“Natural Selection’s [too limited] Reach”

I hadn’t realised that the Biologic Instute had a diary/blog.

February’s article is by Ann Gauger, although it consists largely of quotations from Douglas Axe, and is called Natural Selection’s Reach.

What continues to astonish me about ID proponents is just how ignorant they are of evolutionary theory.  Ann Gauger starts by setting out to address a reader’s query:

A reader wrote us recently to ask why natural selection can’t extract enough information from the fitness landscape to explain complex features.

Well, obviously I dispute the premise of the question, but assuming that the reader and Gauger share the view that natural selection’s “reach” is too limited to “explain complex features”, let’s see how Gauger explains her stance.  She starts by rightly saying that:

It all depends on what you think the fitness landscape looks like

and then lets Axe go on to explain further.  Unfortunately, Axe appears to think it looks like this:

with complex features situated on the high distant peaks, and natural selection only able to move a step at a time, and only upwards.

If this were actually a realistic model of the fitness landscape, of course, natural selection would be doomed.  But what Axe has presented is, at most, a two-dimensional map.  This would be what the landscape would look like if organisms could only vary along two dimensions, say, size and colour. When the population had optimised its size and colour, it would be stuck on the top of one of those little mud ridges, with nowhere to go but down.

Does Axe really think that there are only two dimensions to the fitness landscape of biological organisms?  Or has it simply not occurred to him to extend his metaphor to the harder-to-envisage realm of multidimensional fitness space?

The “limited reach” of natural selection is not the problem – yes, populations generally can only “move” over the fitness landscape step by tiny step. But that doesn’t matter if the landscape consists of many ramps along many dimensions, and the more dimensions there are, the more ramped routes there will be, thus vastly increasing the accessibility of those distant peaks.

Gauger concludes her piece:

What is the mutational reach of natural selection in general? It’s very short. For bacteria, our work suggests the reach is only a few mutations at a time.  That’s not enough to get a genuinely new function for a protein, let alone a new pathway made up of a handful of proteins, or a metabolism made up of hundreds of proteins. For larger multicellular organisms like us, with slower generation times and smaller populations, the problem gets worse. Much worse.

 

So unless someone paved a highway to Mt. Whitney that went uphill every step of the way, Darwin’s engine would never get out of Death Valley. But a paved highway isn’t evolution, it’s design.

Nope. A route that goes uphill (or at least not drastically downhill – drift helps too) every step of the way is highly probable in a multidimensional fitness landscape, and a multidimensional fitness landscape doesn’t have to be designed.  You just need an environment in which there are lots of resources that are exploitable by the kinds of variation possible to biological organisms. And given that we know (and both Axe and Gauger must know, being biologists) that similar phenotypes have similar genotypes, the landscape is not only full of climbing ramps, but is also “paved” – smoothed by the similarities between the phenotypic consequence of similar genotypes.

Honestly, it’s not that I’m “skeptical” of ID – I have just yet to read a pro-ID article, even by the academics in the field, that doesn’t make rookie errors about evolutionary science.  Oh, except for Todd Wood, and he relies on faith, not science, for his belief.

94 Replies to ““Natural Selection’s [too limited] Reach””

  1. Mung Mung
    Ignored
    says:

    I am willing to learn from anyone, even morons.

  2. Mung Mung
    Ignored
    says:

    Elizabeth:

    “Do you think that Dembski says something materially different or new in that (unpublished) paper than he says in No Free Lunch? If so, what is the key new point that Joe has left unaddressed?”

    I can’t read Joe’s mind. Ask him. But first, if we we’re true skeptics, we’d need evidence that he’s even familiar with the paper you claimed contains “rookie mistakes” about “evolutionary science.” So far, that evidence is suspiciously absent. But that does not seem to bother the alleged “skeptics” here at “The Skeptical Zone” in the least. Not Skeptics.

    Your claim, Elizabeth, in case it’s slipped your mind, was that there is not a single article that you have read by any ID academic which does not make “rookie mistakes” about “evolutionary science.”

    Your single allowed exception to this claim is Todd Wood, who is not even and ID a academic.

    I am still waiting for you to point out the “rookie mistakes” about “evolutionary science” that Dembski made in his paper on Specification (a paper that we all know you’ve read).

    Can’t do it? Why not just admit you were employing hyperbole and that you didn’t expect your comments to be taken literally? After all, we’re in “The Skeptical Zone.”

    Why am I the only Skeptic here?

  3. Mung Mung
    Ignored
    says:

    Elizabeth,

    http://www.amazon.com/dp/193659904X

    So now you know.

  4. llanitedave llanitedave
    Ignored
    says:

    Lizzie: And then there’s the fact that the evolving population is itself part of the changing landscape – which can become an arms race.

    This factoid is one I find too often neglected. Populations are not merely navigating a fitness landscape, the landscape itself is changing around and under them. Without any movement at all on the part of the genetic group, the landscape it occupies can change from a peak to a valley, from valley to a slope, from a slope to a ridge, from a ridge to a peak, or any other conceptual form you like.

    And this is one other way of getting around. Ramps can appear and disappear, a cliff wall blocking the way to Mt. Improbable can without any action on the part of the population become a broad ramp.

    Evolving populations don’t just navigate the fitness landscape, they are carried by it.

  5. Lizzie
    Ignored
    says:

    Mung:
    Elizabeth:

    “Do you think that Dembski says something materially different or new in that (unpublished) paper than he says in No Free Lunch? If so, what is the key new point that Joe has left unaddressed?”

    I can’t read Joe’s mind. Ask him.

    It’s not Joe’s mind I’m asking about, but yours. I repeat: what is the key new point, made in the Specification paper, that you think Joe has left unaddressed?

    But first, if we we’re true skeptics, we’d need evidence that he’s even familiar with the paper you claimed contains “rookie mistakes” about “evolutionary science.” So far, that evidence is suspiciously absent. But that does not seem to bother the alleged “skeptics” here at “The Skeptical Zone” in the least. Not Skeptics.

    Joe, above:

    Joe Felsenstein: (Not an April Fools posting): I have read the Dembski article that Mung references. Mung says that it is “of immediate relevance”. It isn’t relevant to the issue I raised — namely whether there is any justification for using the presence of CSI as indicating Design:

    * Nowhere in the article does Dembski present any defense of his Law of Conservation of Complex Specified Information.

    * Does that mean that he no longer uses the LCCSI as his method of ruling out the role of natural selection in putting specified information into the genome? No, because in Addendum I he cites his previous books, including No Free Lunch, and makes clear that

    The changes in my account of these concepts here should be viewed as a simplification, clarification, extension, and refinement of my previous work, not as a radical departure from it.

    Mung:

    Your claim, Elizabeth, in case it’s slipped your mind, was that there is not a single article that you have read by any ID academic which does not make “rookie mistakes” about “evolutionary science.”

    Your single allowed exception to this claim is

    Todd Wood, who is not even and ID a academic.

    Me,above:

    Lizzie: You are probably correct. He is an academic, and his research project is to discover how an Intelligent Designer (the Abrahamic God) made the world, not to prove that an Intelligent Designer did so. So, depending on how you define “ID theory” he may be beyond the pale. Shame. He’s a good man, is Todd.

    Mung:

    I am still waiting for you to point out the “rookie mistakes” about “evolutionary science” that Dembski made in his paper on Specification (a paper that we all know you’ve read).

    Me, above:

    Lizzie: Dembski’s mistake about evolutionary theory in that paper is to indicate that he can subsume “Darwinian and other material mechanisms” into a “chance hypothesis” and treat it as a null.

    Mung:

    Can’t do it? Why not just admit you were employing hyperbole and that you didn’t expect your comments to be taken literally? After all, we’re in “The Skeptical Zone.”

    Why am I the only Skeptic here?

    Me, above:

    Lizzie: But I will modify my claim and say: I have yet to read an ID article about evolutionary theory that does not make rookie mistakes about evolutionary theory.

    Mung, do you even bother to read the responses to your posts?

  6. Lizzie
    Ignored
    says:

    Also, Mung, I notice you say this, at UD:

    Elizabeth admits her ignorance, but claims ignorance is the best place to begin for a true “skeptic.”

    Not only do you apparently not read my posts, but you make shit up, and attribute it to me.

    Please do not do this.

  7. Lizzie
    Ignored
    says:

    Mung:
    Elizabeth,

    http://www.amazon.com/dp/193659904X

    So now you know.

    Thanks. Is this comment by one reviewer true?

    In the last chapter, Ann Gauger makes an argument for a literal Adam and Eve.

    If so, do you find her argument persuasive?

  8. Lizzie
    Ignored
    says:

    And from a favorable review:

    Very well written and gets to the point. In a nutshell the authors present an interesting issue. If at most a cell can go thru 2 mutations at a time, and for a cell to survive the mutations need to be non harmful. How can the cell of a chimp become the cell of a human when the number of mutations needed numbers in the millions?

    I assume the reviewer has misunderstood the book’s argument here. Am I right?

  9. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    Mung:

    “Do you think that Dembski says something materially different or new in that (unpublished) paper than he says in No Free Lunch? If so, what is the key new point that Joe has left unaddressed?”

    I can’t read Joe’s mind. Ask him. But first, if we we’re true skeptics, we’d need evidence that he’s even familiar with the paper you claimed contains “rookie mistakes” about “evolutionary science.” So far, that evidence is suspiciously absent. But that does not seem to bother the alleged “skeptics” here at “The Skeptical Zone” in the least. Not Skeptics.

    I have read the paper and think I understand it. Most of its arguments are in earlier papers of Dembski (ones that I cited in my 2007 article). Mung was asked to point to any defense of Dembski’s Law of Conservation of Complex Specified Information. It was Dembski’s basis for his Design Inference, but I showed that the Law is wrong, that natural selection can put CSI into the genome, and that the LCCSI does not prove that it can’t.

    Mung’s only defense of the Design Inference argument was to point to this particular paper. Now Mung refuses to say what in that paper was new or relevant. Instead Mung diverts the question to me, or to Lizzie’s statements about “rookie mistakes” (which I leave to her).

    Mung, the Design Inference has fallen apart. Yet the statement that observing CSI proves Design still walks the earth. It is a zombie argument.

    In that paper of Dembski’s, there is mostly a repetition of previous arguments, and Dembski says so. Is there any new argument for the validity of the CSI criterion? Let me help find it, since Mung can’t seem to:

    In the Specification paper, Dembski does not bring in any new reason to believe that the LCCSI is correct. He does, however, change his CSI calculation in that paper. He incorporates into the measure “Darwinian and other material mechanisms”.

    In other words, to compute CSI, you have to declare it exists only when “Darwinian and other material mechanisms” cannot explain the specification.

    So there we have it. The CSI argument works this way:

    * If the presence of the specified information could be explained by “Darwinian and other material mechanisms”, we don’t call it CSI, because then the amount of specified information is not improbable, as it could have been put there by natural selection.

    * If it could not be explained by Darwinian and other material mechanisms, we conclude (ta-da!) that Darwinian and other material mechanisms can’t explain it.

    Perhaps Mung was arguing that we are supposed to be impressed by that.

    It also is not the way most ID types calculate CSI: they leave out the part about natural selection being able to explain it. They don’t use Dembski’s altered calculation.

    Without that part, they are relying on the LCCSI. But they (Mung included) are unable to defend the supposed Law. The zombie argument still walks the earth.

  10. Allan Miller
    Ignored
    says:

    I think the “2 mutations” might refer to diploidy (?), and may misrepresent the actual (similarly incorrect) ‘not-enough-time’ argument, detailed in Paul McBride’s extensive critical reviews linked here: http://pandasthumb.org/archives/2012/07/paul-mcbrides-r.html

    Mutation loads from 40-160 per viable individual can be inferred from various techniques. Add in the significant contribution of multi-base insertions and deletions, and there does not appear to be a mutation-based reason to doubt that the overall amount of sequence difference is due to known, inevitable processes causing divergence between commonly descended lineages.

    But if you’re looking for ‘rookie mistakes’, look no further: :http://www.youtube.com/watch?feature=player_embedded&v=7tuZIxDxkxI#! Population genetics = ‘tree-building’ (phylogeny)?

  11. Lizzie
    Ignored
    says:

    Joe Felsenstein:
    Mung:

    I have read the paper and think I understand it. Most of its arguments are in earlier papers of Dembski (ones that I cited in my 2007 article). Mung was asked to point to any defense of Dembski’s Law of Conservation of Complex Specified Information. It was Dembski’s basis for his Design Inference, but I showed that the Law is wrong, that natural selection can put CSI into the genome, and that the LCCSI does not prove that it can’t.

    Mung’s only defense of the Design Inference argument was to point to this particular paper. Now Mung refuses to say what in that paper was new or relevant.Instead Mung diverts the question to me, or to Lizzie’s statements about “rookie mistakes” (which I leave to her).

    Mung, the Design Inference has fallen apart.Yet the statement that observing CSI proves Design still walks the earth. It is a zombie argument.

    In that paper of Dembski’s, there is mostly a repetition of previous arguments, and Dembski says so.Is there any new argument for the validity of the CSI criterion? Let me help find it, since Mung can’t seem to:

    In the Specification paper, Dembski does not bring in any new reason to believe that the LCCSI is correct. He does, however, change his CSI calculation in that paper. He incorporates into the measure “Darwinian and other material mechanisms”.

    In other words, to compute CSI, you have to declare it exists only when “Darwinian and other material mechanisms” cannot explain the specification.

    So there we have it. The CSI argument works this way:

    * If the presence of the specified information could be explained by “Darwinian and other material mechanisms”, we don’t call it CSI, because then the amount of specified information is not improbable, as it could have been put there by natural selection.

    * If it could not be explained by Darwinian and other material mechanisms, we conclude (ta-da!) that Darwinian and other material mechanisms can’t explain it.

    Perhaps Mung was arguing that we are supposed to be impressed by that.

    It also is not the way most ID types calculate CSI: they leave out the part about natural selection being able to explain it. They don’t use Dembski’s altered calculation.

    Without that part, they are relying on the LCCSI. But they (Mung included) are unable to defend the supposed Law. The zombie argument still walks the earth.

    Ah. I had interpreted the paper to be saying that Darwinian “material mechanisms” were part of the “chance” null, and which he appears to equate with a blind search (as in NFL). Which would be a rookie mistake. But if he is in fact allowing for the possibliity that Darwinian mechanisms can create what looks like CSI, but wouldn’t be, solely because it was created by a Darwinian mechanism…

    Could he really be saying that? I mean, he has got two PhDs, in maths and philosophy! He must know what a circular argument is!

    So perhaps all he is saying is that if we did include Darwinian material mechanisms in the null distribution, biological patterns would probably (!) still be in the extreme tail?

    Which wouldn’t so much a “rookie mistake” as completely unsupported assertion.

    It’s a terrible paper.

  12. damitall2
    Ignored
    says:

    Mung,

    I’ve enKindled that book this morning (depriving myself of the wherewithal for 1 1/2 pints of Woodfordes’ Wherry Bitter, which is very well kept in my local 🙁 ).

    I’ve read a few pages,and will finish it when I get back from York this evening

    On the basis of what I’ve read, I will guarantee that none of those authors would dare defend it to a knowledgeable audience, even in such an amiably polite forum as this one.

  13. Lizzie
    Ignored
    says:

    Mung: I am willing to learn from anyone, even morons.

    Good. But can I suggest that the learning will go better if you make the working assumption that the person you are willing to learn from is not a moron?

  14. Lizzie
    Ignored
    says:

    damitall2:
    Mung,

    I’ve enKindled that book this morning (depriving myself of the wherewithal for 1 1/2pints of Woodfordes’ Wherry Bitter, which is very well kept in my local :( ).

    I’ve read a few pages,and will finish it when I get back from York this evening

    On the basis of what I’ve read, I will guarantee that none of those authors would dare defend it to a knowledgeable audience, even in such an amiably polite forum as this one.

    Me too (Kindle is just too easy to do!)

    Just read the Gauger article on Adam and Eve. Will comment later, and look forward to reading your response.

  15. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    Lizzie: Ah. I had interpreted the paper to be saying that Darwinian “material mechanisms” were part of the “chance” null, and which he appears to equate with a blind search (as in NFL).Which would be a rookie mistake.But if he is in fact allowing for the possibliity that Darwinian mechanisms can create what looks like CSI, but wouldn’t be, solely because it was created by a Darwinian mechanism…

    Could he really be saying that?I mean, he has got two PhDs, in maths and philosophy!He must know what a circular argument is!

    So perhaps all he is saying is that if we did include Darwinian material mechanisms in the null distribution, biological patterns would probably (!) still be in the extreme tail?

    Which wouldn’t so much a “rookie mistake” as completely unsupported assertion.

    It’s a terrible paper.

    Well, it does explain specification and the Complex part. But then it throws in this new wrinkle. And makes the whole CSI argument circular.

    Some CSI-like arguments used over at UD are of Dembski’s original type (CSI, FSI), others assume you have to rule out “Darwinian” mechanisms in order to declare the presence of the signal (I think dFCSI is one of these).

    It’s very confusing. The zombie method keeps getting up and walking again, unsupported by any actual logical argument.

  16. damitall2
    Ignored
    says:

    Joe Felsenstein: It’s very confusing. The zombie method keeps getting up and walking again, unsupported by any actual logical argument.

    …or any real-life calculations.

  17. Lizzie
    Ignored
    says:

    Joe Felsenstein: Well, it does explain specification and the Complex part.But then it throws in this new wrinkle. And makes the whole CSI argument circular.

    Some CSI-like arguments used over at UD are of Dembski’s original type (CSI, FSI), others assume you have to rule out “Darwinian” mechanisms in order to declare the presence of the signal (I think dFCSI is one of these).

    It’s very confusing. The zombie method keeps getting up and walking again, unsupported by any actual logical argument.

    Yes, it’s a bit irritating how people like us are constantly being accused of getting ID theory wrong, or misrepresenting it, but if you take any one exposition of it, and show that it doesn’t work, then you are accused of not reading some other exposition of it, even when some of those expositions are mutually contradictory.

    I mean, is the argument supposed to be that Darwinian mechanisms can’t create CSI, or that chemistry can’t create Darwinian mechanisms, or that the universe can’t create chemistry?

    Or all three? If so, 1 is wrong, 2 is probably wrong, and 3 may be metaphysics.

  18. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    Lizzie:
    I mean, is the argument supposed to be that Darwinian mechanisms can’t create CSI, or that chemistry can’t create Darwinian mechanisms, or that the universe can’t create chemistry?

    Or all three?If so, 1 is wrong, 2 is probably wrong, and 3 may be metaphysics.

    Well, when you argue against their dismissals of evolutionary mechanisms, they do like to whiz off to the Origin Of Life, and even to the origin of the universe. Gotta keep those goalposts moving.

  19. Lizzie
    Ignored
    says:

    Joe Felsenstein: Well, when you argue against their dismissals of evolutionary mechanisms, they do like to whiz off to the Origin Of Life, and even to the origin of the universe. Gotta keep those goalposts moving.

    It would seem so. Come on, UD regulars, come and show us why we are wrong here 🙂

  20. damitall2
    Ignored
    says:

    Lizzie,

    Well, I’ve rapid-.read it. Very, um , Christian, and there I was thinking that ID was agnostic on the question of the Designer’s identity.

    From the point of view of science, then the most charitable thing I can say is that Gauger and the rest need to get up to date and address later evidence.

    For instance, in her defence of the Adam’n’Eve origin of humans Gauger addresses only a single paper of Ayala’s from the 1990s, that deals with ancient polymorphisms in a short (270 bp) DNA sequence in an HLA gene in her attempt to bring down mainstream population genetics. However there is subsequent work including some using whole genomes from different ethnic groups which pretty well rules out all humans originating from a single breeding pair of H sapiens.

    This ignorance of the range of scientific publications dealing with the subjects covered in this regrettable book is a constant feature, particularly when it comes to work published in this decade.
    Whether that ignorance comes from willful blindness or from shoddy literature search may never be known for sure, but it is difficult to take Gauger and Axe seriously as cutting-edge scientists if they can’t be arsed to search out and consider recent work relevant to their opinions. (No-one takes Luskin seriously anyway)
    If Mung is interested in pursuing the arguments against this rather pathetic bookette, he can do no better than to google Paul McBride’s comprehensive takedown

  21. Lizzie
    Ignored
    says:

    And to save him googling, here it is.

    Yes, I read it over lunch. So at best, Adam and Eve were not anatomically human. It reads like an attempt to show that Adam and Even were not impossible, rather than a conclusion that they were probable.

    Not a very successful attempt. And she seems to have a very strange notion of what genetic drift is.

  22. Mike Elzinga
    Ignored
    says:

    Eric Anderson captures the ID/creationist shtick pretty well:

    The perception of evolution’s explanatory power is inversely proportional to the specificity of the discussion.

    That follows quite closely the historical tactics of ID/creationist “argumentation.”

    When “What good is a half a wing?” is debunked, the next “challenge” becomes, “If you can’t specify every trajectory from a primordial soup to the final position of every atom in a complex molecule such as a protein, then you can’t explain evolution.”

  23. Allan Miller
    Ignored
    says:

    And then: “this time, actually do it, while I’m watching”.

  24. Mung Mung
    Ignored
    says:

    Elizabeth:

    “Come on, UD regulars, come and show us why we are wrong here.”

    It’s not that you’re wrong, it’s that you live in a fantasy world in which you can never be wrong.

    I finally signed up here at TSZ to show people where they are wrong, but they didn’t want to talk about that.

    When you personally showed back up I posted to how you were wrong. But you, last I checked, can’t admit it.

    Not Skeptics.

  25. Mung Mung
    Ignored
    says:

    damitall2:

    “If Mung is interested in pursuing the arguments against this rather pathetic bookette, he can do no better than to google Paul McBride’s comprehensive takedown”

    I fail to see the relevance.

  26. Mung Mung
    Ignored
    says:

    Elizabeth:

    “Thanks. Is this comment by one reviewer true?
    In the last chapter, Ann Gauger makes an argument for a literal Adam and Eve.
    If so, do you find her argument persuasive?”

    I don’t recall whether an argument was made for a literal Adam and Eve existing on the earth approx 6000 years ago. If such an argument was made I probably did not find it persuasive.

    If you’re really interested in pursuing the topic I still have the book here somewhere, but I fail to see how the chapter is relevant unless you’re claiming it makes “rookie mistakes” about “evolutionary science (whatever that is).”

    FYI:
    I do not believe the earth is only 6k to 10k years old.
    I commonly point out the problems with a YEC view on UD.
    Do try to keep up. 🙂

  27. Mung Mung
    Ignored
    says:

    Joe Felsenstein:

    “Mung’s only defense of the Design Inference argument was to point to this particular paper. Now Mung refuses to say what in that paper was new or relevant. Instead Mung diverts the question to me, or to Lizzie’s statements about “rookie mistakes” (which I leave to her).”

    I hope that Joe F. can substantiate his implication that I was attempting to defend “the design inference argument.” I wasn’t. He can’t.

    “Instead Mung diverts the question to me, or to Lizzie’s statements about “rookie mistakes” (which I leave to her).”

    Some poster in this thread claimed that you, Joe F., had demonstrated the “rookie mistakes” concerning “evolutionary science” made by Dembski.

    Why didn’t you correct them?

    “Now Mung refuses to say what in that paper was new or relevant. Instead Mung diverts the question to me, or to Lizzie’s statements about “rookie mistakes” (which I leave to her).”

    Don’t leave it up to Elizabeth, she’s already backed off her initial claim.

    Now she claims that what she meant was not that Dembski made “rookie mistakes” about “evolutionary science” (whatever that is), but that Dembski made “rookies mistakes” about “evolutionary theory” (whatever that is).

  28. Mung Mung
    Ignored
    says:

    Elizabeth:

    “But can I suggest that the learning will go better if you make the working assumption that the person you are willing to learn from is not a moron?”

    Is that what it means to be a “skeptic”?

  29. Mung Mung
    Ignored
    says:

    Since everyone seems to want to ignore the actual facts: Not a skeptic.

    Here’s the claim from the OP:

    Honestly, it’s not that I’m “skeptical” of ID – I have just yet to read a pro-ID article, even by the academics in the field, that doesn’t make rookie errors about evolutionary science. Oh, except for Todd Wood, and he relies on faith, not science, for his belief.

    Hogwash

  30. Allan Miller
    Ignored
    says:

    So you picked at the claim that Todd Wood was a relevant example ***, then posted a link to a book by Luskin, Axe and Gauger that is shot full of basic misunderstandings (see Paul McBride’s reviews, among others). You have so far only supported the case against ID argumenters and their basic comprehension of evolutionary biology.

    ***[eta: the irony being that YEC Todd Wood puts most ID-ers to shame on the biology]

  31. Lizzie
    Ignored
    says:

    Oh boy, lots of things to respond to here, but also a response from Eric at UD which I think is worth addressing (although why he can’t come over here and say it, beats me, seeing I can’t go there – he could even cross-post if he liked).

    Anyhoo:

    OK, I finally made my way over to TSZ to see what these “rookie mistakes” were that Lizzie is making much of. I have not looked at all the posts, but I did read one about Axe and Gauger and here is the “mistake” they make:

    Without getting all technical, Axe and Gauger apparently feel that the fitness landscape is punctuated by peaks and valleys, with the result that organisms are likely to get stuck at a fitness peak. This is the egregious error Lizzie sees. She acknowledges that natural selection would be “doomed” under such a scenario.

    Now, this is not a new concept with Axe and Gauger. Indeed, many people have argued that the fitness landscape is as described above.

    Lizzie argues, however, that this is not so. The landscape, according to her is like this:

    And given that we know (and both Axe and Gauger must know, being biologists) that similar phenotypes have similar genotypes, the landscape is not only full of climbing ramps, but is also “paved” – smoothed by the similarities between the phenotypic consequence of similar genotypes.
    (emphasis added)

    Now this is certainly a thoroughly Darwinian view of things harking all the way back to Sir. Charles. Darwin felt that there was an unbroken continuum — slight successive changes — such that the fitness landscape would be essentially flat, like colors merging almost imperceptibly on a color chart.

    Unfortunately for Darwin, and unfortunately for Lizzie, that is not at all what we see in nature. We see breaks and leaps and uniqueness and discontinuity. We in fact see organisms occupying disparate points on the map.

    It is possible — logically possible, that is — that these points we currently see are indeed joined together by smoothed, paved, easy-to-access pathways. But that is an assumption, not an empirical fact, and those frequent oases in the organism’s long and directionless path to that distant and dusty peak are more a mirage imagined by the desperate traveler than an actual point of refuge.

    No, Eric, it is an empirical fact. And I did not merely assert it, I cited the evidence. From my OP:

    A route that goes uphill (or at least not drastically downhill – drift helps too) every step of the way is highly probable in a multidimensional fitness landscape, and a multidimensional fitness landscape doesn’t have to be designed. You just need an environment in which there are lots of resources that are exploitable by the kinds of variation possible to biological organisms. And given that we know (and both Axe and Gauger must know, being biologists) that similar phenotypes have similar genotypes, the landscape is not only full of climbing ramps, but is also “paved” – smoothed by the similarities between the phenotypic consequence of similar genotypes.

    Let me try to make that even clearer:

    1) A high dimensioned fitness landscape will have many more horizontal or ramped routes around valleys than a low dimensioned one, and you do not have to look very hard to find vast numbers of dimensions along which organisms can vary to see that the natural fitness landscape is extremely high-dimensioned, and therefore nothing like the rutted mud of Gauger’s photographic metaphor. Thus we have empirical observations that tell us that the fitness landscape is high-dimensioned, and therefore short of impassable ravines.

    2) The tighter the link between genotype and phenotype i.e. the more that organisms with similar genotypes resemble each other phenotypically, the smoother the fitness landscape must be, by definition.

    And so, contra Gauger , we know from empirical data, that the natural fitness landscape is both high-dimensioned and smooth. This is no assumption, it is empirical fact. Fact that Axe ignores.

    Furthermore, there are good reasons to think that many points on the map — from individual biochemical systems to whole organisms — are in fact steep peaks that cannot be so easily traversed.

    Well, no, see above.

    Thus, at most what Lizzie could have objectively said would have been that some people disagree with the idea of a discontinuous landscape and argue for a more level landscape. Fine. But that certainly doesn’t mean that Axe and Gauger have committed some rookie mistake in their description of the landscape.

    Well, yes, it does, because they have assumed a low-dimensioned and rugged landscape, where we know, empirically that it is high-dimensioned and smooth.

    Further, Lizzie’s assertion that the landscape is smooth, and therefore easily traversable by natural selection, is nothing more than that — an assertion. It certainly has not been demonstrated.

    I just demonstrated it for a second time. If you disagree, explain where my reasoning is wrong, do not ignore the fact that I have presented my reasoning, not merely asserted my conclusion.

    Moreover, not only is a smooth fitness landscape not an empirical fact, it is really just a restatement of the theory: namely, that slight, successive changes can lead to just about anything.

    Well, no. See above.

    It thus commits the error of assuming the very thing that needs to be demonstrated. And that is something we (rookies and all) quite accurately understand about evolutionary theory.

    And, therefore, no. Darwin observed, emprically, that heritable phenotypic differences between generations was slight, but did not know why, i.e. knew that the fitness landscape was smooth. He also observed, empirically, that it was high-dimensioned (he cites the very many ways in which phenotypes can vary). He did not use those terms, as the mathematical description of a “fitness landscape” is more modern, but it is all there, in Origins. It was from these empirical observations that he, correctly, deduced that the fitness landscape was smooth and high-dimensioned. He did not assume that it was because it must be if evolution is to happen. He concluded that evolution must happen, because the fitness landscape is smooth (similar phenotypes adjacent to each other in search space) and high-dimensioned (with many routes around valleys).

    And if he did not say it quite like that, it’s how I’m saying it now, and I challenge Eric to explain why a system in which similar genotypes have similar phenotypes, and in which phenotypic variation can be along a vast number of dimensions, is not both smooth and full of upward ramps around valleys.

    And if he responds at UD (where obviously I cannot post, and visit more rarely, not surprisingly) can I repeat my invitation to cross-post his response here.

  32. Lizzie
    Ignored
    says:

    Mung:
    Elizabeth:

    “Come on, UD regulars, come and show us why we are wrong here.”

    It’s not that you’re wrong, it’s that you live in a fantasy world in which you can never be wrong.

    Let me supply context: I posted:

    I mean, is the argument supposed to be that Darwinian mechanisms can’t create CSI, or that chemistry can’t create Darwinian mechanisms, or that the universe can’t create chemistry?

    Can you address this?

    I finally signed up here at TSZ to show people where they are wrong, but they didn’t want to talk about that.

    Of course we do,, but let’s actually converse, which means actually responding on substance to each others’ posts.

    When you personally showed back up I posted to how you were wrong. But you, last I checked, can’t admit it.

    Can’t admit what? Perhaps you should check again. I freely acknowledged that I should have added the rider that I was only talking about ID arguments that actually deal with evolution. Clearly you can’t make a rookie error about something you do not actually touch on.

    And I told you what I thought the rookie error was in Specification. Have you responded? I will go check.

  33. Lizzie
    Ignored
    says:

    Mung: April 7

    Well, it’s a chapter by chapter critique of the book you recommended we read (and which I believe we have both now done. Would you like to post a thread on it? McBride’s critique would seem to be a good starting point, and you can provide counter-rebuttals to his points.

  34. Lizzie
    Ignored
    says:

    Mung:
    Elizabeth:

    “Thanks. Is this comment by one reviewer true?
    In the last chapter, Ann Gauger makes an argument for a literal Adam and Eve.
    If so, do you find her argument persuasive?”

    I don’t recall whether an argument was made for a literal Adam and Eve existing on the earth approx 6000 years ago. If such an argument was made I probably did not find it persuasive.

    No, she doesn’t. She makes an argument that it is possible that the human race is descended from two individuals who lived around 4 million years ago, and may have been intelligently designed. Unfortunately, this conflicts with Luskin’s case, made earlier in the book, that no humans existed 4 million years ago, so if Gauger’s two individuals were Adam and Eve, Adam and Eve were Australopethicines, and, according to Luskin, not human. But her argument isn’t that the population must have been reduced to two at that point, but that a bottleneck of two is consistent with the data, as long as we go back 4 million years. However, there are flaws even in that argument, as McBride points out.

    If you’re really interested in pursuing the topic I still have the book here somewhere, but I fail to see how the chapter is relevant unless you’re claiming it makes “rookie mistakes” about “evolutionary science (whatever that is).”

    Evolutionary science is the scientific domain that deals with the evolution of life forms over time. Gauger’s glaring error in that chapter (which I had not seen before, and which therefore was a potential black swan to my claim) is to define genetic drift as: “the stochastic loss of genetic information due to failure to reproduce”. This is not the definition of genetic drift, and is highly misleading, and she then duly misleads by saying that it “tends to reduce the power of natural selection to drive change, especially in populations of a million or less”. No, it does not. In fact, genetic drift, which is usually defined as the change in allele frequency due to random sampling of the gene pool in each generation, can be an important enabler of natural selection (non-random sampling, where the frequencies certain alleles increase or reduce in frequency due to phenotypic effects that affect an organisms chances of successful breeding), in that alleles that are near neutral when they first appear can, by drift, propagate through the gene pool, increasing the amount of allelic variance, and therefore the capacity for adaptation. It is of course true that in small populations, genetic drift can result in a net loss of allelic variance, but that, of course, is an argument against very tight bottlenecks in our ancestry.

    FYI:
    I do not believe the earth is only 6k to 10k years old.
    I commonly point out the problems with a YEC view on UD.
    Do try to keep up. :)

    I was aware of this, Mung, but thanks for the reminder.

  35. Lizzie
    Ignored
    says:

    Mung: April 7

    Mung:
    Since everyone seems to want to ignore the actual facts: Not a skeptic.

    Here’s the claim from the OP:

    Honestly, it’s not that I’m “skeptical” of ID – I have just yet to read a pro-ID article, even by the academics in the field, that doesn’t make rookie errors about evolutionary science.Oh, except for Todd Wood, and he relies on faith, not science, for his belief.

    Hogwash

    As I’ve said, several times, now, I have amended my claim to cover only articles that actually address evolutionary theory.

    I may yet come across a pro-ID article that does not make rookie errors in evolutionary theory, but Gauger’s chapter in the book you recommended is not one of them. Nor is Dembski’s “Specification” paper, for the reason I gave. If you disagree that Dembski’s was an error, please say why, but in my view, his is a rookie error. In fact, it’s one he has de facto conceded, by accepting that evolutionary processes can in fact produce patterns that would be unlikely to be found by blind search, but that evolutionary processes themselves are highly improbable to be found by blind search.

    But feel free to return the ball.

  36. Lizzie
    Ignored
    says:

    Mung:
    Elizabeth:

    “But can I suggest that the learning will go better if you make the working assumption that the person you are willing to learn from is not a moron?”

    Is that what it means to be a “skeptic”?

    Yes, in a way, it is – It’s being open to the idea that the person you are talking to may have a point you have not considered, rather than taking the default view that a dissenting view must be incorrect.

    A skeptic, in my view, is a person who neither accepts nor rejects ideas without serious scrutiny. That entails, inter alia, the assumption that what appears to be a flaw in the other person’s argument might in fact be a flaw in your own understanding, and vice versa.

    For instance, Mung, although I find you rude and evasive, and that you misrepresent my views to the point of what looks like mendacity, I do not assume you are a moron, nor do I assume you are incorrect. That is why I keep addressing your posts, and asking for clarification.

    I shall keep doing so. I am a patient woman.

  37. petrushka
    Ignored
    says:

    It strikes me that it woud be good to have a place for meta comments. Those that are about the conduct of the discussion rsther than about the topic itself.

    I know you have guano, but that seems best reserved for rude and off topic comments. You have the sandbox, but I think that would best be reserved for suggestions.

    I’m thinking there should be a place for comments that do nothing but complain about the conduct of the discussion.

  38. Lizzie
    Ignored
    says:

    Mung:

    Don’t leave it up to Elizabeth, she’s already backed off her initial claim.

    Yes, but only by adding the rider (which I would have assumed was implicit) that I am not including in my generalisation papers that do not actually address evolutionary science/theory.

    Now she claims that what she meant was not that Dembski made “rookie mistakes” about “evolutionary science” (whatever that is), but that Dembski made “rookies mistakes” about “evolutionary theory” (whatever that is).

    geez louise.
    This is what I wrote:

    But I will modify my claim and say: I have yet to read an ID article about evolutionary theory that does not make rookie mistakes about evolutionary theory.

    I did not “back off” my claim by substituting “evolutionary theory” for “evolutionary science”. I “backed off” my claim by adding the rider that my claim only applies to articles that actually address evolutionary theory. But the same is true for “evolutionary science”.

    So let me modify it once again:

    I have yet to read an ID article about evolutionary theory or science that does not make rookie mistakes about evolutionary theory or science.

    I also said:

    Lizzie: Dembski’s mistake about evolutionary theory in that paper is to indicate that he can subsume “Darwinian and other material mechanisms” into a “chance hypothesis” and treat it as a null.

    No where did I say that Dembski’s error was in evolutionary theory rather than evolutionary science. In this context, the two terms are interchangeable, and his error applies to both theory and empirical findings. Ergo, I did not “back off” at all. I simply explained his error, which was, and I quote myself:” to think he can subsume ‘Darwinian and other material mechanisms’ into a “chance hypothesis’ and treat it as a null.” And as I have also stated above, Dembski himself has moved on from this error, getting very hot under the collar with people who criticise him for it for not addressing his more recent work in which he does clearly states that evolutionary processes are possible that are perfectly capable of finding specified targets that would be vanishingly unlikely to be found by blind search. Which is of course true. But he now argues that evolutionary processes that do this are themselves vanishingly unlikely to be found by blind search. Which may be true, but is yet another rookie error, because it seems not to have occurred to him that fitness landscapes that result in specified targets that are unlikely to be found by blind search, are themselves not found by blind search – the universe is highly structured – chemistry and physics are not blind searches. And if all his argument boils down to: a structured universe can’t have arisen by blind search, then his whole argument from improbability dissolves because we cannot calculate the odds of a structured versus a non-structured universe.

    Which is not to say: therefore the universe was not designed. It is simply to say: therefore we cannot infer that it was designed.

    The objection raised by most people to ID is not an objection to the idea that the universe may have been designed with the purpose of creating human life, but to the inference that life was designed, because, look, specified complexity!

  39. Lizzie
    Ignored
    says:

    petrushka:
    It strikes me that it woud be good to have a place for meta comments. Those that are about the conduct of the discussion rsther than about the topic itself.

    I know you have guano,but that seems best reserved for rude and off topic comments. You have the sandbox,but I think that would best be reserved for suggestions.

    I’m thinking there should be a place for comments that do nothing but complain about the conduct of the discussion.

    I agree, and I think we are growing out of blog format. I’m working on forum that will be integrated with the blog, and, hopefully, provide the benefits of each. Still debugging though!

  40. davehooke
    Ignored
    says:

    One of the annoying things many IDists do is conflate OOL with TOE. They are doing it right now in comments at UD. How about a very clear post on how a theory such as TOE has a domain of applicability?

    Perhaps something like the below, although I may have made lay errors.

    The theory of evolution requires self-replicators. Those self-replicators do not need to pass our criteria (whatsoever those may be) for “life”. We know that the replication is by means of DNA.

    *Origin of DNA-using self-replicators*

    There are three broad alternatives for the origin of DNA-using self-replicators.

    1) Natural processes led to the first DNA-using self-replicators.
    2) Artificial processes led to the first DNA-using self-replicators.
    3) There was a supernatural cause of the first DNA-using self-replicators.

    The theory of evolution proceeds on the basis that one of those is true. However we got DNA-self-replicators, once we have them, and they are imperfect copyists, evolution can occur as described by the scientific theory.

    *Domain of applicability*

    The argument ‘we don’t have a satisfactory theory for OOL therefore evolution is incorrect (or improbable)’ is equivalent to ‘we don’t have a satisfactory theory for baryogenesis therefore atomic physics is incorrect (or improbable).’

    A theory has a domain to which it applies. I do not need to know how to make ovens in order to bake a cake (which is to apply, loosely speaking, the “theory of baking cakes”). The theory describes certain processes, not all processes. Every theory has its domain, a set of phenomena it applies to.

    *Origin of life*

    How did non-life become life?

    I think the alternatives are as follows:

    1) What we call “life” is emergent from chemical behaviour.
    2) A supernatural entity breathed life into one generation of self-replicators.

    The theory of evolution can proceed on the basis that one of those is true. It really doesn’t matter to the theory of evolution which is true. A supernatural origin of life does not prevent the theory of evolution from describing the changes to the inherited characteristics in populations of organisms. That is what the theory of evolution is about, so it does not matter to the theory how the organisms got here. The origin of life is simply outside of the domain of the theory of evolution.

  41. Patrick Patrick
    Ignored
    says:

    Lizzie,

    A forum that provides threading and remembers what you’ve read and supports killfiles and . . . damn I miss Usenet.

  42. Lizzie
    Ignored
    says:

    Patrick:
    Lizzie,

    A forum that provides threading and remembers what you’ve read and supports killfiles and . . . damn I miss Usenet.

    Yeah, Scoop would be my first choice, but I don’t think it’s supported any more.

  43. Lizzie
    Ignored
    says:

    davehooke:
    One of the annoying things many IDists do is conflate OOL with TOE. They are doing it right now in comments at UD. How about a very clear post on how a theory such as TOE has a domain of applicability?

    Perhaps something like the below, although I may have made lay errors.

    The theory of evolution requires self-replicators. Those self-replicators do not need to pass our criteria (whatsoever those may be) for “life”.We know that the replication is by means of DNA.

    *Origin of DNA-using self-replicators*

    There are three broad alternatives for the origin of DNA-using self-replicators.

    1) Natural processes led to the first DNA-using self-replicators.
    2) Artificial processes led to the first DNA-using self-replicators.
    3) There was a supernatural cause of the first DNA-using self-replicators.

    The theory of evolution proceeds on the basis that one of thoseis true. However we got DNA-self-replicators, once we have them, and they are imperfect copyists, evolution can occur as described by the scientific theory.

    *Domain of applicability*

    The argument ‘we don’t have a satisfactory theory for OOL therefore evolution is incorrect (or improbable)’ is equivalent to ‘we don’t have a satisfactory theory for baryogenesis therefore atomic physics is incorrect (or improbable).’

    A theory has a domain to which it applies. I do not need to know how to make ovens in order to bake a cake (which is to apply, loosely speaking, the “theory of baking cakes”). The theory describes certain processes, not all processes. Every theory has its domain, a set of phenomena it applies to.

    *Origin of life*

    How did non-life become life?

    I think the alternatives are as follows:

    1) What we call “life” is emergent from chemical behaviour.
    2) A supernatural entity breathed life into one generation of self-replicators.

    The theory of evolution can proceed on the basis that one of those is true. It really doesn’t matter to the theory of evolution which is true. A supernatural origin of life does not prevent the theory of evolution from describing the changes to the inherited characteristics in populations oforganisms. That is what the theory of evolution is about, so it does not matter to the theory how the organisms got here. The origin of life is simply outside of the domain of the theory of evolution.

    And at least Dembski is smart enough to have realised that he needs to focus on OOL, not evolution, he’s realised that evolution can do what he used to say can’t do, given an appropriately parameterised fitness landscape.

    Gauger and Axe are simply wrong that the natural fitness landscape is rugged and low dimensioned – we directly observe that it is smooth and high-dimensioned.

    Dembski claims that a smooth, high dimensioned fitness landscape must be intelligently parameterised.

    It sounds as though they all realise that a smooth, high-dimensioned fitness landscape accounts perfectly well for anything after OOL, so that either the landscape must really not be smooth (Axe and Gauger) or must have been designed (Dembski).

    Both are unsupported.

  44. petrushka
    Ignored
    says:

    Denton seems to have come to this conclusion more than a decade ago in “Nature’s Destiny”

    It’s unsupported but not incoherent. It’s just Deism on steroids. Lots of sane and bright people have thought that existence is designed, or whatever.

    To me the more interesting question is contingency. Would rewinding the tape allow a completely different scenario to develop? I think so, but I wouldn’t know how to prove it.

    I get into arguments with perfectly credentialed scientists because I think humans might be unique, the product of innumerable contingencies. By human, I mean intelligent beings having civilizations. For some reason a lot of people want to believe we are commonplace. I put that in the same bucket as believing in god because it makes you feel good.

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