Friday, May 16, 2008

Oops, I Did It Again!

I have this dirty feeling again...

I tend to start up interesting debates at sites where discussion on the evidence for (or lack thereof) evolution is not the intended topic for discussion. I've already unintentionally "hijacked" the discussion at Tom Gilson's blog, which has abruptly ended both there and here (in fairness, the debate never got started here, dangnammit!). :(

Over at Steve Martin's blog, "An Evangelical Dialogue on Evolution", an interesting debate with RBH is about to blossom. However, Steve has made it clear that the intent of his blog is not to debate evolution itself. Therefore, out of respect for Steve's wishes, let's move the debate here.

First comment is reserved for RBH. After that, the floodgate's are open. Let the fun begin!

"Keep your stick on the ice"
Red Green

13 comments:

  1. This is the comment I left on An Evangelical Dialogue on Evolution, which JJS invited me to repost here so as not to hijack that thread.

    JJS P.Eng. wrote

    But if you mean that there's a HDSC in common ancestry based on the evidence, well I believe Drs. Gould (sudden appearance and stasis), Doolittle (Multiple Common Ancestors), and Koonin ("bush" of life) would disagree, and this is just a short list of dissenters. Plus, IMO, the fossil evidence and the "speciation" evidence do not support common ancestry, either.

    I'll restrain myself, also in deference to Steve's point, and confine myself to remarking that anyone who can find doubt about common ancestry in Gould's "sudden appearance and stasis" (which I take to mean punctuated equilibrium theory) really needs to read what Gould (and Eldredge) actually wrote. JJS might start with Gould's Punctuated Equilibrium, which is Chapter 9 (separately published) of his doorstop The Structure of Evolutionary Theory. If JJS can find anything in that chapter -- any evidence -- that contradicts or casts doubt on common ancestry I'll eat The Structure of Evolutionary Theory.

    The others JJS mentions deserve comment, too, but as I said, I'll restrain myself. I'll just whisper molecular phylogenies. :)

    ====

    I'll suggest for the sake of a reasonably coherent thread that we start with with Punctuated Equilibrium -- "sudden appearance and stasis" -- and see where, if anywhere, Gould and Eldredge's conception casts doubt on common ancestry. Later we can circle back to other issues raised on your comment over there. For now let's focus on the one question, How does Eldredge and Gould's punctuated equilibrium hypothesis reduce the certainty of the common ancestry/descent conclusion -- the High Degree of Confidence Steve attributes to it?

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  2. RBH,

    Correct me if I'm wrong, but is not PE a way of explaining "sudden appearance and stasis" within a Darwinian framework? "Sudden appearance and stasis" is evidence against "Classic Neo-Darwinism" (NDES), and PE, to the best of my knowledge, it not widely accepted (although I do not put much argumentative stock in "consensus science").

    I have not read Punctuated Equilibrium by Dr. Gould (just ordered it today and looking forward to reading it), but I have read Dr. Phillip E. Johnson's critique of PE in Darwin on Trial. When I have more time (busy long weekend), I'll lay out the critique in detail when time permits.

    Thank you for posting here, RBH. I am looking forward to this discussion.

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  3. I'm not sure what "Classical Neo-Darwinism" means to you, but PE is not in opposition to the (Darwinian) view that speciation occurs by incremental changes in the genetic composition of populations that take place over time typically measured in thousands of generations.

    Punctuated Equilibrium theory is a proposal to explain the pattern of "sudden appearance and stasis" in the fossil (geological) record. (The italicized phrase is important.) PE was laid out over a number of publications starting in 1971. Eldredge and Gould argued on the basis of four main points -- I'll condense here:

    1. The geological record is relatively coarse-grained. One cannot discern series of events that occur on a finer time scale than the time grain of the record allows. As an analogy, consider a movie that shows images at a rate of 24 frames per second (roughly 40 milliseconds per frame). The record of successive images that frame rate provides cannot represent events that happen, say, at a microsecond rate. The steps of an incremental process that takes just a few milliseconds to play out would be invisible in a 24 frame per second movie -- it would display a 'punctuated' appearance with the actual incremental process being invisible to the representation.

    2. Genetic changes potentially leading to speciation can occur relatively rapidly in small isolated populations. For example, genetics teaches us that the rate at which new alleles fix in a population as a function of pure genetic drift is an inverse function of population size. The genetic composition of a small isolated population also can differ from the parent population due to founder effects. So small populations are prone to relatively rapid changes in their genetic composition.

    3. Most speciation is allopatric (cladogenesis) -- it occurs in small geographically isolated populations that "bud off" from a parent population -- and is incremental in nature, proceeding in a step by step fashion.

    4. If a new species is formed in a small isolated population and then the geographical barriers between the parent population and the offspring population are later breached, the offspring population can overspread the area occupied by the parent population very rapidly in geological terms, and thus appear 'suddenly' in the geological/fossil record over the range of the parent population. The speciation process would be invisible unless one can find the small geographic area in which it occurred and there was preservation of fossils of the graded series.

    For a more detailed introduction see TalkOrigins (note that the "peripatric" speciation mentioned there is a variety of allopatric speciation). One might also read the original 1972 PE paper available here (pdf). Notice that in that paper they provide data on a couple of fossil series that illustrate PE. Notice also that they exaggerate for rhetorical effect the phyletic gradualism against which they argued. Even Darwin foreshadowed the role of isolated populations in speciation and was not himself a "constant speedist," though if he had a leaning it was probably toward phyletic gradualism (anagenesis) rather than cladogenesis. But then we've learned a but since Darwin wrote.

    The processes that PE invokes are in fact accepted in 'standard' evolutionary theory and have good evidential support. What is mostly rejected are the rhetorical claims of a revolutionary shift in thinking that Gould especially made. Eldredge and Gould actually built on pre-existing ideas of Mayr, and invoked no new processes or mechanisms. That is, PE is an outgrowth and elaboration of existing theory to explain a pattern in the geological data, not an ad hoc attempt to explain away those data. Their main novel claim was the degree of heavy predominance of allopatric speciation over sympatric speciation.

    Now, the question we are addressing -- your claim that initiated this discussion -- is whether PE casts doubt on common ancestry. I see no indication that it does.

    Finally, I would be wary of taking a lawyer's representation of a technical issue in biology as a veridical account of that issue. I'm not much interested in Johnson's critique without evidence that Johnson knows enough about PE to accurately represent both it and 'standard' evolutionary theory. I've not seen such evidence in what I've read of Johnson, though my reading of him has been confined to essays available on the web and reviews of some of his books. I'll be interested to read your summary of his critique.

    RBH

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  4. By the way, while you're reading, you might follow this series of posts on An Evangelical Dialogue. The first content post, by Keith B. Miller, just went up.

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  5. RBH, thank you for your extensive reply. I was going to try to "clean up" my original response when I had time (like now), but I see you've pretty much covered much of what I wanted to.

    RBH said:
    "Punctuated Equilibrium theory is a proposal to explain the pattern of "sudden appearance and stasis" in the fossil (geological) record. (The [bolded] phrase is important.)"

    My point is that Gould recognised the "dirty little secret" of paleontology and with PE, tried to explain - or explain away, depending on one's point of view (at this time, not mine) - the "sudden appearance and stasis" in the fossil record. As for your summary of PE, I thank you for it and all the links with it. I need to read over it a couple times to be able to personally comment on it.

    RBH said:
    "The processes that PE invokes are in fact accepted in 'standard' evolutionary theory and have good evidential support."

    I would ask you what the "Standard evolutionary theory" is. My understanding of the Neo-Darwinian Evolutionary Synthesis (NDES) is the "party line" by Dawkins, Mayr, Wilson, et al. IOW, NS governs as the evolutionary mechanism for gradual changes required for animal macroevolution (I accept microevolution as can be seen from an earlier debate here and summarised here).

    RBH said:
    "Now, the question we are addressing -- your claim that initiated this discussion -- is whether PE casts doubt on common ancestry. I see no indication that it does."

    I believe that implied in my original claim was that Gould recognised a problem with the standard tree of life (ToL) which I see as the NDES evidence of universal common descent (UCD). I accept that he tried to explain it with PE, but he still recognised a problem with the NDES ToL.

    RBH said:
    "Finally, I would be wary of taking a lawyer's representation of a technical issue in biology as a veridical account of that issue. I'm not much interested in Johnson's critique without evidence that Johnson knows enough about PE to accurately represent both it and 'standard' evolutionary theory."

    I would be careful taking this position, and I am assuming that this is not your main point in your overall argument since it comes last. IMHO, this is an elitist position and does not become a scientist at all. I believe it was Richard Feynman who said that scientists should be open and honest with critiques from non-scientists (this is a generalised paraphrase; I'll locate the specific quote when time permits).

    Dr. Johnson's argument was good enough to gain support from Dr. David Raup (as mentioned in "Doubts About Darwin"). Dr. Johnson's story - before and after "Darwin on Trial" - is fascinating and I encourage everyone to read about it.

    I would also caution about using reviews as evidence. Science can be quite polarised and politicised - especially in this field. That's why I personally want to read about both sides from the source.

    More again soon...

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  6. Two other points I would like to make.

    1. In Steve's post at Evangelical Dialogue, I accept UCD to have a"high-degree of scientific certainty" among evolutionary biologists only because it is the consensus view. However, IMO, the evidence does not support presenting UCD as fact.

    When I used Gould as supporting evidence, I did not mean to imply that Gould did not accept UCD, but rather that he recognised a significant problem and tried to explain it. This is the same for Dr. Doolittle's multiple common ancestors and Dr. Koonin's "bush of life". They all recognised a problem with UCD and then try to explain it in their own way.

    2. Another problem I have with UCD is the fossil evidence is used to "prove" UCD. However, this "proof" entails arranging the fossils using UCD as an a priori assumption. This is circular reasoning, not proof.

    Now if UCD was presented side-by-side of another theory, say archetypes, I would have no problem with it. But both UCD AND archetypes have to be recognised for what they are: assumptions, nothing more, nothing less.

    More soon...

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  7. I would ask you what the "Standard evolutionary theory" is. My understanding of the Neo-Darwinian Evolutionary Synthesis (NDES) is the "party line" by Dawkins, Mayr, Wilson, et al. IOW, NS governs as the evolutionary mechanism for gradual changes required for animal macroevolution (I accept microevolution as can be seen from an earlier debate here and summarised here).

    That's a fairly accurate brief summary, though it neglects the synthesis of organismal evolution and genetics that is usually referred to as the modern synthesis. The main (though not sole) variable driving biological evolution at all levels of analysis is natural selection operating on variation that is at bottom generated by genetic mutations that affect selectable traits of organisms. I myself prefer using "incremental changes" rather than "gradual changes", since the latter phrase carries connotations over and above the step by step character of evolutionary change.

    I believe that implied in my original claim was that Gould recognised a problem with the standard tree of life (ToL) which I see as the NDES evidence of universal common descent (UCD). I accept that he tried to explain it with PE, but he still recognised a problem with the NDES ToL.

    Not at all. Eldredge and Gould did not address a perceived problem with the ToL, they addressed a perceived problem with a pattern in the fossil data that did not match what a pure phyletic gradualist (incremental, slow, and involving the whole population/species) speciation hypothesis would predict. That is, they didn't see a problem with the ToL or common ancestry, but with the explanation of a pattern in the fossil data. Once again, they exaggerated the 'orthodox' commitment to anagenesis (phyletic gradualism), and heavily emphasized the role of allopatric speciation over sympatric, with special attention to small isolated populations. They were addressing how speciation occurs, not whether it occurs.

    I would be careful taking this position, and I am assuming that this is not your main point in your overall argument since it comes last. IMHO, this is an elitist position and does not become a scientist at all. I believe it was Richard Feynman who said that scientists should be open and honest with critiques from non-scientists (this is a generalised paraphrase; I'll locate the specific quote when time permits).

    My remark addressed knowledge. It's not elitist in the pejorative sense to require of a critic -- be he professional or amateur -- that he display at least a working knowledge of the position he criticizes. An enormous volume of creationist critiques of evolution (with which I've been involved for 20 years) are founded on misunderstandings or misrepresentations of evolutionary theory. Like structural engineering, evolutionary biology is a highly developed discipline that can't be learned in a month or two of casual reading of secondary sources. So one looks for evidence that the critic actually knows enough about the subject matter of the discipline to produce criticisms that are worth looking into. Life is finite, and not every criticism is worth spending time on.

    Dr. Johnson's argument was good enough to gain support from Dr. David Raup (as mentioned in "Doubts About Darwin"). Dr. Johnson's story - before and after "Darwin on Trial" - is fascinating and I encourage everyone to read about it.

    I can find no independent source for that claim aside from Johnson's reported recollection of a remark at a conference, the recollection only reported by Johnson 10 years after the conference. And "Johnson's argument" is a little vague: What part of Johnson's argument did Raup actually support?

    I would also caution about using reviews as evidence. Science can be quite polarised and politicised - especially in this field. That's why I personally want to read about both sides from the source.

    Erm, I didn't use a review as "evidence." I said I had read only some of Johnson's essays and reviews of his books, and therefore looked forward to your descriptiion of his argument.

    When I used Gould as supporting evidence, I did not mean to imply that Gould did not accept UCD, but rather that he recognised a significant problem and tried to explain it.

    Except that the problem Eldredge and Gould saw was not with common descent, but with the explanation of how speciation mainly occurs. Nowhere in their writings (and I've read a whole lot of both Eldredge and Gould) do they suggest, imply, or state that the pattern in the fossil record that they advanced PE to account for was a problem for common descent.

    Another problem I have with UCD is the fossil evidence is used to "prove" UCD. However, this "proof" entails arranging the fossils using UCD as an a priori assumption. This is circular reasoning, not proof.

    The fossil evidence is part of the evidence for common descent, but I know of no evolutionary biologist or paleontologist who would claim that it "proves" universal common descent. There are multiple independent lines of evidence that underpin the inference of common descent, not merely the fossil evidence. In Gould's phrase (cited here, "... a scientific fact is not 'absolute certainty', but simply a theory that has been 'confirmed to such a degree that it would be perverse to withhold provisional consent'." In the case of common descent, the evidence is sufficient -- at least in the eyes of the professionals who study it -- that it would be perverse to withhold provisional consent. Now, one is perfectly free to reject that view and regard the professional consensus as flawed, but that requires very good reasons and evidence to be worth spending time on.

    Further, your remark that using the fossil record as evidence for common descent "entails arranging the fossils using UCD as an a priori assumption" is false. The fossils are "arranged" chronologically by age and morphologically by means of comparative anatomy. Neither assumes common descent; common descent is the inference that follows from the patterns observed in those chronologically and morphologically "arranged" data. There are conceivable patterns in those data that, if they were actually observed, would disconfirm ("falsify") common descent. In J.B.S. Haldane's phrase, finding fossil rabbits in the Precambrian would overthrow the theory of common descent. But we don't find those rabbits, not because the data are "arranged" so as to conform to the theory but because the data, "arranged" by methods that are independent of the theory, are universally consistent with the theory.

    Common descent is far from an assumption. It is an inference -- a conclusion -- based on a wide range of data from multiple independent sources. It is the consilience of those multiple independent lines of evidence that gives the conclusion its "fact" character. Eldredge and Gould never questioned that. They questioned some specifics of how common descent -- via speciation -- occurred, but not the fact that it occurred.

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  8. RBH,

    Let me address the "elitist" comment first. In no way was that meant to be an insult to anyone's training and research and work ethic. In fact, I believe we have moved beyond (for the most part) the elitist argument. Your knowledge on the subject is superb and, it has become apparent, way beyond mine.

    However, I think I was getting close to crossing the line of "pretending" to be an expert. Both the "elitist" and "pretender" position are easy (and wrong) to take. So allow me to retreat back to "sideline observer" status.

    That said, I do have a few clarifying questions:

    1. RBH said "The geological record is relatively coarse-grained. One cannot discern series of events that occur on a finer time scale than the time grain of the record allows."

    I understand the analogy given, but what is actually a "time grain" as it relates to P.E.?

    2. RBH said "Most speciation is allopatric (cladogenesis)" and "For a more detailed introduction see TalkOrigins (note that the "peripatric" speciation mentioned there is a variety of allopatric speciation)."

    Just so we're on the same page, please define, in layman's terms, allopatric and peripatric speciation. Also, is there observational evidence that this occured, and finally, is it different from TalkOrigins summary of speciation here?

    3. RBH said "The fossil evidence is part of the evidence for common descent, but I know of no evolutionary biologist or paleontologist who would claim that it "proves" universal common descent."

    Fair enough. Two questions: what is the rest of the evidence for UCD and could UCD be supported by this evidence without the fossil evidence (I'll elaborate on this later)?

    4. For the sake of space, points 4a thru c are with reference to RBH's final two paragraphs on the comment posted 16:50, 19 May 2008:

    a. You mention UCD is an "inference". IMO, inferences are generally made based on one's prior assumptions and experiences. Therefore, what difference is there between UCD and say design/archetypes?

    To clarify my position, I am NOT saying ID should overide UCD, but rather the two should be considered "inferences of equal leverage". (On a side note, I have posted on my problems with the design inference here and here, which also could be applied to the UCD inference.)

    To elaborate from point 3, if UCD and design/archetypes are on equal footing regarding interpreting the fossil evidence, then the fossil evidence becomes a weaker argument to support the UCD inference. (When I say "equal footing", I mean in the narrowly defined terms of inference and interpreting the fossil record).

    b. The debate on origins is off-topic, so I'll keep this short. IMO, Haldane's "rabbit" exists, but not in the specific rabbit form. The fossil record shows most of the phyla we see today (plus others we don't) appear suddenly during the Cambrian period where previously only bacteria and some sponges and jellyfish appeared. This is not what one would expect in a "bottom-up" system. That said, let me grant that neither NDES nor PE seeks to explain origins. Therefore, I won't use the "Cambrian Explosion" against them.

    However, the Cambrian Explosion does count against UCD/ToL since it would appear that the chronological arrangement of fossil would suggest multiple "trunks" exist rather than a single "trunk". The ToL UCD concept is a bottom-up concept. Thus, multiple trunks suggest either a different form of common descent (i.e. "front-loading" or Doolittle's MCD) or an incomplete UCD, far from the "high-degree of scientific certainty", IMO.

    Points 4a and b are off-topic, but do address some of the weaknesses of UCD, IMO.

    c. Let me clairfy again: I do NOT doubt that Gould NEVER questioned UCD. However, he did see a weakness with the NDES description/explanation of "sudden appearance and stasis", and thus developed PE to explain it better. If we can agree on this point, then let me propose that we move our discussion forward to whether the "high degree of scientific certainty" regarding UCD is more assumption/inference than evidence (see point 6).

    5. RBH said "In Gould's phrase (cited here, "... a scientific fact is not 'absolute certainty', but simply a theory that has been 'confirmed to such a degree that it would be perverse to withhold provisional consent'.""

    IMO, Gould's playing around with the meaning of words, which was one of the overarching themes of Johnson's "Darwin on Trial". To say evolution is both a theory and a fact only welcomes confusion rather than understanding.

    IMO, a better definition of "scientific fact" would be the objective observations and measurements made and accumulated over time. Following from this definition, UCD is thus a construct based on facts (both observed and measured) that is accepted by most biologists of all disciplines (including some IDers like Dr. Michael Behe), IMO. However, UCD is not a fact and could potentially be overturned, altered, or discarded in the future.

    6. It is quickly becoming clear to me that there are multiple research lines within biological evolution research (PE being only one). Unfortunately, this is not clearly communicated to the public at-large, and contributes to a lot of "misunderstanding" that goes on. Thus, for future comments, I propose we stick to debating the "high-degree of scientific certainty" of UCD rather than picking apart specific theories. (I am still interested in your answers of 1 and 2 for future debates).

    Let me stress again that these are merely observations from the sidelines. I appreciate you giving me a "sneak peak of the playbook".

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  9. RBH said:
    "I can find no independent source for that claim aside from Johnson's reported recollection of a remark at a conference, the recollection only reported by Johnson 10 years after the conference. And "Johnson's argument" is a little vague: What part of Johnson's argument did Raup actually support?"

    While independent evidence would be nice, it doesn't take away from the main point which is: Even though Dr. Raup disagreed with Dr Johnson's conlcusions, he did appear to give general support to Dr. Johnson's interpretation of the science. So unless Dr. Raup has personally disavowed this version of events, I am comfortable with Dr. Johnson's testimony.

    I realise this is off-topic, but it needed to be said.

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  10. I understand the [film frames per second] analogy given, but what is actually a "time grain" as it relates to P.E.

    Essentially, fossils tend to be found in fossil beds composed of successive bedding planes -- fossil bearing strata -- which can be laid down at intervals on the order of 100K or 200K years per plane or more, give or take, of course, depending on the particular conditions. In that neighborhood, though, the 100s of thousands of years. That's analogous to the 24 frames per second. So we see fossils of a species in a given bedding plane, maybe in the one above it, and then in the third bedding plane it's gone, replaced by fossils of another species that looks (morphologically) like it's related to the first species. Now, unless the bedding planes are temporally very fine-grained, say in the single-digit hundreds of years, and unless the particular place one happens to be digging up those fossils is where the isolated population made the transition from the first to the second species, it will look as though the first species just disappeared and the second species suddenly appeared. Eldredge and Gould argued that what really happened was that speciation took place in some isolated population occupying a fairly small area and the new species later overspread and replaced the old species. So the new species' appearance in the wider area looks sudden but that's an artifact of the combination of the coarse time grain of the bedding planes and the fairly rapid (a few thousand or tens of thousands of generations) speciation event. Eldredge and Gould reported data on occurrences where they found the transitional fossils of the isolated population undergoing speciation, where the local bedding planes were very fine-grained temporally.

    Just so we're on the same page, please define, in layman's terms, allopatric and peripatric speciation. Also, is there observational evidence that this occured, and finally, is it different from TalkOrigins summary of speciation here?

    Pretty good definitions here with a handy illustration. As I noted, Eldredge and Gould describe two fossils series illustrating peripatric speciation.

    The link you gave is to a list of brief sketches of speciation events, not to a summary of speciation. Some of those are peripatric, some allopatric, some (one at least) sympatric, and some it's hard to tell from the brief descriptions. Noe have apparently progressed far enough to illustrate PE. For a summary of the modes of speciation see the link I provided above.

    Fair enough. Two questions: what is the rest of the evidence for UCD and could UCD be supported by this evidence without the fossil evidence (I'll elaborate on this later)?

    In addition to the fossil record, there's a range of evidence mainly from comparative anatomy, biogeography (important in Darwin's original thinking), molecular biology and genetics, and recently from evolutionary developmental biology (evo-devo). Interestingly, the fossil evidence is today probably among the less important of those lines of evidence. If there were no fossils at all the evidence from molecular biology and comparative genetics alone would nevertheless make a powerful case for common descent.

    a. You mention UCD is an "inference". IMO, inferences are generally made based on one's prior assumptions and experiences. Therefore, what difference is there between UCD and say design/archetypes?

    Inferences in the sense that I'm using it here -- somewhat misleadingly, I suspect -- are (tentative) conclusions drawn from data that are then tested in independent data. That is, they are hypotheses formed to account for the data in hand that provide tests against new independent observations. At least that's how it went historically in the formulation of evolutionary theory by Darwin. Since Darwin the theory of common descent has been tested against independent data from a range of disciplines, as I noted above, and it has passed all those tests. That is, it predicted patterns that one would find, say, in comparative genetic analyses, and the observed patterns match the predicted patterns.

    As far as I know, "design/archetypes" makes no predictions about the patterns to be found in new observations. Can you provide any, as well as provide a summary of the "design/archetypes" hypothesis that generates those predictions of observations? What, for example, about "archetypes" predicts the consistent animal phylogenies derived from both morphological and molecular data?

    However, the Cambrian Explosion does count against UCD/ToL since it would appear that the chronological arrangement of fossil would suggest multiple "trunks" exist rather than a single "trunk".

    That ignores taphonomical considerations associated with the Precambrian, and wholly ignores the molecular data. Once again, it's the consilience of multiple independent lines of evidence that underpins common descent.

    Later we may get into the Russ Doolittle vs. Ford Doolittle stuff. The basic question there is whether the Last Universal Common Ancestor was some specific very early single-celled organism or was in effect a population of critters that was dominated by horizontal gene transfer so that a single lineage of descent can't be reconstructed from present data. Front-loading in any naive sense (and that's the only sense in which I've seen it -- a la Behe) immediately falls afoul of the inability to retain front-loaded 'information' in the absence of stabilizing selection. Genetically, the world is a 'use it or lose it' proposition. In the absence of selection to retain genetic info, it is degraded by mutations, so any front-loaded genetic info would be degraded by mutations well before it is time to unpack it.

    However, he [Gould] did see a weakness with the NDES description/explanation of "sudden appearance and stasis", and thus developed PE to explain it better.

    Subject to the qualification that Eldredge and Gould exaggerated the degree to which 'standard' theory treated the rate and nature of speciation, I can accept that.

    IMO, Gould's playing around with the meaning of words, which was one of the overarching themes of Johnson's "Darwin on Trial". To say evolution is both a theory and a fact only welcomes confusion rather than understanding.

    Blame the fact (!) that "evolution" (like, say, "force") has multiple meanings, and one has to keep track of context to know which meaning is intended when.

    IMO, a better definition of "scientific fact" would be the objective observations and measurements made and accumulated over time. That's generally called "data."

    Following from this definition, UCD is thus a construct based on facts (both observed and measured) that is accepted by most biologists of all disciplines (including some IDers like Dr. Michael Behe), IMO. However, UCD is not a fact and could potentially be overturned, altered, or discarded in the future.

    Common descent is an inference from data, a "fact" in Gould's sense, just as, say, the "fact" that the planets revolve around the sun is an inference from data. Both of those "facts" are corroborated by multiple lines of independent evidence. It is (remotely) possible that either or both could potentially be overturned, altered, or discarded sometime in the future, but that's the way life is: We don't have complete and absolute knowledge. All science is 'as best we know now.' Those two particular "facts" are ones in which we have very high degrees of confidence on account of the multiple lines of independent evidence (data) that have been gathered over the decades and centuries since they were proposed. The heliocentric model of the solar system no longer depends solely on Galileo's observations, and the theory of common descent no longer depends solely on Darwin's observations of the fairly gross properties of organisms.

    It is quickly becoming clear to me that there are multiple research lines within biological evolution research (PE being only one). Unfortunately, this is not clearly communicated to the public at-large, and contributes to a lot of "misunderstanding" that goes on. Thus, for future comments, I propose we stick to debating the "high-degree of scientific certainty" of UCD rather than picking apart specific theories.

    Then we will have to consider those multiple research lines, because once again, it is the convergence and consilience of multiple lines of independent evidence that provides the high degree of confidence in common descent.

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  11. While independent evidence would be nice, it doesn't take away from the main point which is: Even though Dr. Raup disagreed with Dr Johnson's conlcusions, he did appear to give general support to Dr. Johnson's interpretation of the science. So unless Dr. Raup has personally disavowed this version of events, I am comfortable with Dr. Johnson's testimony.

    And I'm not comfortable accepting a self-serving and vague claim made 10 years after the fact in the absence of an independent corroborating source, particularly when "the science" in what I have read of Johnson's stuff available on the web is consistently flawed.

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  12. While you're reading Gould, keep in mind this sentence from the Introduction to his Punctuated Equilibrium (p. 12-13):

    When I was myself how all these disparate thoughts and items gfell together into one long argument, I can only cite--and I don't know how else to put this--my love of Darwin and the power of his genius. Only he could have presented such a fecund framework of a fully consistent theory, so radical in form, so complete in logic, and so expansive in implication. No other early evolutionary thinker ever developed such a rich and comprehensive starting point. From this inception, I had only to explicate the full original version, tease out the central elements and commitments, and discuss the subsequent history of debate and revision for these essential features, culminating in a consisten reformulation of the full corpus in a helpful way that leaves Darwin's foundation intact while constructing a larger edifice of interestingly different form thereupon.

    Gould is amnything but modest there, but he is clearly building on Darwin's foundation, not abandoning it.

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  13. Sorry for not commenting for a while. Between family, work and contractors tearing up my yard, I don't have much time to investigate and read your links.

    That said, I ran across 29+ Evidences for UCD on the Talk.Origins FAQ site. I have just skimmed through it so far, but I think it makes for a good "project" of mine. Details to come in a future post.

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