral mutations even with the be full sexual reproduction and error correcting mechanisms functioning. One of the most critical parameters is the ratio of harmful to beneficial mutations. Sanford cites literature estimating this at least 1,000 to 1, and possibly one million to one. I believe this ratio dominates all neo Darwinian hopes of "development". Please clarify how your 2) follows. I do not see how that would invalidate Sanford's arguments, as they would apply in both cases.
"Once again, genomes do not construct organisms; organisms construct organisms, in concert with their environment."
I agree with you here. See Jonathan Wells comments on embryology where he gives much more detail on the importance of the embryo vs the genome.
. . .extract fragments of dinosaur DNA from fossilized mosquitoes, splice them together with DNA from living frogs, then inject the combination into ostrich eggs which had had their own DNA inactivated. . . . In every case, if any development occurred at all it followed the pattern of the egg, not the injected foreign DNA. . . .DNA does not program the development of the embryo.
Your comments point back to the Origin of Life.
Omne vivum ex vivo The foundational observation of biology: Omne vivum ex vivo (Latin: Only life from life) is first attributed to William Harvey, c. 1630 (1) — William Harvey, c. 1630 (1). (Also referred to as: Omne vivum ex ovo - Latin: only life from an egg.) Louis Pasteur disproved the prevailing theory of spontaneous generation, showing conclusively that biological life was never observed rising spontaneously from sterilized media.
i.e., Both the genome AND the surrounding cell are essential to self reproducing life. This points to the recursive nature of life. From mathematics and controls, this consequently means that the starting conditions are also essential to life. {DLH corrected from (10,000 -1 million) to (1,000 to 1 million) per Sanford (2005) p 24.}DLH_{March 6, 2008
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DaveScot:
“The only criticism I had of Sanford’s book is he cites literature supporting a background mutation rate orders of magnitude higher than the commonly given rate.
Actually, I'm not sure its the mutation rate that is the trouble. It seems rather that he counts mutations that are in DNA that is not (yet) known to do anything. That said, even if you eliminate the mutatations in apparently inactive DNA, he still has a fundimental case. As far as I can see, even optimal natural cannot work in an environment with greater than 1 mutation per generation. In higher organisms, the generation that must be considered is when a male and female get together to reproduce, not the generation of a single cell, because it is the organism from birth to reproduction that is tried in the fire of natural selection. Alas, whether we are degrading fast or slow, if we are degrading, this would be a problem. It is still frustrating when cases are exaggerated. The exaggeration gets shot down, and the baby goes out with the bathwater.bFast_{March 6, 2008
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DaveScott "The only criticism I had of Sanford’s book is he cites literature supporting a background mutation rate orders of magnitude higher than the commonly given rate and by that means makes a case for genetic entropy destroying a genome in thousands of years. . ." Since mutations, hybrids etc appear to be Sanford's expertise and commercial involvement, I would think he would be well abreast of those parameters. Can you suggest any reviews or papers on the mutation rates that show values significantly differ from the values Sanford cites?DLH_{March 6, 2008
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Above: I think that all of us software types find the idea that man is described by 25,000 genes, or 4 * 25,000(genes) * 300(nucleotides/gene) bits of information to be a bit inconcievable. I do understand that epigenics is that which is not in the DNA, and that the above only calculates the "coding" DNA. However, even the entire human DNA, if none is junk, is some darn impressive tight code if it produces a human with all of his inhereted characteristics.bFast_{March 6, 2008
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Allan_MacNeill:
Indeed, I am not conversant with systems level evolution at all. My specialties are ...
I appreciate your honesty. As with many IDers, I am solidly in the common descent camp. Not to say that I totally reject any challenge to common descent, but that I have seen compelling evidence for common descent, including man from "apes", and I have seen no compelling case to challenge common descent. Basic evolutionary theory seems to hold significant components of truth. This includes variation, and natural selection. I am not prepared to go as far as Dembski when he suggests that new useful information cannot be generated via these natural mechanisms. It seems compelling to me that if a gene is duplicated, then each copy becomes the followed copy for two separate tasks, a divergence from the original in one of those copies is both expected, and information increasing. Ie, I don't by any means throw out all of neo-Darwinian biology. However I am compelled by Behe's case of Irreduceable Complexity. I think, however, that he has taken off too big of a bite when he looks at genes as single non-morphing units (he recognizes that the do morph, but doesn't account morphing in his discussion.) I prefer to examine irreduceable complexity found on the point mutation level, such as with the HAR1F. We have 150 million years * some 20,000 species of evidence that the thing is non-mutating (it is ultra-conserved). Yet in man it has taken on 18 mutations, 18 that cause a slip-cog in its 3d shape. I think it a much simpler, therefore less refuteable, case of IC. I think that the clearest published thinker on the issue of systems evolution is Behe. I think the best text on the subject is Darwin's Black Box. I appreciate your discussion of epigenics. I think that all of us software types find the idea that man is described by 25,000 genes, or 4 * 25,000(genes) * 300(nucleotides/gene) bits of information to be a bit inconcievable. That said, I think that epigenic replication is similar to DNA replication in many ways. The epigenic portion of the cell clearly gets copies. There are surely copying errors (mutations). These copying errors most usually would be destructive to an organism. As such, by adding the epigenic data to the mix, we increase the count of copying anomolies that are experienced per cell duplication. My computer simulations challenge that a maximum of one mutation in active information can be tolerated per generation to allow nautral selection to select for it. Whenever the copy error rate goes beyond 1 deleterious copying error (copying errors, as far as I can see are either in inactive regions or are nearly always destructive) even idealised, computer generated selection could not maintain the code. As we know, however, humans have far more than one destructive mutation per reproductive cycle. That's just in the DNA, let alone the epigenic data. The net result is that there seems to need to be another data preservative beyond natural selection. Additional evidence for the need of an additional data preservative includes the discovery of ultra-conserved DNA sequences that do not have any obvious function in the organism. We recently discussed evidence of a data preservative in plants (barley, wasn't it?) However, we also get to the interesting topic that you brought up w/ DaveScot, re the six-leg thing. I started an interesting thread in ISCID's brainstorms about polydactilism (six-finger syndrome). When quadrupeds first appear in the rock record, they had 8, and 6 digits per limb. At some point early on, they settled on 5. Five has been the maximum for any prototypical (not a mutatant within its species) quadruped since then, as far as I can tell. Nature has experimented with 4, 3, 2 and 1 digit creatures. Nature has extended the wrist bone of the pandas to produce a simulated 6th digit. Yet despite all of the variety of quadrupeds, none have concluded that 6 digits would be an easy way to make a large foot (rabbits, polar bears, desert animals) or a large flipper (aquatic quadrupeds). You would think, based upon this data, that the code for 5 digits would be deeply engraned in the hox genes or something. But no, polydactilism has shown up as an anomoly in humans, cats, dogs, and mice. It is, in all cases, caused by a single point mutation. The six-digit creatures appear to have no deleterious side-effects. Some human cultures have valued six-digitism, even killing their five-digit young. Yet pentadactilism has proven to be universal. Why? I think that the only explanation is that there is another preservative.bFast_{March 6, 2008
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And a partial qualification: Echinoderms actually have hundreds or even thousands of "legs" - the little "tube feet" that sprout from their ventral surfaces. I suspect that the "arms" of sea stars are so structurally and functionally different from the appendages of both arthropods and vertebrates that they follow completely different developmental rules. So perhaps the "paired appendages" rule is intrinsic to jointed legs?Allen_MacNeill_{March 6, 2008
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What it will take for me to accept it, however, is a rigorous and long-term program of intensive empirical testing of hypotheses that clearly differentiate between alternative hypotheses. Until this has been accomplished, all we are doing is speculating without evidence.
I agree 100%. Unfortunately, it then becomes an issue of funding and resources. Which is why I suggest a middle ground as a starting point, so that ID proponents won't find their careers endangered or funding taken away. ID research is generally almost a "hobby" in comparison to the needed income the day job brings*. There is some work slowly being done, but it's not enough in comparison to what could be done. But even if a middle ground does not work out the good news is that the equipment is getting cheaper every year. So salaries will be the largest cost. So funding such a research program should become attainable I'd hope. *No insult intended. Honestly, is there anyone where ID research IS their primary source of income?Patrick_{March 6, 2008
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And touché: I had forgotten about the pentaradial Echinoderms and the Bivalvia. Exceptions that test the rule, eh?Allen_MacNeill_{March 6, 2008
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DaveScot: Yes, I did read John's book (I was given a free copy when he came to our class), and was impressed with his arguments, but once again not convinced. Once again, his argument is essentially that without some "magical" input, all lineages of organisms should eventually degenerate and disappear because their genomes "decay". However, that would only be the case if their genomes 1) had no built-in error correction mechanisms (which all do, and which use "sex" – that is, exchange of genetic material — as part of the mechanism); and 2) depended completely on the genome for assembling and operating the organism. As you yourself have repeatedly pointed out, the latter is clearly not the case. I agree. As to your chicken's egg example, you have amply supported precisely the point I was trying to make. If you don't provide heat and turn the egg every now and then, you don't get a chicken. Therefore, at least two external sources of information are absolutely essential for the production of newly-hatched chicks from eggs. We don't yet know how many such sources of information there are, nor what effects they have on developmental programs, nor how such programs work, nor how they change over deep evolutionary time. That's what empirical investigations are for, right?Allen_MacNeill_{March 6, 2008
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In case any of you are interested in the (literally) gory details, I have now finally posted an explanation of why I have been out of commission for so long. It's at my blog: http://evolutionlist.blogspot.com/2008/03/on-problem-of-pain.htmlAllen_MacNeill_{March 6, 2008
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Allen This “external” information is absolutely essential for regulating development. Ever hatched a chicken egg under a light bulb? I did. Try it and get back to me about how much information the environment provided. You can roll the egg over from time to time like a mother hen does if you want, or not. I fail to see how even gravity is providing any information to the egg when its rolled over at odd intervals. The chick that hatches is pretty much just a tiny adult chicken. I could simply use a budding yeast cell in isolation instead of chicken egg to get around your assertion that the egg gets information while it's still inside the chicken. Clearly all the information (essentially) to build an organism is contained within a single cell. re; John Sanford You should probably read Sanford's book (I did) before criticizing it. What you took from the lecture is not an entirely accurate reflection of what he wrote in the book. For one he discusses the whole genome not just coding genes. Second your objection that he doesn't include epigenetic information (which is true, even in the book to the best of my recall) is irrelevant because the genome, if not the sole repository of heritable information, is a repository of very critical information which quite easily renders the organism unviable when there are mistakes in it. Epigenetic information or not, the genome is critical and failure to maintain it well results in disability and death. The only criticism I had of Sanford's book is he cites literature supporting a background mutation rate orders of magnitude higher than the commonly given rate and by that means makes a case for genetic entropy destroying a genome in thousands of years (I presume to be in accord with Young Earth Creationism) while the testimony of the fossil record is that species persist (relatively unchanged) for an average of 10 million years before they mysteriously disappear as abruptly as they entered the record. I wrote an article here last week asking not why almost all species go extinct without spawning any new species(genetic entropy explains that quite well) but rather how a lucky few cell lines managed to avoid the catastrophic effect of genetic entropy for hundreds of millions or billions of years. I speculated that there's a disaster recovery mechanism at work that restores a genome to a previously known working state. This is how we address the problem of "software entropy" in computer systems and my experience has been that anything human engineers invent to solve problems likely has an analog in the machinery of life for the same class of problem. There are no animals of which I am aware that have unpaired appendages Starfish (5 legs) and clams (1 leg) come immediately to mind as animals without paired legs but if you restrict the discussion to articulated legs then you have me stumped for an answer. DaveScot_{March 6, 2008
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Patrick asks: "...would the majority of Darwinists find such a hypothetical scenario acceptable?" I can't speak for my colleagues (nor would they let me ;-), but I do not reject such a possibility out of hand. What it will take for me to accept it, however, is a rigorous and long-term program of intensive empirical testing of hypotheses that clearly differentiate between alternative hypotheses. Until this has been accomplished, all we are doing is speculating without evidence.Allen_MacNeill_{March 6, 2008
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Hi Allen, Thanks. Yes, that does make me feel better. And actually, I have read the Huxley letter - you've quoted from it and linked to it several times previously. CharlieCharlie_{March 6, 2008
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I agree, and for the same reasons that I assert that the “modern evolutionary synthesis” is now outmoded. ... We now know that both of these are inadequate to explain observed patterns of development and descent with modification. This is why I am advocating that we all recognize that the “modern synthesis” has for at least fifty years been gradually replaced by what could more precisely be called the “evolving holistic synthesis”, one that recognizes at least four different modes of evolutionary change (i.e. genetic, epigenetic, behavioral, and symbolic) and includes a much larger role for information exchanges between organisms and their environment.
In regards to the modern synthesis I think that ID successfully refutes it. But even if ID is rejected at the outset or is not included in considering the evidence it should now be obvious that the modern synthesis is an inadequate model of biological reality. So now the real question is whether ID holds true in regards to the “evolving holistic synthesis”. I don't think anyone could say for certain at this point; it's too early. It's a different question with a potentially different answer. I've said this before over the last couple years but I think that ID proponents have been focusing way too much on the modern synthesis. Part of this focus is due to there still being so many supporters of the modern synthesis. And most of the public discussion still involves the modern synthesis. But I say it's dead, it's gone, let's move on and ignore those supporters. Back in #56 what I was trying to say was that BOTH ID and the “evolving holistic synthesis” could turn out to be true. (I'm about to get in trouble with everyone... ;) ) In order to function, the “evolving holistic synthesis” requires OOL, which is its own separate question. Dembski's recent work shows that in order to find the targets in search space active information is required. Besides "directed front-loading" (what I'm calling Behe's and Mike Gene's hypothesis in order to differentiate it from other variants) there is the potential that ID only holds true in regards to the OOL. The front-loaded active information is the design of the system (modular components, plasticity in the language conventions, etc), which allows the “evolving holistic synthesis” to function without there being a directly embedded plan. Thoughts? I've actually been mulling over this concept for a while but never got around to posting it. Now here is the real question: would the majority of Darwinists find such a hypothetical scenario acceptable? As in, is it even possible to have a middle ground where both ID and Darwinism* hold true? Can't we just all get along? Even though I'm suggesting this idea I'm not convinced of it myself. I just think it a good starting point where both sides could potentially stop the arguing, the hating, and the career-busting and work toward finding the truth. *of a kind...obviously I'm not referring to concepts that ID proponents already accept.Patrick_{March 6, 2008
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Hi Allen: I do not have an explicit definition for intelligence any more than I have a definition for life. In the realm of logic, mathematics, and physics we call these undefined terms or primitives. I prefer to let intelligence be an undefined term or primative. Hofstadter in the book, Godel, Escher, Bach goes in to the difficulty of defining intelligence explicitly. [Hofstadter, by the way, was a good freind of Dennett] However, it does not mean that merely because we leave a term undefined that we cannot define characteristics which are sufficient to say something exists. For example even though no one in the world can sufficiently what life is, a doctor has a set of identifying criteria to rule whether someone is dead or alive. In like manner there are identifying criteria for intelligent actions by intelligent agents. One such criteria are the artifacts left behind by an intelligence, i.e. 1. Beaver Dams 2. Bird Nests 3. Human Houses At issue is whether evolutionary processes can create such artifacts. My personal view is that it complicates the issue by insisting on whether intelligence is required to do this or that. A more empirical approach is to ask whether evolutionary processes can create artifacts that have strong analogy to engineered artifacts in our technological world. Further, is the perception of these analogies merely a postdiction like seeing faces in the clouds? These are the sort of things subject to empriical and theoretical investigation without having to make recourse to arguments about intelligent causation. Even though I believe in ID, proof in the ultimate sense is hard. For example, can any one formally prove he is not the only conscious intelligent being in the universe? That said, we can at least demonstrate the existence of improbable analogies in life to engineered artifacts. That was what the book Design Inference was about. That part can be subject to empirical investigation. Further it can be theoretically and empirically investigated whether evolutionary processes can create sturctures analogous to human artifacts. My favorite example is the Turing Machine (computer) which we find in the modern world of technology as well as in the cell. Discussion of ultimate causation is another story, and perhaps lies outside the bounds of direct empirical, operational science.scordova_{March 6, 2008
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Hi Sal: So that we're all on the same page, would you please define "intelligence" in a way that one might confirm its operation empirically (i.e. without reference to any "hidden" — that is, unobservable — qualities)?Allen_MacNeill_{March 6, 2008
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And for what it's worth, the only way I have ever driven to the City (and the only way I ever will) is down Rte. 17 (soon to become I-86). I once worked a whole summer in a field crew surveying a mountain for a timber company outside of Hancock. Ate breakfast every morning at the Hancock Diner, where George Ivanitsky was the most efficient and graceful short-order cook I have ever had the delight to watch. Besides, the Roscoe Diner isn't on I-81, and I don't like driving through Scranton...Allen_MacNeill_{March 6, 2008
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Dr. MacNeill, It is a delight as always to hear from you and along with others I hope you are well and getting better. The environement has a lot of information necessary to build a system, but I do think it is sufficient. Aerospace engineers need to gather large amounts of information from the environment about the atmosphere -- this is necessary information, but I do not think such information is sufficient information to build an airplane. Even if the environment has large amounts of information, it requires machinery (or intelligence) to translate the information into something useful in the construction of systems. I have no doubt that environmental information is used by organisms to drive their evolution. I think James Shapiro is doing great work in this area as well as people studying develpmental plasticity. Shapiro was actually so bold as to suggest cellular intelligence and thus finds a middle ground in the ID debate. See: Bacteria as Engineers. My only issue with Shapiro is that if an organism's own intelligence shapes its evolution, from where did the first intelligence originate?scordova_{March 6, 2008
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Sal wrote: "Thus I hold out hope that hard-nosed empiricism can settle the question once and for all." So do I; while mathematical models have their place in science, they rise or fall on whether the universe actually operates in a way that is reflected in those models. That is, the math doesn't "run" the universe; math simply describes the universe in ways that are irreducibly inadequate. So (to quote "Thought Provoker" at Telic Thoughts) "Let's do science!" Let's formulate hypotheses about how something in nature is constructed and operates, let's formulate predictions that flow from such hypotheses, then design experiments or further observations that will reliably either confirm or disconfirm such predictions, and then let's publish the results and argue publically about what they mean. And while we do so, let's treat each other as if there were "that of God in every person" shall we?Allen_MacNeill_{March 6, 2008
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Sal wrote: "Both Stuart Kaufmann and Massimo Pigliucci are favoring the idea that somehow the physics laws of physics can explain biology." If this is in fact the case, I must strongly disagree with Kaufmann and Pigliucci. As Ernst Mayr forcefully asserted, biology is characterized by emergent properties that cannot be reduced to physical laws (unless those laws are modified to include them). Indeed, I have a huge problem with the whole idea of "reduction" in science, and especially evolutionary biology. As I have been discussing in my correspondence with Hannah, I think the term "reduction" is itself part of the problem. I would prefer the term "transformative expansion" rather than reduction. For example, consider the so-called "reduction" of chemistry to physics. Physical chemistry ("Honk if you passed P Chem!") doesn't so much "reduce" chemistry to physics as it "expands" both physics and chemistry to explain phenomena that neither one can explain alone. The elegant equations that were developed to "explain" the orbital structure of the hydrogen atom don't work for more complex atoms, and certainly don't apply to molecules in any meaningful way. Why not? Because atoms with more subatomic particles (and molecules composed of many atoms bonded together) have properties that isolated atoms do not have. These properties are emergent properties, and as such cannot be "reduced" to anything, but rather can only be explained by "expanding" our previous understanding and "transforming" it on the basis of new empirical knowledge. This is what makes science so fascinating; it never "holds still". New discoveries are constantly forcing us to revise our old models of how nature is put together and how it operates. "The 'modern synthesis' is dead; long live the 'evolving synthesis!'"Allen_MacNeill_{March 6, 2008
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Sal wrote: "Further, from an empirical standpoint, if John Sanford’s hypothesis of Genetic Entropy is confirmed by improved sequencing technologies (such as Solexa), it will empirically disconfirm the possibility of self-organization or even any sort of “new synthesis” which the Altberg 16 might suggest." Will Provine and I invited John Sanford to make a presentation in our evolution course at Cornell last fall. He did so, and was very grateful to us for our respectful treatment of him. However, I attacked his ideas directly using the same arguments I have in this thread. Ironically, Sanford bases his models on precisely the same outdated assumptions that formed the mathematical basis for the "modern evolutionary synthesis": 1) that genes are the only significant "causes" of the phenotypes of organisms; 2) that changes in genes are the only signicant "causes" of changes in the phenotypes of organisms; 3) that the only way that traits can be inherited is via the inheritance of genes that code for them; and 4) that, given the foregoing, it is impossible for changes in genes alone to explain the origin of biological diversity. I agree, and for the same reasons that I assert that the "modern evolutionary synthesis" is now outmoded. For reasons of mathematical convenience, it reduced the "causes" of evolution to two mechanisms (natural selection and genetic drift) operating on a single medium of inheritance (Mendelian, and later molecular inheritance). We now know that both of these are inadequate to explain observed patterns of development and descent with modification. This is why I am advocating that we all recognize that the "modern synthesis" has for at least fifty years been gradually replaced by what could more precisely be called the "evolving holistic synthesis", one that recognizes at least four different modes of evolutionary change (i.e. genetic, epigenetic, behavioral, and symbolic) and includes a much larger role for information exchanges between organisms and their environment.Allen_MacNeill_{March 6, 2008
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Sal et al: I am uncomfortable with the concept of "front loading" — "front" with respect to what? Time, I suspect, as in Michael Behe's suggestion in DBB that the first cells were "front-loaded" with all of the information necessary to produce all of the biodiversity we see today. This suggestion is absurd, if by "information" Behe (and MikeGene and other "front-loaders") mean genetic information. Once again, genomes do not construct organisms; organisms construct organisms, in concert with their environment. As I hope should be obvious from some of my previous comments, the environment within which an organism develops contains immensely more information than can possibly be encoded within the organism's genome. This "external" information is absolutely essential for regulating development. As just one example, the homeotic genes that produce the first orientation "fields" in a developing animal require positional information to operate. Part of this positional information is an axis from "top" (i.e. dorsal) to "bottom" (i.e. ventral). "Top" and "bottom" are positional information that requires, at a bare minimum, a gravitational field (their is no "top" and "bottom" in a microgravity environment). Hence, the operation of the homeotic genes absolutely requires "external" information. So, I would prefer to call the kinds of information we are talking about as "external", or even better "holistic", as they include relational information both within and around the organism (and this information also includes and requires sequential time as another axis).Allen_MacNeill_{March 6, 2008
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Both Stuart Kaufmann and Massimo Pigliucci are favoring the idea that somehow the physics laws of physics can explain biology. Without going into detail, this would be like trying to explain the origin of software soley in terms of the hardware it runs on. What Trevors and Abel and others have pointed out in various papers is that biological phenomena can not be reduced to explanations which soley appeal to the laws of physics. Thus self-organization can not possibly work! Further, from an empirical standpoint, if John Sanford's hypothesis of Genetic Entropy is confirmed by improved sequencing technologies (such as Solexa), it will empirically disconfirm the possibility of self-organization or even any sort of "new synthesis" which the Altberg 16 might suggest. Thus I hold out hope that hard-nosed empiricism can settle the question once and for all.scordova_{March 6, 2008
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With respect to natural selection, irrespective of questions of ID and irreducible complexity, Kimura made sound mathematical arguments about the limits of the power natural selection can exert. If a population of 100,000 has 100 individuals each with a selectively advantatged trais, it would be essentially impossible for natural selection to preserve the 100 selectively advantaged individuals or their traits. In such cases random drift is a far more accurate model for the evolution of the population. Think then of the implications for the evolution of complex proteins or binding sites in such a scenario! Kimura argued non-Darwinian evolution successfuly for the MAJORITY of molecular evolution. I think he gave an obligatory salute to Charles Darwin by saying his math didn't apply to adaptive traits, but in truth it does! Masotoshi Nei (an NAS member) has taken the next step and argued that Kimura's arguments against Darwinian evolution at the molecular level are extensible to anything else, including adaptation. Salthe (named in Mazur's article) cited a critique by Lewontin (also named in the article) that demonstrated that Darwinian evolution cannot even be stated in a way clear enough mathematically that it can be tested. The main problem is the inability to define fitness. If a theory cannot even measure its central quantity, one has to wonder if its scientific. [See the Santa Fe Bulletin Winter 2003 "Four complications in understanding the evolutionary process" which regretably is no loger online.] Central to modern Darwinism is the idea that mutations and variations are random with respect to fitness. The math shows that if this is true, natural selection does not have the population resources to shape a trajectory toward any more than a few adapatations at a time. This was known as Haldane's dilemma, and Kimura and Ohta appealed to Haldane in defense of their neutral theory. I have not even to mentioned that random mutation poses the problem of weeding out bad mutations, and not just favoring good ones. See: Nachman's U-Paradox. Thus if one begins to suggest mutations (whatever mechanisms create them) are not random with respect to adaptive fitness, one is skirting near the possiblity of front loading, which is right around the corner from ID.scordova_{March 6, 2008
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There is a substantial issue on the table. Kindly address it.
KF, officious tone notwithstanding, your role at this blog is betrayed by the fact that your comments don't appear with a white background. If my defense of Dr. Dembski is inappropriate I trust he will tell me so and I will respect his wishes. {DLH kairosfocus is one of the best contributors here. Heed him well! Stay on focus and don't distract the thread.}poachy_{March 6, 2008
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DaveScot wrote: "Because the that’s an artificial classification. Insects by defintion have six legs. If they have more than six they’re an arthropod but still have all the other identifying characteristics of insects. Even in the case of insects a butterfly is an insect but its larval form has dozens of legs. I don’t get the point you’re trying to make." The point I'm trying to make is that, given that the larval form of many insects have many pairs of "legs" (I don't want to get into a semantic argument about legs versus parapodia), how is it that when they become adults, they all have only three pairs, whereas the Chelicerata have four pairs, the Crustacean have lots of pairs, and tetrapod vertebrates only two pairs (yes, the name says so, but that's not the causative reason). And why pairs? There are no animals of which I am aware that have unpaired appendages. Why not? What is the "constructive logic" whereby appendages only develop in pairs, and that in most cases the numbers of pairs is strictly regulated? I strongly suspect that the answers to these questions cannot be simply reduced to "that's what the genes prescribe". As I tell my students, genes don't "do" anything at all. DNA just sits there, as inert as a blob of melted glass. It takes a whole functioning organism living in a hugely complex and interrelated environment to translate the genetic information in DNA into a functioning organism. Focusing exclusively on the genetic material is to commit the same fallacy as (some of) the founders of the "modern evolutionary synthesis." We know better now.Allen_MacNeill_{March 6, 2008
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bFast wrote: "It is clear that Allan MacNeill is unprepared to provide a defense when systems level evolution is presented." Indeed, I am not conversant with systems level evolution at all. My specialties are the evolution of human sexual behavior, the evolution of the capacity for religious experience, and the history and philosophy of biology, especially evolutionary biology. Could you please recommend a reference that a complete tyro might be able to learn from without tearing out his already very thin hair?Allen_MacNeill_{March 6, 2008
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Charlie wrote: "And, speaking of Hannah and your summer course, aren’t you the same Allen MacNeill who had to shut his own blog down for a couple of days’ cooling-off-period after violating his own rules against ad hominems and calling somebody a liar?" Yes, and I credit Hannah (and my friend and mentor, Will Provine) with gently but persistently teaching me to attack people's ideas, but not their person. Here's what I wrote at the end of that course: "One person in particular deserves special mention: that is, of course, Hannah Maxson, without whom I suspect we might not have achieved anything like what we eventually did. She helped us all immensely in understanding and wrestling with these issues, faithfully attended every class session despite not being an enrolled student (the only “invited participant” from either side to do so), consistently presented an example of how to respectfully but forcefully argue for one’s positions, and spent uncounted hours setting up and moderating the two websites associated with this course, while at the same time holding down a demanding day job. For all of us, I humbly say “thank you, Hannah.” Unfortunately, the web preserves every gaff we have ever committed, without attaching any subsequent apologies, retractions, or other modifications. So, if it will make you feel better (and Dr. Dembski, this is for you as well), I most humbly apologize for every time that I attacked you as a person, rather than your ideas. As I have said before, I assume (now) that we are all committed to an unbiased search for understanding about how the universe operates. It is only by adhering to three simple rules that we can accomplish this: 1) Never attack people 2) Always attack their ideas (and be especially critical of your own) 3) If someone attacks your own ideas, and succeeds in convincing you of their position, say so immediately and move on Here's what Huxley said about this in the letter I cited earlier: "Surely it must be plain that an ingenious man could speculate without end on both sides, and find analogies for all his dreams. Nor does it help me to tell me that the aspirations of mankind–that my own highest aspirations even–lead me towards [a particular doctrine referenced in the letter]. I doubt the fact, to begin with, but if it be so even, what is this but in grand words asking me to believe a thing because I like it. Science has taught to me the opposite lesson. She warns me to be careful how I adopt a view which jumps with my preconceptions, and to require stronger evidence for such belief than for one to which I was previously hostile. My business is to teach my aspirations to conform themselves to fact, not to try and make facts harmonise with my aspirations. Science seems to me to teach in the highest and strongest manner the great truth which is embodied in the Christian conception of entire surrender to the will of God. Sit down before fact as a little child, be prepared to give up every preconceived notion, follow humbly wherever and to whatever abysses nature leads, or you shall learn nothing." Let me repeat the core of this idea: "She warns me to be careful how I adopt a view which jumps with my preconceptions, and to require stronger evidence for such belief than for one to which I was previously hostile." 'nuff said.Allen_MacNeill_{March 6, 2008
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DaveScot wrote: "Clearly though the information IS contained within a single cell (all the information needed to build a chicken resides inside the shell of the egg)." I think it would be more accurate to say that the information needed to build a newly hatched chicken resides inside the shell of the egg." However, even that assumption is just that: an assumption. And it is probably wrong insofar as the egg itself does not sit in a vacuum, but rather inside its mother, and then inside a nest. As just one example, without the body heat from the mother (or an incubator), a chicken egg with all of its self-contained information becomes, not a cute little ball of animated yellow fluff, but a nasty, smelly mass of decomposing slime in a surprisingly short time. What you are arguing (and I agree) is that genetic information alone isn't close to enough to explain how a fertilized unicellular zygote becomes a fully integrated cooperative community of 100 trillion connected individuals...wait, that leaves out the mitochondria and the undulapodia. Okay, assuming that every cell has at least one kineticore and 100 mitochondria, the real number is more like 20 quadrillion. IOW, if one leaves out the environment within which the organism develops and lives, one is blind to the real causes for the organism's existence.Allen_MacNeill_{March 6, 2008
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Charlie wrote: "But thanks for telling me to read and learn from Huxley. Is there a quote in there about the phrase “lie for Jesus”?" No, and the fact that you asked this clearly indicates that you didn't read it.Allen_MacNeill_{March 6, 2008
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