We’ve finished Blind Watchmaker and probably won’t be posting much more about it, simply because we dealt with it pretty thoroughly in class and it doesn’t seem quite interesting enough to merit further discussion. If you disagree and particularly want to debate some part of it you can use this thread to do so; and if you want to challenge our basic conclusions here they are, for the chapters covered Friday.
I’m going to call them opinions, though, and not facts, because I can’t promise any of us will defend them– we’re pretty much ready to move on. :) Still, if you’d like to offer a well-reasoned contrary opinion we’d love to hear it.
• Chapter 9: Puncturing Punctuationism. More of a chapter in the Dawkins-Gould feud than part of the book’s logical progression; moreover, in the years following 1986 the evidence has been leaning more in favor of punctuated equilibrium than gradualism.
• Chapter 10: The one true tree of life. Dawkin’s aim in this chapter doesn not seem very ambitious, as he suggest that, because of its necessary assumptions, cladistics can’t logically support evolution; but it fails even as description. Our general conclusion: his “perfect” scheme is too perfect to have much resemblance to reality, and there is no “one true tree of life”.
• Chapter 11: Doomed rivals. Dawkins would do much better if he could be a bit less dismissive of ideas he disliked, and actually address them in a meaningful way. We didn’t find either his rejection of Lamarckism or neutral theory (the two issues that were focused on) at all convincing.
Question: Are we moving back to a modified version of Lamarckism with the “genotype follows phenotype” of evo-devo?
Right now we’re reading Darwin’s Black Box, by Michael Behe, and discussion of that begins on Tuesday.
I think Hannah has captured our general evaluation of the last few chapters of Dawkins The Blind Watchmaker fairly well, if a little telegraphically. Here’s my take on them:
Chapter 9: Puncturing Punctuationism – Most people familiar with this issue will be familiar with the long-running feud between Dawkins and Stephen J. Gould, one of the co-founders of the theory of punctuated equilibrium. In evaluating this chapter, several people contributed the following points:
• Dawkins’ main objection to the theory of punctuated equilibrium stems from his own philosophical position as one of the strongest proponents of the “genes first and foremost” school of evolutionary theory. Gould, on the other hand, is quite representative of the “phenotype first and foremost” school, which is not surprising, given his avocation as a paleontologist. As a dedicated promoter of the “genes” school of thought, Dawkins apparently argues against “punk eek” primarily because it undercuts the “genetic gradualist” arguments of R. A. Fisher, J. B. S. Haldane, and Sewall Wright, upon which the “modern evolutionary synthesis” is based. “Punk eek” theory represents a direct contradiction to some of those arguments, and in 1986 (when Dawkins wrote this book) there wasn’t that much evidence either way. Now, however, the theory of “punk eek” is steadily gaining support, especially among paleontologists, with evo-devo devotees providing potential mechanisms whereby relatively “sudden” shifts in phenotype can occur.
Does all this “invalidate” the theory of evolution? Not at all; it simply updates it, on the basis of new data and new theoretical interpretations of that data.
Chapter 10: The One True Tree of Life – Again, the criticisms of this chapter stem primarily from new information that tends to undermine Dawkins’ argument. As Will Provine has pointed out, the work of Lynn Margulis (of “serial endosymbiosis” fame), along with advances in our understanding of lateral gene transfer have undermined the assumption that the phylogeny of life on Earth has a single “root and trunk” and that the only thing that happens is continual branching (i.e. diversification) over time. On the contrary, horizontal gene transfer (via viruses, cell fusion, hybridization, and good old sex) results in an irreducible “bushiness” at the base of the “tree of life”, with separate lines of descent fusing together higher in the tree (for example, in the origin of eukaryotic cells).
Once again, this new view of “descent with modification” violates the overly simplified version of phylogeny supported by Dawkins, but once again it does not “violate” or “disprove” evolutionary theory – it simply updates it, based on new information.
Chapter 11: Doomed Rivals – As Lord Kelvin repeatedly demonstrated, it’s never a good idea to declare any branch of science “dead” or “finished”; new information can always revitalize a discipline. Several members of the class (including yours truly) pointed out that new information in the area of epigenetics and evo-devo point to a kind of “neo-Lamarkism”, albeit with solid genetic mechanisms to explain it. And the neutral theory of Kimura, Ohta, et al is solidly embedded in current evolutionary theory. Finally, the “mutationist” theory (a la De Vries, Bateson, and Goldschmidt), far from being conclusively defeated, has gained a new reincarnation in some of the findings of evo-devo. Given the evolutionary genetics of homeotic genes, it does seem possible for relatively small genetic changes to result in relatively large phenotypic shifts in relatively brief periods of time.
To cite Will Provine once again, many of the major tenets of the “modern synthesis” have been rendered outdated by new discoveries and interpretations in the constantly evolving field of evolutionary biology. “Young Earth creationism” is still without any empirical foundation or scientific support, but our views of how teleology (a la Mayr/1974) can evolve in natural systems provide an interesting counterpoint to “intelligent design theory”, a counterpoint that we intend to investigate as we critically analyze the arguments and evidence for ID.
Taken together, Dawkins’ assertion in the last paragraph of the book that “slow, gradual, cumulative natural selection is the ultimate explanation of our existence” seems in hindsight to be both contrary to the evidence from paleontology, epigenetics, and evo-devo. While it may be understandable, given Dawkins commitment to the “genes first” school of evolutionary theory (i.e. the “modern synthesis” and its descendents), there now seems to be sufficient evidence to indicate that this dominant paradigm may be in the process of mutating to another, in which evolution is still the explanation, but the mechanisms that drive it are more complex, less “random,” and more interesting than what Ernst Mayr called “bean-bag genetics.”
Comment by Allen MacNeill — July 10, 2006 @ 12:31 pm
Thanks, Allen! I guess my post– and the telegraphic quality of it– was the combination of feeling guilty that no-one had posted on anything past chapter five, and so could we exactly blame people for going off-topic?– and then at the same time being in lab, with work that didn’t really admit long breaks. But it’s much better to have the reasoning behind the conclusions.
As a side note: I’ve been posting our “general opinons” for this book since it seemed we really didn’t have any major differences in our evaluation of it– the interesting discussions that took place were more on tangents. If/when we begin focusing on issues where I’m more out of the class mainstream someone else should take over impartial “class notes”!
Or if it turns out we all take sides and no-one is impartial I guess we’ll all have to write warring commentary :).
Comment by Hannah — July 10, 2006 @ 12:49 pm
Allen:
I commend your open-mindedness as to where science is heading:
I didn’t think it possible for Ph’Ds in biology to even mention the name of Goldschmidt.
Which makes me think that the failing of ID is perhaps that it seems to come with a religious world-view already attached. (IDers try to help by staying away from identifying the ‘D/designer’.) Yet, if we allow ourselves to be troubled by this world-view, aren’t we then denying ourselves a potentially very fruitful heuristic?
From what I’ve read of some noted scientists they ask themselves (relative to microbiology and such), “How would I have built it/done it?” In a sense, then, ID might already be the prevailing paradigm without anyone realizing it.
Just some thoughts. But, again, I find your open-mindedness refreshing. In fact, having this blog strikes me as being very open-minded. Thanks.
Comment by Lino D'Ischia — July 10, 2006 @ 1:35 pm
Lino wrote:
“Which makes me think that the failing of ID is perhaps that it seems to come with a religious world-view already attached.”
Wow! You can say that again! I just finished a 2.5 hour discussion on this very topic (with one of the students in this class), in which I lamented the fact that the three people most identified with ID (Behe, Dembski, and Johnson, and especially the last two) have a very obvious theological axe to grind. How much more interesting (and potentially fruitful) this debate might have been if accusations of theism/atheism didn’t creep in so close to the beginning of every thread. For example, if we were debating the kind of “self-organization” that Stuart Kaufman has proposed were the focus of debate, or the “thermodynamics far from equilibrium” of Ilya Prigogine, we might have some really interesting insights and come up with some fascinating hypotheses for field and lab folk to investigate. Instead, the debate degenerates into ATHEISM!!!!! no CHRISTIANITY!!!!! (just take a look at almost any thread at Uncommon Descent or Pharyngula for examples). I have to say, I really envy Newton his pronouncement: “I make no hypotheses!”
Indeed.
Comment by Allen MacNeill — July 10, 2006 @ 3:42 pm
Lino also wrote:
“ID might already be the prevailing paradigm without anyone realizing it.”
As we will see when we read the papers on teleology by Ayala, Mayr, Nagel, etc. biologists do this all the time. Indeed, biochemists, microbiologists, physiologists, geneticists, ecologists…the list goes on…all operate on a kind of implicit teleology/design hypothesis. When you observe something new and strange, you ask “What’s this for?”, which is a flat-out teleological approach. This is why Dawkins has to constantly reiterate that biology is a science in which the objects have all the appearance of design, without having design.
As Ayala, and especially Mayr have argued, this isn’t mistaken practice: even if you accept Lewontin and Gould’s perspective that the characteristics of organisms are “exaptations,” rather than “adaptations,” analyzing them functionally (as if they were solutions to problems) is almost always the most fruitful way of figuring out what they do and how they do it. Then, once that’s all done, you go on to say that the answer to why they do it doesn’t involve design at all, and expect that most people won’t get whiplash from the abruptly shifted gears?!
Right, I know, I’m starting to sound like an IDer, but I have to admit that at least IDers (and a few EBers, like Mayr) have the motivation to talk about the problem of purpose. Clearlly, it exists in natural objects and processes (at least insofar as we, ourselves, are natural entities, and the things we do are natural processes…that is, they don’t violate natural laws). What we are trying to come to clarity on in this course is how teleological entities (i.e. living organisms) can get that way as the result of what have all the appearances of being non-teleological processes (i.e. the laws of nature). Yes, along the way “there be dragons”, but a person of stout heart and open mind should be able to either defeat them or show how they’re just big lizards after all…
Comment by Allen MacNeill — July 10, 2006 @ 3:54 pm
That’s a strong statement. Do you want to dispute it (elsewhere, maybe, or we’ll get in trouble for hijacking the thread and discussing motivations)?
I definitely agree there; but surely the same effect could be achieved by recognizing the complete irrelevance of such accusations and sticking to the interesting part of the question? It doesn’t matter for the substance of the debate whether or not Behe, Dembski or Johnson have a theological axe to grind; and in fact I don’t think it matters for the practical part either, as people who’ve decided you’re on the “wrong side” tend to be quite imaginative with their conspiracy theories whether or not they have any base.Have I gone too far on this tangent, and should I start a “motivations” thread? Or save that for when we’re going over it in the course…?
Comment by Hannah — July 10, 2006 @ 3:56 pm
Hi, Hannah:
Maybe I didn’t qualify my statements enough: Dembski and Johnson have publically and repeatedly written on precisely the necessary connection between their theology and their ID (see, for examle, Dembski’s contributions to B. Wiker’s Moral Darwinism and Johnson’s arguments in Reason in the Balance). So, I therefore exempt Behe from my generalization.
I’m not sure a “motivations” thread would be a good idea right, now. When we read Johnson/The Wedge of Truth, I’m sure we’ll get into this some more.
So, here we are, the only two people actually in the course, lobbing balls back and forth across the net. Anyone else in the course want to join in and make it more than just volleying?
Comment by Allen MacNeill — July 10, 2006 @ 4:37 pm
Chapter 10: The One True Tree of Life – Again, the criticisms of this chapter stem primarily from new information that tends to undermine Dawkins’ argument. As Will Provine has pointed out, the work of Lynn Margulis (of “serial endosymbiosis” fame), along with advances in our understanding of lateral gene transfer have undermined the assumption that the phylogeny of life on Earth has a single “root and trunk” and that the only thing that happens is continual branching (i.e. diversification) over time. On the contrary, horizontal gene transfer (via viruses, cell fusion, hybridization, and good old sex) results in an irreducible “bushiness” at the base of the “tree of life”, with separate lines of descent fusing together higher in the tree (for example, in the origin of eukaryotic cells).
I’d like to point out that horizontal gene transfer(HGT) makes no sense at all without a shared genetic code. Therefore, I maintain that there was likely one root of organisms that use translation. I believe that the ribosome only developed once, and was a “winner take all” step. Therefore I object to such depictions as the “mangrove of life” which has multiple separate roots.
Comment by ivy privy — July 10, 2006 @ 6:47 pm
I hope I was clear enough there. I believe the ribosome originated once. It obviously subsequently developed independently in different branches (stems, whatever).
Also, I would suggest that the “Tree of Life” not be considered “wrong” any more than Newtonian mechanics is “wrong”. More advanced investigation shows that those ideas do not account for all the complications of the relevant systems, but they are still fine for introductory teaching tools. I was taught Newtonian (non-relativistic) physics in high school; I suspect it is still taught. (It is probably clear that I am arguing against Wells’ Icons of Evolution here.)
Comment by ivy privy — July 10, 2006 @ 6:57 pm
The case for Evo-Devo or Goldshmidt’s ideas has serious sympathy in ID circles (Davison, Denton, others). There are probably some in YEC Baraminology who are sympathetic to some aspects Evo-Devo (primarily because a belief in a recent Global flood which implies all creatures today must have descended from only a few ancestors).
I point this out to say, one must not presume all naturalistic scenarios are rejected by IDers out right. There is a larger diversity of opinion on the ID side than one might suppose at first glance….
For me, as far as evo-devo, probably a direct approximation of radical phenotype changes is the transformation of a caterpillar to a liquefied pupa to a butterfly. If one looks at the body plan at each stage, one would almost hardly think it was the same creature! The genome is identical at each stage, but there are two proteomes (two sets of different proteins from the same genome!, one for the caterpillar stage and one for the butterfly stage). It is thus not hard to imagine a radical transformation is possible in principle, if it is programmed into the organism.
The IDers will insist it still takes pre-programmed design to accomplish large scale transformation (as evo-devo suggests), but one will find that IDers do not disdain the work of evo-devo or Kimura or Haldane or Fisher or Gould like they disdain ultra-Darwinism or neo-Darwinism.
The issue of hierarchical patterns in morphology and molecules has many twists. The creationists prior to Darwin said the hierarchy was evidence of common design and evolutionists today argue it is evidence of common descent.
Curiously, not all evolutionists prior to today were supportive of viewing biology through the lens of hierarchical patterns (this was prior to molecular taxonomy, and afterall hierarchies were a creationist conception of Linnaeus and others). A good explanation of the history of the taxonomy debate is by geneticist Michael Denton (an ex-creationist turned Darwinist turned ex-Darwinist).
He shows the hierarchical view of nature acatually can be used to argue against the existence of intermediates ( hierarchical patterns resist transitionals). Denton argues this in Evolution a Theory in Crisis (the book which made an IDer out of Behe, even though Denton is would probably be better described as a pseudo-IDer).
In fact, a purely secular counterpart to Dawkins book would be Denton’s book, not Behe or Dembski’s book. Denton’s book is assigned reading by Dembski and Behe in their ID classes. The treatment of morphological and molecular taxonomy by Denton is still the best that I’ve ever seen available in pop literature (still pretty heavy reading!).
Denton’s treatment of molecular taxonomy and the molecular clock and some of Kimura’s work 20 years ago anticipated problems which I see in the peer-reviewed literature today.
The divide between IDers is along the lines of absolute common ancestry. I think the strongest case for evolution is in common ancestry arguments. But even the YECs have their conceptions of limited common ancestry (descent from a few kinds of creatures, and Man having no ancestor). The bigger issues are the mechanisms, and the origins of the mechanism.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 10, 2006 @ 7:01 pm
Allen writes,
Well, I hate to be the curmudgeon, but unfortunately I am going to have to disagree with much of what both Hannah and Allen say in posts #0 and #1, because in many places I think they are passing on confusions about evolutionary buzzwords — confusions that are common in the media and public (and universal with creationists), but which don’t really have much to do with the actual scientific debates among biologists! (Keep in mind I say all of this criticism with a big ;-) ).
Punctuated Equilibria
First, Hannah gives us several opinions that are really just classic creation-science talking points, later inherited by the ID movement. For example:
First, “gradualism” is not in opposition to Punk Eek. Punk Eek is really a gradualist model of speciation, based upon applying Ernst Mayr’s model of geographically localized speciation (”allopatric speciation”) to the fossil record. Ernst Mayr, you may recall, was not some revolutionary against the NeoDarwinian modern synthesis — instead, he was the personification of and leading proponent of the Modern Synthesis. Gould and Eldredge simply took his model and applied it to the fossil record to explain the common (but not universal) pattern of stasis in a species followed by “rapid” (10,000 - 1,000,000 years “rapid”) change to another species (another closely related species, mind you (think horses and zebras) — the differences that paleontologists describe in fossil species separated by Punk Eek events are typically small enough that creationists (but not evolutionists) would call them “microevolution.”
What Punk Eek actually opposed was “constant rate-ism”, as in fact Dawkins rather carefully explains in The Blind Watchmaker. Even here, it is debatable if Darwin or anyone else ever actually believed in “constant rate-ism.” Keep in mind that for Darwin, the term “gradual” meant not “smooth”, but “step-like.” He once described an earthquake in South America that raised the seashore 15 feet into the air. He said this change was “gradual”! The original meaning of “gradual” is related to “graduation”, as in college graduations and graduated cylinders. One could quite legitimately argue that the species-to-closely-related-species pattern described by “Punk Eek” is itself “gradual” in exactly Darwin’s sense.
Finally, now that the misconceptions are cleared up, we should discuss the results of the paleontologists who have actually done empirical studies assessing the question of whether or not evolutionary change in a group of (closely-related!) species, with a detailed fossil record, tends to be more continuous or episodic. Basically, the studies say: some of both. Groups like horses show both patterns. Marine plankton (huge populations, incredibly fine fossil record in ocean sediments) tend to show more continuous change. Molluscs etc. on contintental shelves tend to show a more punctuated pattern. Fossil hominids for the last few million years, on the other hand, tend to show a quite continuous pattern of change:
Here is chart from a 1994 PNAS article showing the change in hominid brain size over the last few million years. Here are photos of some of the skulls. There are no obvious “punctuations” in this particular fossil record — unfortunately for the creationists, who are convinced that no transitional fossils whatsoever exist, based on their misinterpretations of Punk Eek, and they are especially convinced of this for hominid fossils.
In any case, the real Punk Eek discussion is about patterns of speciation in the fossil record. These are relatively small changes to most people. This point is almost universally misunderstood outside of paleontology and those who study speciation explicitly. Macromutations, evo-devo, the origins of “higher” taxa like phyla, adaptive radiations, etc., are all different topics that don’t really have much to do with Punk Eek, even though Gould talked about all of these other topics as well in his popular books, getting everyone thoroughly confused about them. Enough confusion reigns that scientists themselves will sometimes put lines in their papers like “and my results might explain punctuated equilibria!”, not realizing that mundane processes like allopatric speciation are sufficient.
Cladistics
Hannah writes,
This description of cladistics is a travesty. Kevin Padian, the paleontologist who testified in support of evolution in the Kitzmiller v. Dover trial, explicitly used cladistics as his method throughout his presentation to the judge. Padian showed, with statistically rigorous cladistic analyses published in the peer-reviewed literature, that the creationist assertions found in Of Pandas and People — asserting that there were no transitional fossils between fish and tetrapods, early tetrapods and mammals, dinosaurs and birds, and land mammals and whales — were all absurdly, horribly wrong.
Cladistics is in fact more Darwinian and evolutionary than the old Linnean taxonomy was. Linnean taxonomy retains essentialist elements and leads to contradictions where extremely closely related fossil species (like the mammal-like reptiles) can be placed in different “classes” depending on where one arbitrarily draws the line between “reptiles” and “mammals”. Cladistics, on the other hand, simply estimates the pattern of the phylogenetic tree and assigns names to groups that share a common ancestor not shared with other groups. Linnean ranks are not assigned. Fossils are not shoe-horned into groups defined by living organisms (like e.g. mammals), rather they can be placed into “stem groups” which have some, but not all, of the features of the living “crown groups” (i.e., they are transitional). What used to be called “mammal-like reptiles” are now placed in the stem of the crown group mammals.
Now that cladistics has basically “won” the scientific debate (which was not completely the case in the 1980’s), many “mysteries” in evolution are becoming clearer. For example, the “Cambrian Explosion of phyla” is evaporating as it is shown to be an artificial product of Linnean taxonomy. See the PT post “Down with Phyla!.” Or see this description of the fossil record for the origin of the arthropod phylum, from an expert on Cambrian arthropods:
In other words, cladistics has enabled paleontologists to identify the transitional fossils that have some, but not all, of the defining features of arthropods, and this gives us some sense of the steps by which the defining features of the arthropod phylum were acquired. Basically this destroys the typical creationist arguments about the “sudden” origin of phyla.
So the idea that “cladistics can’t logically support evolution” is totally ridiculous. This bit of rhetoric is derived from the creationist misinterpretation of the cladistic principle that you can never be sure that a particular fossil is a direct lineal ancestor of a certain group, or simply a close cousin. Creationists say that cladists have given up on finding transitional fossils. But in fact cladistics has been an immense help in finding transitional fossils, by quantifying relationships rather than treating then in a qualitative, essentialist fashion.
The Tree of Life
This is wrong to a high degree of statistical approximation. Sure, there are exceptions like hybridization in plants and lateral gene transfer in microbes, but overall the tree pattern of life is extremely rigorously documented, and the specific tree scientists have constructed is continually supported by new data, although of course minor revisions are continually ongoing. The statistics of comparing the similarity of phylogenetic trees are important to understanding this; rather than reinvent the wheel, I refer everyone to this extremely excellent page on the topic, especially the subpage on Statistical Support for Phylogenies.
Lamarkism/neutral theory
I can’t remember exactly what Dawkins says about these topics, but I doubt he has any real problem with neutralism, which is just what happens when selection is about equal to zero. He probably does have a problem with calling neutralism an alternative to the neo-Darwinian synthesis, because it is in fact a product of it.
Regarding Lamarkism, my only general remark is that a great deal of uncritical hype occurs every few months when someone comes out and loudly proclaims that they’ve discovered an allegedly “Lamarkian” or other allegedly non-Mendelian/non-Darwinian phenomenon. Many times a more careful examination reveals that process involved is actually at root Darwinian, just with some selection process going on that the experimenters don’t initially notice. Here is an example where a much-balleyhoed claim of RNA-based inheritance in Arabipdopsis was called into serious question by a blogger’s selection hypothesis, which was later published.
Moving on to Allen MacNeill on Punk Eek:
Again, Punk Eek was derived from Mayr’s model of allopatric speciation. This is not exactly what I would call a “direct contradiction” of the “modern evolutionary synthesis.”
I think this is mixing two very different issues: one, involving Punk Eek, is how speciation appears when viewed in the fossil record. The other, evo-devo, involves the origin of morphological “novelty”. These two issues are not necessarily connected at all, especially since the differences between sister species (which is what Punk Eek is looking at) are not typically of the “dramatic macromutation” sort. Assuming “sudden” macromutations are an important evolutionary process at all, they might be correlated with speciation events and explain some punctuations, but they could just as well happen during anagenetic change within a single species, or only once every few hundred speciation events. Just because Stephen Jay Gould liked to talk about both Punk Eek and macromutations does not mean they are part of the same phenomenon.
Allen on “The One True Tree of Life”
This opinion is regularly expressed (by scientists who are tooting their own horn for having “overturned” “Darwin’s tree of life”), but unfortunately I think this is hype also. Once you get to multicellular organisms with isolated germlines — which is what zoologists like Dawkins are talking about — lateral gene transfer (LGT) becomes an almost negligible force relative to linear descent, and even for microbes there is clearly a huge amount of treelike structure despite the possibility of LGT events. Endosymbiosis is an obvious exception that everyone recognizes, but it is not new and was not new in 1986 either — it was well-accepted by the early 1980’s.
To continue in my curmudgeonliness here, if one going to brazenly include things like “hybridization” and “good old sex” as violations of the “Tree of Life” paradigm, then one is clearly just setting up a silly strawman of what the “Tree of Life” paradigm is, probably for the purposes of knocking it down to show how amazingly revolutionary and open-minded one is (I am not blaming Allen here, but I think certain scientists have been less than circumspect here). The “Tree of Life” model was always a tree of species, implicitly or explicitly gene pools of interbreeding organisms, and the branches on the tree occurred when the gene pools split into separate gene pools. Hybrids were always a well-recognized ambiguous case, tied up with the inherit ambiguousness (expected, of course, if evolution is true) of what exactly a real “species” is.
And, once we remember that the “Tree of Life” paradigm is about gene pools, what then becomes of the hullaballo over the “tangled roots” of the “tree of life”? If indeed we think that the “Last Common Ancestor” was not a single microbe but a community of microbes trading genes (and did anyone ever really think the Last Common Ancestor was literally a single microorganism? Or was it a species?), couldn’t we just draw a line around this community, call it a “species” with a shared gene pool, and poof, we’re back to a standard “Tree of Life” model!
“[S]low, gradual, cumulative natural selection”?
How could evolution be “less ‘random’” than “slow, gradual, cumulative natural selection”? If you are strong selectionist, you think that selection basically dominates other processes in evolution, resulting in adaptations appearing in response to environment in a rather predictable fashion. Simon Conway Morris and Richard Dawkins are basically identical in this respect. Conway Morris, of course, interprets this as matching a theistic worldview where God set up a Universe that would sooner or later produce sentient beings, while Dawkins interprets it (when he uses the world “ultimate”) as meaning that there is no cosmic purpose to existence — but either way, it is not meaningfully more random than the newer views.
As for the newer views specifically, I have already explained my issues with the various contentions about paleontology and evo-devo. For epigenetics, I again worry about hype — is there any particular reason to think that epigenetics can make macromutation any more likely than it is under genetics? The real problem with making macromutation work is not with genetics or epigenetics, but with natural selection — it seems unlikely that “large” phenotypic changes will be adaptive enough to be favored by selection, compared to a series of smaller phenotypic changes building up an adaptation step-by-step. I think that it is more likely that “moderate” sized phenotypic mutations — like the duplication of segments, identity shifts in appendages, etc. — are the kind of phenotypic mutations that the evodevo people are really talking about when they deal with the question of the origin of novelty, and not the kind of “poof” model where a complex adaptation appears all at once, which is basically what the macromutationists were arguing for. And I suspect Dawkins would agree with the importance of these “moderate”-sized phenotypic mutations. For evo-devo, I would only add that the whole point of evo-devo is to synthesize developmental biology with good old neo-Darwinian population genetics — basically “bean bag genetics” if one wants to be crude. Instead of just treating variation as a black box somehow connected to genes — something we were forced to do until the 1990’s — we can now incorporate the details. This is not a paradigm shift IMO.
I doubt Dawkins would/does have an issue with any of it, because I don’t see that any of it contradicts “slow, gradual, cumulative natural selection”, for reasonable understandings of those terms (”slow” = process operates by population genetics over many generations, which may seem “fast” relative to the huge timescale of the fossil record; “gradual” = step-by-step, not totally smooth; “cumulative” = adaptations are built up from many mutations, not all at once).
All IMHO of course. ;-)
Nick
PS: Denton’s “biochemical equidistance” argument. In a later post I just noticed, Sal cites Denton as some kind of genius:
Sal fails to mention that:
(1) Denton fundamentally misunderstood taxonomy when he mistakenly assumed that we should see a linear, ladder-like pattern in DNA (i.e., fish->frogs->lizards->dogs->humans), rather than an evolutionary tree, which is what Darwin said (all living organisms are at the tips of the branches; modern, living frogs are not “in between” modern fish and reptiles, instead, each of these groups has been evolving and changing for hundreds of millions of years). This misunderstanding was then copied into the ID textbook Of Pandas and People, where Behe was made to admit it was flat wrong during cross-examination at the Kitzmiller trial.
(2) Denton himself argued for the “Biochemical Echo of Typology” in the book Sal cites, the 1985 Evolution: A Theory in Crisis. But in his 1998 book Nature’s Destiny, Denton gave all of that up, completely dropped the “biochemical equidistance” argument, and argued for the genetic continuity, and now bashes IDists (Denton is not one) for denying the overwhelming evidence pointing to common ancestry.
A handy popular critique of Denton’s “biochemical equidistance” misunderstanding is online here.
Comment by nmatzke — July 10, 2006 @ 10:19 pm
I just sent a big long post, it is probably in the spam buffer for having links in it. Post at your leisure…
Comment by nmatzke — July 10, 2006 @ 10:20 pm
Thank you! It was getting boring :).
This is funny because I don’t think I’ve every heard any ID’er or creationist talk about punctuated equilibrium– all I know about it– which is admittedly very little– is from my professors or evo grad students here at Cornell.
So perhaps it is a talking point, but I used it quite innocently. Especially as I really don’t have any opinion on punctuated equilibrium myself, but was trying to relay the general consensus of our (non-creationist-majority) class. Surely it is not quite heresy to consider them as ideas that have been in opposition?
You’re bringing up fossils; not me. There may be reasons from the fossil record why “cladistics can’t logically support evolution”; but I wasn’t basing my statement on on any creationist handbook, unless Blind Watchmaker qualifies. :)
Dawkins states (pg 276; third paragraph) that working without assuming evolution is necessary if you want to use the results of your taxonomic work to support evolution. He also states (pg 280, paragraph 1), in discussing what he calls the “average-distance measurers”, who try to work without these assumptions, that “it is probably fair to say that methods are not really available for achieving their aim.” Therefore, if he is right, methods are not available to use taxonomy to support evolution. That’s all.
At least, that’s all as of 1996. Has there been a revolution in cladistics since then?
I’ll save more discussion of the “one true tree of life” for sometime when it isn’t so late, as that tends to get rather long…
Comment by Hannah — July 10, 2006 @ 11:41 pm
Salvador:
That seems regrettable since Denton’s treatment seems to be somewhat flawed. Wesley Elsberry for instance showed how Denton was quite wrong in his treatment and conclusion of the cytochrome-C data.
Interestingly enough it seems that many creationists have gotten their arguments from Denton’s book and unwittingly repeat the flawed analysis.
As such I find it quite surprising that scientists like Behe and others relied on Denton in their conversion rather than on more accurate peer reviewed research.
Don Lindsay has collected a set of reviews of Denton’s book
One of the better reviews are by Korthof who shows how Denton in a later book seems to have reversed on some of his earlier positions.
Denton’s treatment of the fossil record and intermediates also seems quite lacking, and his book would do even more poorly given the recent finds of many excellent examples of transitional fossils.
As far as the tree of life is concerned, let’s first establish that excellent data exist which show a statistically consistent picture of the tree of life (see for instance Douglas Theobald’s talkorigins article on 29+ evidence for macroevolution).
Douglas shows how a picture of a statistically significant tree emerges. He quotes
The stunning degree of match between even the most incongruent phylogenetic trees found in the biological literature is widely unappreciated, mainly because most people (including many biologists) are unaware of the mathematics involved (Bryant et al. 2002; Penny et al. 1982; Penny and Hendy 1986). Penny and Hendy have performed a series of detailed statistical analyses of the significance of incongruent phylogenetic trees, and here is their conclusion:
“Biologists seem to seek the ‘The One Tree’ and appear not to be satisfied by a range of options. However, there is no logical difficulty in having a range of trees. There are 34,459,425 possible [unrooted] trees for 11 taxa (Penny et al. 1982), and to reduce this to the order of 10-50 trees is analogous to an accuracy of measurement of approximately one part in 106.” (Penny and Hendy 1986, p. 414)
The argument by some is that in the early stages horizontal gene transfer was significantly large to destroy much of any evidence of common descent.
Also research has suggested that horizontal gene transfer may have been quite limited
The net of life: Reconstructing the microbial phylogenetic network Victor Kunin1, Leon Goldovsky, Nikos Darzentas and Christos A. Ouzounis2
AbstractIt has previously been suggested that the phylogeny of microbial species might be better described as a network containing vertical and horizontal gene transfer (HGT) events. Yet, all phylogenetic reconstructions so far have presented microbial trees rather than networks. Here, we present a first attempt to reconstruct such an evolutionary network, which we term the “net of life.” We use available tree reconstruction methods to infer vertical inheritance, and use an ancestral state inference algorithm to map HGT events on the tree. We also describe a weighting scheme used to estimate the number of genes exchanged between pairs of organisms. We demonstrate that vertical inheritance constitutes the bulk of gene transfer on the tree of life. We term the bulk of horizontal gene flow between tree nodes as “vines,” and demonstrate that multiple but mostly tiny vines interconnect the tree. Our results strongly suggest that the HGT network is a scale-free graph, a finding with important implications for genome evolution. We propose that genes might propagate extremely rapidly across microbial species through the HGT network, using certain organisms as hubs.
Comment by PvM — July 11, 2006 @ 12:19 am
Much discussion has been given to computer simulations like Dawkins WEASAL.
Supposed imporvements or supposed better examples of Darwinian evolution were given by Avida and Dave Thomas, Elsberry and Shallit. I have begun takin on those issues, especially since Avida has been said to refute Behe’s co-option. As a transition from Dawkins to Behe, I take the issue of Avida on. See:
Tautologies and Theatrics (part 1): adventures in Avida
Regarding Denton, I don’t endorse all of what he said, and the one flaw in his argument was in Pandas and People. However, what he pointed about the molecular clock (which Dawkins mentions) is devastating, and peer-reviewed literature today has affirmed the main point of his position.
Denton has not abandoned the typological perception of nature, and in fact his Cuvierian view of platonic forms in proteins was the topic of his paper in the journal of theoretical biology.
See The Protein Folds as Platonic Forms: New Support for the Pre-Darwinian Conception of Evolution by Natural Law
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 11, 2006 @ 1:07 am
Hanna wrote:
You can “hear” a creationist talking about punctuated equilibrium at the IDEA Center web site. Go look for the article by Casey Luskin titled “Punctuated Equilibrium and Patterns from the Fossil Record”. It’s even got that graph creationists love to use that shows “the actual fossil record” of all the phyla except one poofing into existence during the Cambrian. This version even has a little quote mine from Dawkins thrown in.Comment by alienward — July 11, 2006 @ 1:40 am
But transformed cladism to support evolution is a self-defeating affair. It is exactly as you say, ” you can never be sure that a particular fossil is a direct lineal ancestor of a certain group, or simply a close cousin.” Which cripples cladism from supporting common ancestry.
It is counter intuitive, but morpholgical classification schemes actually resist common ancestry, contrary to popular opinion.
For example, as the evolutionary story goes, a fish ought to be the ancestor of reptiles, mammal, birds. But from a taxonomic standpoint, that makes little sense! One can see the structural relationship just as well, if not better, between fish, reptiles, birds, and mammals without assuming fish are the ancestors.
What happens in forming these nested sets is that NO creature ends up being seen as ancestral. One wouldn’t make fish the ancestor of man unless one had a prior pre-disposition to do so.
So then one is left with a classification scheme (much like Linnaeus) where common ancestors aren’t there.
Trying to create a classification scheme by forcing fish to be the superset of reptiles, birds, and mammals hardly fits. The taxonomy doesn’t justify it.
Richard Dawkins gives an account of the taxonomists (the transformed cladists)
Comment by Salvador T. Cordova, IDEA GMU — July 11, 2006 @ 1:55 am
Hannah wrote:
But Dawkins doesn’t say this in the Blind Watchmaker. He does say cladists (of the time, cladistics has evolved methodologically since Dawkins wrote this) try to avoid the assumption of evolution before they draw their trees.
Comment by Ian Musgrave — July 11, 2006 @ 2:02 am
Hannah wrote:
Nick M wrote
And he doesn’t, what he is saying is that neutral evolution (which he agrees with, and he says that the bulk of genetic changes is due to neutral mutations) is not the source of adaptions. I don’t think any biologist would disagree that while the majority of genetic mutations are neutral (while they may dispute the precise proportion), they are not the source of phenotypic adaptions. Dawkins spent a lot of time explaining his position on this and the reasons that Lamarkisim is fundamentally flawed. It is hardly dismissive to point out severe problems with a proposed mechanism.
Comment by Ian Musgrave — July 11, 2006 @ 2:12 am
Sal claim:
However, what he pointed about the molecular clock (which Dawkins mentions) is devastating, and peer-reviewed literature today has affirmed the main point of his position.
Could you please explain to us what Denton’s claims are and could you explain what peer-reviewed literature has affirmed the main point of his position?
Quoting from the new rules: If a statement of fact is challenged, the person challenged should make a good faith effort to either provide supporting evidence or make a logical argument as to why such supporting evidence is unnecessary.
It seems that Denton’s book may not be that good a treatment of taxonomy etc as Sal may have believed.
It’s important to realize how such ‘popular science’ books may be at odds with scientific theory.
As far as Avida is concerned, it seems to be off topic for this thread so I suggest we take it to a more suitable thread for discussion as there are quite a few flaws in your claims.
Avida, is an excellent tool at exploring the validity of ID claims regarding complex specified information (CSI), irreducible complexity (IC). But I think much of the relevance of Avida has been minimized when we realize that IDers have accepted that CSI as well as IC can be generated by natural processes. The argument now has become that the information was somehow ‘front loaded’.
On Pandasthumb Richard B Hoppe presented a good overview of the actual arguments based on Avida as well as the many strawmen objections by IDers
RBH In his testimony at the Dover trial on September 28, Rob Pennock described a study that has particularly irritated ID creationsts, The evolutionary origin of complex features, published in Nature in 2003. In that paper Lenski, Ofria, Pennock and Adami showed that there are circumstances under which structures that meet Behe’s operational criterion for irreducible complexity (IC) — loss of function due to knockout — can evolve by random mutations and selection. Since IC is the core negative argument of ID — IC structures and processes allegedly cannot evolve by incremental “Darwinian” processes — the demonstration that they can evolve by Darwinian processes knocks out IC as a marker of intelligent design. And since IC is a special case of Dembski’s Specified Complexity, it also weakens Dembski’s core argument.
RBH continues to address the claims about co-option, pointing out the evidence that shows that co-option is quite ubiquitous in nature.
What the Avida study showed is how Similarly, assembly language programs that performed the input-output mapping corresponding to EQU evolved, not EQU itself. That’s not a trivial distinction. A given function can be performed by a number of different structures.)
In fact many different solutions ‘evolved’ in the different lineages.
RBH lays to rest most of the objections to Avida as it pertains to the Lenski study.
See wwwDOTpandasthumbDOTorg/archives/2005/09/desperately_dis.html
and replace DOT with the period
RBH does mention that he extended a challenge to IDers
Given a data set (i.e. a long string) that represents a computer program (such as Avida), and the inputs to that (a population of digital organisms and a fitness landscape), measure (algorithmically) the ‘CSI’ (or whatever he asserts is ‘conserved’) in that data set.
Given a 2nd data set that also represents a computer program (Avida), and any inputs to that program (a different population of organisms, and the same fitness landscape), measure (algorithmically) the ‘CSI’ in that data set.
RBH: I posed a similar sort of challenge to the IDists on ARN a few months ago. Not surprisingly, none took it up (including Salvador, who didn’t find it “interesting”). I find it very telling that IDists who advertise a methodology for detecting design (IC, SC, CSI, or whatever it’s called) decline the invitation to validate and calibrate their methodology on phenomena of known provenance. It almost looks like they don’t care whether it’s reliable and valid. Does that surprise anyone? Luskin was identified in a DI press release as a “scientist”. Perhaps that is a worthy extramural project he could do as a new employee to get in good with his new bosses. Or maybe not.
In an earlier posting RBH addressed the Lenski paper as well as what he calls an error ridden objection by Truman
wwwDOTpandasthumbDOTorg/archives/2004/03/evolving_comple.html
I believe that understanding Avida and how it is relevant to the issues being studied can be helpful to lay to rest many of the criticisms of this excellent platform.
Comment by PvM — July 11, 2006 @ 2:29 am
As far as platonic forms are concerned, again I find it fascinating how science has uncovered how simple processes of duplication and preferential attachment leads to scale free systems in which a few common forms exist and many uncommon forms. It’s a combination of the neutrality of codon encoding, combined with the natural laws guiding the folding of proteins which explains the existence of the set of proteins. I am not sure what the relevance to ID is when natural law is used to explain an observation in nature.
In “A comment on the protein folds as platonic forms” Jayanth R. Banavar et al Journal of Theoretical Biology Volume 223, Issue 2 , 21 July 2003, Pages 263-265 explore the arguments presented by Denton et al
This novel phase of matter (Banavar and Maritan, 2003; Banavar et al., 2003a) has been exploited by Nature to house protein folds because of many of its advantages including those described by Denton et al. (2002) and Finkelstein and Ptitsyn (2002):
(1) The presence of a limited number of folds arises because of the constraints of the tube anisotropy. In the marginally compact phase, one requires that a space-filling conformation is created (in order to expel water from the hydrophobic core) with a preferentially parallel orientation of nearby tube segments.
(2) The native state folds may be thought of as “pre-existing Platonic molds” (Denton et al., 2002; Denton and Marshall, 1999) that a sequence must choose from for its native state structure.
(3) The limited number of folds that a sequence can adopt explains the relatively large basin of attraction (in a dynamical sense) for each of them. The thousand or so putative native structures allow for both diversity and stability, which are dual characteristics required for evolution to be successful (Anderson, 1983).
(4) The marginally compact phase exists in the vicinity of a phase transition which accounts for the exquisite sensitivity of protein conformations to the right types of perturbations.
(5) Because the set of protein folds are pre-determined by physical law, the sequence and the functionality evolve in order to best make use of these folds.
(6) Proteins are able to fold dynamically in an all-or-none transition into the native state (Bogatyreva and Finkelstein, 2001). This can be accounted for in the tube picture by noting that in the marginally compact phase, the energy scale of interaction is relatively weak and therefore the transition temperature is low and entropic effects are not important. The careful orientational positioning required of nearby tube segments ( Banavar et al., 2002b) leads to the tube snapping into its native state structure.
(7) The tube picture explains in a simple way the formation of fibril-like structures called amyloids which are implicated in a variety of diseases (Dobson, 2002).
The authors conclude
We are intrigued by the suggestion of Denton et al. (2002) that “the lawful nature of the folds together with the intriguing fact that many of the 20 protogenic amino acids—out of which the folds are constructed—are amongst the most common amino acids found in meteorites and the easiest amino acids to generate in pre-biotic syntheses is surely of considerable significance, consistent with and supporting a deterministic theory of the origin of life (or at least of proteins) and by extrapolation the whole Platonic cosmogony—raising the possibility that all organic forms and indeed the whole pattern of life may finally prove to be the determined end of physics and life a necessary feature of the fundamental order of nature.”
Of additional interest may be the work by A Framework for Globular Proteins , TIMOTHY LEZON, Pennsylvania State University —
Due to their remarkable chemical specificity and diversity, globular proteins play a crucial role in the network of molecular interactions of life. Over the past several decades, much experimental data has been accumulated on proteins, but the overarching principles that govern the general features of proteins remain largely unknown. Here, a novel framework for understanding many key attributes of globular proteins is presented. This framework suggests that the characteristics of globular proteins that make them well-suited for biological function are the emergent properties of a unique phase of matter. Implications of this picture include the provision of a fixed backdrop for molecular evolution and natural selection and design restrictions on molecular machinery. The work described here was carried out in collaboration with Jayanth Banavar and Amos Maritan.
Finally some well reasoned advice
A consideration of the protein structures used in biology has led some to conclude that the protein folds are a limited set of possible structures determined by chemical laws (Denton, 2002) - and that all evolution does is to search out and find these Platonic forms. The reason that this is a viable hypothesis is that each of the common protein folds can be specified by an enormous number of distinct sequences - in other words, finding these forms by random search processes is simply not that difficult a task. What is the number of distinct protein folds? Structural analysis of biological proteins reveals that many proteins that carry out different functions use the same basic folded structure (for example, the α-β barrel fold is used by hundreds of distinct enzymes). This structural analysis may be converging on an estimate of a few thousand distinct folds. It is important to realize that more folds continue to be discovered almost daily, so the end result is uncertain. However, there is a larger issue that cannot be addressed by the analysis of biological proteins alone, and that is whether biology is revealing to us a small subset of all possible protein folds, or alternatively, whether we are seeing that biology uses essentially all of the possible folds. Biology might very well use just a subset of the possible folds either as a result of historical accidents (i.e. contingent on the sequences that were sampled early in evolution), or because a subset of the folds have some advantages not shared by other folds. In my opinion this remains an open question, subject to experimental investigation.
in Explaining the Universe Without a Clue Jack W. Szostak
In other words, finding folding proteins using random search may not be that hard after all, something which seems to go against the hopes of IDers, who seem to insist that protein evolution is (close to) impossible.
In the end, if natural law explains proteins and their evolution then it seems that there is little room left over for ID to play in.
Perhaps IDers can help understand how this may be resolved?
Comment by PvM — July 11, 2006 @ 2:54 am
Ian–
I posted page numbers for the passages I based this on. Could you maybe elaborate on why you draw a different conclusion from them?
Comment by Hannah — July 11, 2006 @ 8:34 am
In comment #10, Salvador wrote:
“IDers do not disdain the work of evo-devo or Kimura or Haldane or Fisher or Gould like they disdain ultra-Darwinism or neo-Darwinism.”
That’s interesting news, as R. A. Fisher and J. B. S. Haldane are considered by virtually all evolutionary biologists and historians of science to be two of the founders of the “modern (i.e. neo-darwinian) synthesis” of evolutionary biology. Kimura simply extended some mathematical concepts implicit in the work of Fisher and Haldane.
On the other hand, Gould (and Eldrege) presented a major challenge to one of the major tenets of the “modern synthesis”: the idea that all significant evolutionary change must, of necessity, be extremely gradual. This idea is explicit in R. A. Fisher’s mathematical models of selection (which are primarily based on random mutation and selection at individual allele loci), and it is precisely this idea that the theory of “punctuated equilibrium” attacks.
However, and despite creationist/ID assertions to the contrary (and as Nick Matzke has masterfully shown elsewhere in this thread), the theory of “punctuated equilibrium”, rather than “undermining” the “modern synthesis”, simply built on and extended ideas that were implicit in the work of some of the founders of the synthesis. In particular, G. G. Simpson’s Tempo and Mode in Evolution is widely recognized as having the germ of the idea of “punctuated equilibrium”, a point recognized by both Eldrege and Gould in other publications on the subject. And, as Nick has pointed out, Ernst Mayr also takes some credit for part of the core theory of “punctuated equilibrium”, and no one could ever accuse Mayr of not being part of the “modern synthesis.” Indeed, he “wrote the book” on the subject (along with Will Provine).
Comment by Allen MacNeill — July 11, 2006 @ 9:30 am
And may I say, at the risk of being accused of “hijacking”, that this thread epitomizes precisely the kind of disciplined, respectful, and citation-loaded discussion that we hoped this website would encourage. Bravo (and brava) one and all!
Comment by Allen MacNeill — July 11, 2006 @ 9:31 am
I realize that what I said may sound horribly contradictory, but IDers like John Sanford and Walter ReMine were able to critique NDE because of Fisher and Haldane’s foundation of population genetics.
For example, Haldane’s dilemma, inspired by his 1957 paper The Cost of Natural Selection has been topic of interst in ID circles. Kimura and Crow are cited heavily in Sanford’s book.
Fisher’s work outside of NDE has been the foundation of Dembski’s design detection method.
That’s not to say IDers agree with everything these men say, but one gets the sense many IDers revere their mathematical accomplishments.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 11, 2006 @ 10:14 am
There is a subtlety to this discussion that I wish to point out, which I think will explain Hannah’s point. There are two aspects to neutral evolution:
1. The justification neturality is based on the cost issue
2. The mechanisms of neutrality must then be something like a stochastic processes decoupled from selection
#1 and #2 are not completely identical, although at first glance they might seem so. Because of the varieties of protein forms (polymorphisms), it became evident that populations could not create enough excess offspring for natural selection to be the cause of this diversity (this is the population cost issue). Ohta and Kimura used Haldane to show that neutrality applied to historic molecular evolution (not just protein polymorphism).
Dawkins brushes aside the fact such considerations could be fatal to NDE. In fact, many neutralists (like Crow) agree to Dawkins’ attempts at reconciling neutralism with Darwinian ideas. But the seeds have been planted for a major crisis, and this reconcilation can only be tentative.
What is not evident in all of this is that something slipped through the cracks, and this something IDers have been keen to seize upon. IDers fully agree with #1. But IDers point out, what if there are functional systems that agree with #1 (can’t evolve by natural selection) but are not explained by #2 either (purely stochastic processes)! Voila, a potential opening for ID!
Example, contingency functions are exactly the kind of function that would tend to be weakly selectable (effectively neutral), but yet functional.
Dawkins argues natural selection must be highly involved in creation of functional complexity. The IDers assert #1 (cost issues refute NS as a major cause of functionality) and then point out #2 fails to explain functionality of these weakly selectable systems.
In answer to PvM, regarding Denton’s prediction, Denton merely pointed out selectionists and neutralists have found fatal flaws in each others theories. Sample peer reviewed papers showing a growing crisis would be:
Missense Meanderings by DiPristo, Weinreich, and Hartl.
The neutralist can then hammer DiPristo’s side with the cost issue, and then point out the selectionist arguments offered in critique are circular. Each side (selectionist versus neutralist) continues to find fatal flaws in each other’s theory, just as Denton pointed out 20 years ago in his chapter on biochemical typology.
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 11, 2006 @ 11:09 am
Hannah wrote:
To back this up Hannah wrote:
The problem is, that when you look at the context and detail of what Dawkins is saying, it doesn’t support Hannah’s interpretation. Let’s look at what Dawkins actually says.
“One advantage of doing this is [not assuming evolutionary theory true before you build your trees] is that, if you have any doubts about it [evolution], you can use the pattern of resemblances to test it. If evolution is true, resemblances amongst animals should show certain predictable patterns, notably the pattern of hierarchical nesting.”
Now, an “independent test of” is not the same thing as “can’t logically support”. As we already saw back on page 275, we can recover consistent hierarchically nested trees which independently support evolutionary theory. Even if we start out assuming that organisms were evolutionarily related, if we could not recover independent nested hierarchies (as we do), we would soon know something was wrong.
As to your second quote, it helps to quote the full sentence in context:
“[The average distance measurers don’t just avoid evolution in building their trees]… They try to ask Nature to tell them whether she really is organized hierarchically. This is not any easy task, and it is probably fair to say that methods are not really available to achieve their aim.”
You can see that the “not really achievable” relates to a separate and much harder aim, rather than recovering evolutionary relationships. And evolutionary relationships can be uncovered, maximum likelihood is a phenetic method that is statistically well founded. It is computationally intensive, but the revolution in computer power means that maximum likelihood methods are used routinely now. And maximum likelihood methods routinely recover consistent nested hierarchies. Technical issues make the separate issue of independently determining if Nature is hierarchical at all difficult (but not impossible), but again, current limitations in methodology do not equate to “can’t logically support evolution”.
What “fails even as a description” means I have no idea, unless Hannah is focusing only on transformed cladists (who are weird), rather than the other taxonomists.
Comment by Ian Musgrave — July 11, 2006 @ 11:11 am
Ian perhaps has good points in how one might properly represent what Dawkins actually said, and I give him credit for that and appreciate his input.
However this still leaves hanging the issue of whether taxonomy supports common ancestry.
Prior to Darwin, the hierarchies which were readily apparent were explained by creationist as descending from a common forms in the mind of the Creator.
Sure, on the surface it may seem that a common ancestor is reasonable because of the hierarchical layout of similarities, but slight change in perspective, and one sees a hierarchical layout argues equally well against common ancestry!
It is understandable that paternity tests would make one think molecular similarities alone could establish common ancestry, but extrapolating (ah yes that nasty word, extrapolating) paternity tests to all of biology rather than to a single species is a different story.
Consider the Dayhoff Diagram which measures the differences in proteins between species. The diagram shows what is intuitively obvious, horses are similar to kangaroos relative to plants:
Cytochrome C and species divergence
But what is less obvious is that although one can see the sister relationship clearly, who the ancestors are is completely ambiguous.
For example horse, dog, … tobacco moth all have sisterly relationships when compared to wheat.
But do those sister relationship give any clue whatsoever WHO the common ancestor would be? From that diagram would we argue wheat is the common ancestors of horses and moths?
That is the challenge taxonomy poses to evolution. It shows that while sisterly relationships exists, there is no way to say which set of creatures were the ancestors.
One has to force fit pre-conceptions onto taxonomy to argue for common ancestry. But it’s like trying to argue one sister is actually a mother of the others.
One of course gets the impression of a common ancestor by the similarities, but then is left with the question, who could the ancestor be, they all look like sisters, not mothers?
Evolutionists say fish are the ancestors of horses, and might use the Dayhoff diagram to justify their conclusion, but one could easily re-order the columns and rows of the Dayhoff diagram and argue horses are the ancestors of fish!
Salvador
Comment by Salvador T. Cordova, IDEA GMU — July 11, 2006 @ 12:13 pm
Sal’s confusion with Dayhoff is understandable as it even confused Denton. Despite this, as Elsberry showed one can use the cytochrome-c data to determine the cladogram.
It’s the fact that independent sources give such a consistent picture of common descent that has made common descent the fact it is. I encourage any reader to check out Douglas Theobald’s FAQ on talkorigins on 29+ evidences of macroevolution which explores the vaste amounts of evidence supporting common descent.
ID should embrace the facts of science rather than reject them, like for instance YECers, based on religious faith.
When I asked Sal to support his claim about Denton, I expected some significant problems that Denton had pointed out and which science has failed to resolve. Imagine my surprise when Sal mostly repeated his claim and failed to present much of any argument which reflects the scientific understanding of protein evolution
Sal: In answer to PvM, regarding Denton’s prediction, Denton merely pointed out selectionists and neutralists have found fatal flaws in each others theories. Sample peer reviewed papers showing a growing crisis would be:
Missense Meanderings by DiPristo, Weinreich, and Hartl.
Fatal flaws require some detailed explanations and I thus once again invoke the rule of the board and encourage Sal to present his claims and support them in a manner suitable for these boards.
From the paper Sal references
We then advance a biophysical model of protein evolution that helps us to understand phenomena that range from the dynamics of molecular adaptation to the clock-like rate of protein evolution.
A biophysical model which explains wide ranges of observations… I’d love to see a similar model from IDers but despite several repeated requests, it seems that ID research is a bit behind here.
Protein evolution is something I have been studying (as a layperson) and my findings suggest that protein evolution seems to be quite well captured by natural laws (as Denton so clearly argued in his paper on platonic forms), that protein formation is ruled by natural law is of significant relevance as it undermines any ID hypothesis which relies on eliminating said natural laws.
Of course, ID can always move the goalposts and argue ‘front loading’ but then it merely underlines its scientific vacuity.
From the scientific literature (recent)
Jayanth R. Banavar Lattice Tube Model of Proteins, Phys. Rev Let, 93, 238101 (2004)
Gustavo Caetano-Anolles An Evolutionarily Structured Universe of Protein Architecture, 2003 13: 1563-1571 Genome Res.
Johannes Soeding and Andrei N. Lupas
More than the sum of their parts: on the evolution of proteins from peptides,
macromolecule: the folded protein. BioEssays 25:837 – 846, 2003.
Comment by PvM — July 11, 2006 @ 1:44 pm
Sal: Example, contingency functions are exactly the kind of function that would tend to be weakly selectable (effectively neutral), but yet functional.
Indeed, which is why many of the gene duplications do not survive as backup systems but rather diverge into new functions or disfunction. I fail to understand why such a big deal is made of the simple fact that neutrality is an essential mechanism of evolution.
Neutrality allows the genome to explore sequence space without destroying the function of the structure it maps to.
In fact, the findings that proteins map to few structural shapes shows that while sequence space can diverge, structure space can remain the same. While this may surely confound phylogenies which are based on sequence similarity rather than structure similarity, these examples show how neutrality is an essential mechanism in evolution.
In fact, gene duplication and preferential attachment is a simple yet powerful mechanism to explain the scale free nature of protein networks. In other words, we have a simple mechanism (natural of course) which explains protein evolution and thus any hopes for ID have been destroyed that such forces of nature cannot explain protein evolution, which would have triggered a design inference.
I cannot stress this enough. Any time science explains, ID remains powerless and another gap has been closed.
In the case of protein evolution, science is advancing our knowledge and doing quite well in resolving the many open issues.
May I politely inquire as to how ID has contribute in a non-trivial matter to this knowledge? Any empirical or theoretical contributions worth mentioning here?
I have already pointed out that in biology, degeneracy seems to be quite prevalent, and is not typically found in intelligently designed systems, showing that ID cannot rely on analogy (one of the weakest logical arguments) to make its claims.
The presence of degeneracy in biology however follows trivially from the above described mechanisms. In other words, science shows a coherent and consistent picture of biology and its mechanisms.
In fact, if Sal is correct and gene duplications are weakly selectable at best, then gene duplications would not survive long and thus would seem to make poor solutions to robustness. In other words, Sal’s argument seems logically contradictory. Unless Sal can explain to us how such weakly selectable systems are being maintained in the genome?
Comment by PvM — July 11, 2006 @ 2:04 pm
Sal:
Please present your analysis in sufficient detail that allows us to determine if you are correct.
Reconcile the plausible diagrams with known fossil evidence and other phylogenetic data to show that horses are ancestors to fish is equally well or better supported by the available data.
It’s the consistent picture that arises in evolution which makes common descent such a powerful fact. No consistent and coherent alternative picture has been described so far that would undermine these facts.
Comment by PvM — July 11, 2006 @ 2:07 pm
Salvador poses a “challenge based on taxonomic relationships”:
Gven that Salvador evidently accepts that the taxonomic data establish some sort of ancestor-descendant relationship, how on earth could we establish which way that relationship goes? Why, by searching for independent evidence. If we consult paleontologists, they tell us that fish preceded horses in time. Now we have two pieces of coordinated evidence, and together they tell us that (lobe-finned) fishes are ancestral to mammals via an established series of intermediates. See how one can use multiple lines of evidence to narrow the possibilities?RBH
Comment by Richard B. Hoppe — July 11, 2006 @ 2:11 pm
Sal writes,
Must…control…urge…to…use…ad.hom…
There are three or four levels of really incredible misunderstanding that Sal is operating under here, but the most important is that the Dayhoff matrix, published in the 1970s, does not exactly represent the sum total of sequence data available from living forms.
You can rigorously determine whether or not the ancestral state was a “horse” or a “fish” by including more data. When you do this you see that “fish” make up a long series of groups basal to tetrapods (let alone horses), and therefore the most parsimonious reconstruction of the ancestor of tetrapods is a “fish” (defined as a water-breathing vertebrate with fins — fish are not an official group in cladistics because tetrapods nest within the “fish” tree).
You can see how tetrapods nest within “fish” just about anywhere, e.g. the Tree of Life page on Sarcopterygii.
Comment by nmatzke — July 11, 2006 @ 2:28 pm
This constraint on structural shapes seems to represent a major problem for RM+NS. This means that the number of solutions for protein structure is small, thus lowering the already incredibly low probability of finding such ‘solutions’ in sequence space. And Dembski’s NFL theoroms point out the virtual impossibility of searching out these solutions in sequence space using ‘random walks’ (or, neutral mutations).
Could you please explain what you mean by ‘preferential attachment’?
That degeneracy is not found in “intelligently designed systems” can just as easily be ascribed to a superior intellect, thus negating your argument against ‘analogy’. Albert Einstein thought just the way that you and I do—that is, in an analogous manner; but Einstein’s thinking was superior to both yours and mine.
How is this so? Does it involve ‘preferential attachment’?
Comment by Lino D'Ischia — July 11, 2006 @ 5:32 pm
Let me salute Nick on his efforts at civility. I know he must be steaming. The readers are witnessing why pure taxonomists (like the transformed cladists) send others up the wall, everyone except creationists that is….
But not purely taxonomic data (both molecular and morphological). And I would challenge the statement that more recent purely taxonomic data establishes horses are nested within fish, stripped of ANY other pre-conceptions.
To contradict my position, one would have to show that most sequenced proteins when laid out in the manner of Dayhoff’s diagram would not be consistent with the nesting patterns of cytochrome-C. I just don’t see that happening.
I’m afraid I must object here. Someone can force fit a pre-conception and say human beings are fishes, but that doesn’t mean it makes sense in terms of purely morphological nor molecular taxonomy.
Primates nest within mammals. Rodents nest within mammals. How does one taxonomically say mammals nest within fish! Taxonomically, saying mammals nest within fish makes no sense. This is borne out in pure morphological taxonomies and molecular taxonomies. Mammals are not fish, no way. The only reason mammals would be nested in fish is to fit the into existing pre-conceptions (not necessarily right or wrong).
It is exactly these morphological hierarchies in existing biotic reality that are such a nasty barrier to evolutionary conceptions. Hierarchy suggests fish beget fish, and never mammals, not today, nor perhaps ever. One cannot use the hierarchy argument “all fish descended from a progenitor fish, because all fish share certain diagnostic characters” to also argue horses come from fish.
And from taxonomic considerations, one can see, in general, hierarchies resist the notion of transitionals (like those between fish and horses).
Taxonomy need not assume evolution. Recall this bomb dropped in middle of the transformed cladism controversy:
Dawkins was too abstract in his description in his book, regarding taxonomy. But I hope it is apparent why pure taxonomy is anathema to evolutionary biologists.
The hierarchical pattern which was thought to argue for common ancestry begins to actually argue against it. And that’s why the pure taxonomists have ready friends in the creationists.
Morphological taxonomies show amongst species relationships of: sisters, cousins, 2nd cousins, 3rd cousins, etc. But there is a difficult wrinkle to all of this. What would the mother, grand mother, great grand mothers look like? What if we can’t assert what the ancestor looked like, what then?
Consider 2 ways how we might assert an ancestor:
1. Form an ancestral creature with only the basic features for its body parts. Well, this has the unfortunate problem of making mostly dead creatures or something from the X-files. For example if the common ancestor of all Bilaterians only had salient features of a bilaterian and nothing else, it would be dead or look like a creature from the X-files. See: Problems with Characterizing the Protostome-Deuterostome Ancestor
2. Take an existing cousin (like an ant) and claim it’s the ancestor of all it’s cousins. This has the unfortunate problem of working in reverse at the whim of the observer. For example one could argue (in the absence of paleontological pre-suppositions) that within the bilaterians humans are the ancestors of fish or even ants! Thus taxonomy does not logically support evolutionary conceptions very well at all, except to assert sister, cousin, 2nd cousin. etc relationships. But this is consistent with common design as much as common ancestry, with the consideration that the hierarchy makes the characterization of the actual ancestor suspect.
Sisters, cousins, 2nd cousins, and 3rd cousins can be established both in morphological and molecular taxonomies (i.e primates have very similar DNA and proteins, and thus are cousins). If it were pure molecules alone that were considered, one might be persuaded that common ancestry is fact. That is reasonable on the surface. But again morphological hierarchies make the assertion of common ancestry difficult.
Comment by Salvador T. Cordova, IDEA GMU — July 11, 2006 @ 5:38 pm
RBH:
There are about, what 30-35 different accepted body-plans. Just wondering, if you eliminated the vertebrate body-plan entirely, would there be any evidence for evolution?
Comment by Lino D'Ischia — July 11, 2006 @ 5:38 pm
Nick:
If cladistics can’t make a distintion between ‘fish’ and ‘tetrapods’, with ‘fish’ not even being defined but rather ‘nested’ alongside tetrapods, then, to my mind, we’re no longer dealing with the case of the ‘missing link’, but with the case of the ‘missing order’. Pardon the pun, but doesn’t it strike you as fishy that ‘fish’ aren’t placed in their own separate domain?
Comment by Lino D'Ischia — July 11, 2006 @ 5:50 pm
PvM:
I’m puzzled by this statement in this sense: what could possibly be more ‘front-loaded’ than the idea that “natural laws” came into existence already containing within them the constraints necessary for the production of proteins? Personally, Denton’s thesis is TOO ‘front-loaded’. If you press his arguments too far, then the whole idea of ‘chance’ seems to almost disappear. I like Monod’s characterization of life: Chance and Necessity. (Like ‘flesh and bones’)
Comment by Lino D'Ischia — July 11, 2006 @ 6:12 pm
Cladistics can make a distinction (tetrapods are a highly modified subgroup of “fish” that moved to land), but in cladistics you just can’t say that “fish” are one group and tetrapods another, because tetrapods actually fall within the “fish” group.
Comment by nmatzke — July 11, 2006 @ 8:35 pm
Sal, whatever are you talking about? What does “pure taxonomy” even mean? Just earlier the creationists were telling us that cladistics was great because it didn’t assume evolution — isn’t this exactly what you want?
As for transformed cladists, I think they may be extinct since their issues were basically a debate of the early 1980’s which was resolved for everyone but the creationists, who keep dragging out the same old bootlegged quote mines from Colin Patterson’s criticisms of pre-cladistic taxonomy, 25 years+ after the fact, and long after everyone has become a cladist and people like Padian have used cladistics to bash creationist arguments even more thoroughly than they were bashed before.
Comment by nmatzke — July 11, 2006 @ 8:46 pm
Lino D’Ischia wrote:
They are. It’s called the clade Osteichthyes. Now I have a question about ID. Fish and tetrapods belong to the phylum Chordata. According to ID, the creation of fish and tetrapods involved common design, but the creation of the phylum Chordata during the Cambrian involved novel design, right?Comment by alienward — July 11, 2006 @ 9:35 pm
Lino I’m puzzled by this statement in this sense: what could possibly be more ‘front-loaded’ than the idea that “natural laws” came into existence already containing within them the constraints necessary for the production of proteins?
I fail to see the problem, natural law exists and determines which folds exists, evolution uses what is available.
Front loading is such a meaningful concept as it adds an unnecessary component to natural law, namely that it was somehow ‘front loaded’.
In fact, Denton’s concept hardly leaves no room for chance. I have quoted some example papers which show how chance still plays a role.
I find the objections of IDers interesting since on the one hand IDers argue that natural law does not constrain evolution so how could proteins have come into existence and evolved, or how could the genetic code have evolved. And when science shows how there is actually chemistry and/or physics linking the genetic code and/or proteins to lawlike behaviors, the argument becomes that there is no room for chance.
Of course, since ID relies on rejecting regularity and chance, the real conclusion seems to be that there is no room for ID to ‘play’ in.
Do you disagree? If so, how does ID play a role in protein evolution if protein evolution can be explained by natural law?
Comment by PvM — July 11, 2006 @ 11:31 pm
Sal makes so many unsupported assertions about cladistics and taxonomy that it seems irrelevant to invoke the ground rule to have him support his claims of fact.
So instead let me point out that Sal has failed to explain why so many different sources of information all lead to a common tree? Now it may be hard for some to conceptualize the relationship between mammals and fish and yet, the data are clear. So rather than ignoring the data, it may perhaps be more effective to change one’s thinking about the fact of common descent.
I fail to see why common descent is such a big issue. It seems to be of little relevance to ID and only young earth creationists seem to make a big deal of this.
If ID believes that there exists a better explanation for the observed data, let them present the hypotheses and show indeed that they explain the data better than evolutionary theory.
Common descent may cause some a certain amount of discomfort or confusion, and it is our goal in this group to help explain why common descent is such a well established fact even though it may seem to go against ‘common sense’. One cannot really argue against the facts.
Again I point the interested readers to the excellent overview by Douglas Theobald at talkorigins.org
29+ Evidences for Macroevolution Part 1: The Unique Universal Phylogenetic Tree
Perhaps Sal can explain to us why we should reject these facts just because we are unable to explain some minor puzzles?
Taxonomy, phylogeny and many other relevant aspects of biology all strongly support common descent as well as provide fascinating insights into the mechanisms of evolution.
So far, I have yet to see any mechanisms of ID. Any takers?
Comment by PvM — July 11, 2006 @ 11:39 pm
Lino
This constraint on structural shapes seems to represent a major problem for RM+NS. This means that the number of solutions for protein structure is small, thus lowering the already incredibly low probability of finding such ‘solutions’ in sequence space.
No, no that does not logically follow from the fact of scale free networks, in fact scale free networks tend to extend throughout sequence space as has been found for RNA where it is easier to calculate the secondary structures. In other words, finding such structures from other structures is almost trivially simple since neutral paths connect most any of these structures, all that is needed is one or a few non-neutral mutations and voila.
Lino
And Dembski’s NFL theoroms point out the virtual impossibility of searching out these solutions in sequence space using ‘random walks’ (or, neutral mutations).
Sadly enough, Dembski’s NFL does no such thing. Why is it that so many seem to be so unfamiliar with Dembski’s work? Could Lino present the factual support for his claims as per rules of engagement for this board?
Lino
So absence is now evidence for presence because well, analogy is a flawed concept and we should in fact be looking for dis-analogy and conclude design was involved.
And people wonder why I argue that ID is scientifically vacuous. Lino’s comments here exemplify exactly what is wrong with ID as it matches about anything as long as one has enough imagination.
On the one hand ID argues that analogy between design in nature and design in technology should be evidence of ‘intelligent design’, on the other hand ID argues that absence of such evidence is evidence as well.
As far as the concept of preferential attachment, check out the work by barabasi. Preferential attachment has been shown to be an evolutionary process. Imagine that… Theory and empirical evidence actually support eachother.
So if gene duplication and preferential attachment can explain the scale free nature and the level of degeneracy in the genome, why should these natural processes be seen as indicative of intelligent design? And please don’t give us the ‘Dembski’s NFL shows us’ because Dembski’s NFL does little to support his own claims and when we get to discuss his work, I would be more than happy to explain in straightforward terms why Dembski is wrong.
Hint: Under NFL, random search is trivially simple and effective.
Surprised? I thought you would be as you would never get that information from ID sources.
Comment by PvM — July 11, 2006 @ 11:49 pm
PvM: Could you rephrase the following? I’m just not sure what you mean, so it’s hard to respond:
“Front loading is such a meaningful concept as it adds an unnecessary component to natural law, namely that it was somehow ‘front loaded’.
In fact, Denton’s concept hardly leaves no room for chance. I have quoted some example papers which show how chance still plays a role.
I find the objections of IDers interesting since on the one hand IDers argue that natural law does not constrain evolution so how could proteins have come into existence and evolved, or how could the genetic code have evolved. And when science shows how there is actually chemistry and/or physics linking the genetic code and/or proteins to lawlike behaviors, the argument becomes that there is no room for chance.”
Again, I’m a little unclear. But I’ll say this, the formation of ’structure’ is very likely just a function of quantum mechanical forces, and, as such, is determined by natural law. But the amino acids that are linked together, and their sequence, determine, ultimately, how those quantum forces will act (it’s almost like you have a ‘quantum computer’, and the amino acid sequence is the ‘input’ with the ’structure’ being the output). But I don’t think that ‘natural law’ determines the genetic code, and hence, the amino acid sequences. That’s pushing ‘natural law’ too far in my estimation.
The $64,000 question is how did the code come about. The $1,000,000 question is whether RM+NS is capable of even modifying this code. As I roll these words over in my head, the first question that pops up is: we call it the ‘genetic code’; have we ever encountered ‘code’ where it WASN’T produced by some form of intelligence? Doesn’t calling it ‘code’ simply give the store away?
Comment by Lino D'Ischia — July 12, 2006 @ 12:11 am
I’m not following you. Can you elaborate?
Comment by Lino D\'Ischia — July 12, 2006 @ 12:13 am
As I roll these words over in my head, the first question that pops up is: we call it the ‘genetic code’; have we ever encountered ‘code’ where it WASN’T produced by some form of intelligence? Doesn’t calling it ‘code’ simply give the store away?
What store?
Comment by Michael Hubl — July 12, 2006 @ 12:35 am
Well, no, actually. Since you are arguing from analogy based on human design and human usage of the term ‘code’, the logical conclusion would be that humans designed life.
Do you believe we designed ourselves?
(This comment won’t see the light of day because I’ve been banned despite assurances to the contrary)
Comment by Don Baccus — July 12, 2006 @ 1:04 am
Lino D’Ischia asked
Is that a serious question?Mullusca phylogeny
Arthropoda
Bryozoa
And so on. And yes, both fossil data and molecular data in those invertebrate groups and more provide convergent evidence for evolutionary theory.
Alienward remarked
Actually, it’s now pretty clear that Chordata predates the Cambrian.RBH
Comment by Richard B. Hoppe — July 12, 2006 @ 1:19 am
Except that tetrapods fall within Osteichthyes, so it’s not really “separate.”
Also, the diagram in that page shows that cartilagenous fish (sharks and rays), the extinct placoderms, and the hagfish & lamprey fall outside of Osteichthyes, even though colloquially most would call them “fish.”
Comment by Nick (Matzke) — July 12, 2006 @ 1:55 am
The $64,000 question is how did the code come about. The $1,000,000 question is whether RM+NS is capable of even modifying this code. As I roll these words over in my head, the first question that pops up is: we call it the ‘genetic code’; have we ever encountered ‘code’ where it WASN’T produced by some form of intelligenc