Maybe Carl Zimmer is free to read Science and Human Origins now …

_{Denyse O'Leary

July 23, 2012

Human evolution, Intelligent Design, News}

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We may have answered his question. A little background:

Recently, we noted that prominent science writer Carl Zimmer was in a tangle with Discovery Institute’s David Klinghoffer arising from a discussion on a Facebook page: His issue here was this paragraph:

But the idea of such an event having occurred at all is itself far from sure. The telomeric DNA parked in the middle of chromosome 2 is not a unique phenomenon. Other mammals have it too, across their own genomes. Even if it were unique, there’s much less of it than you would expect from the amalgamation of two telomeres. Finally, it appears in a “degenerate,” “highly diverged” form that should not be the case if the joining happened in the recent past, circa 6 million years ago, as the Darwinian interpretation holds.
I was baffled, so I asked on Facebook for the evidence that the form of the chromosome wasn’t what you’d expect if it fused six million years ago.

What followed was a ridiculous runaround, some of which I’ll reproduce here: More.

Well, a reader writes to say, here is where the idea might have originated:

This 1991 Pub Med paper:

Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees.

Chen FC, Li WH., Department of Life Science, National Tsing Hua University, Taiwan.

If the fusion occurred within the telomeric repeat arrays less than ~6 Mya, why are the arrays at the fusion site so degenerate? The arrays are 14% diverged from canonical telomere repeats (not shown), whereas noncoding sequence has diverged There are three possible explanations: (1) Given the many instances of degenerate telomeric arrays within the subtelomeric regions of human chromosomes (Riethman et al. 2001), the chromosomes joined at interstitial arrays near, but not actually at, their ends. In this case, material from the very ends of the fusion partners would have been discarded. (2) The arrays were originally true terminal arrays that degenerated rapidly after the fusion. This high rate of change is plausible, given the remarkably high allelic variation observed at the fusion site. The arrays in the BAC and the sequence obtained by Ijdo et al. (1991) differ by 12%, which is high even if some differences are ascribed to experimental error. (3) Some array degeneracy could be a consequence of sequencing errors. We have not been able to PCR successfully across the fusion site, which would be required to assess the contribution of sequencing errors to this measure of fusion-site sequence polymorphism. However, explanation 2 is supported by the high variability among allelic copies of other interstitial telomeric repeats and associated regions sequenced by Mondello et al. (2000) (AF236886 and AF236885). Considering the high mutability of interstitial telomere repeat arrays, the fusion partners could have joined either within terminal or subterminal arrays to form chromosome 2.

Was this where the idea originated?

Now Carl Zimmer is free to read the book anyway.

See also: Here, Cornelius Hunter addresses the Zimmer-Klinghoffer conflict.

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Comments

Pardon, I seem to be extra prone to typos this morning.kairosfocus_{July 27, 2012
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PM: I am sorry, your response above is simply not good enough. It is not that "oh this cannot be shown in an abstract," but that the logical pattern revealed by the abstract shows the ways in which controlling evolutionary materialist assumptions have been injected and control the process. We did not and cannot observe the deep past of origins. We may only infer from signs and traces in the present per provisional inference to best explanation. That holds for deisng theory inferences and it holds for the evolutionary materialist paradigm. Origins science, simply does not have the luxury of direct empirical observation that obtains in other fields of science, and in turn experimental sciences that allow controlling of variables and circumstances provide a yet higher degree of accountability before observations. In that context, it is NEVER appropriate to speak of how one has shown or demonstrated one's conclusions, or that one has consulted a record comparable to the records of history. That is basic, driven by the limitations of the logic of induction. If you cannot see this, then it must be evident to the astute onlooker that an alien to the system such as I [and it is the undersigned who was the alien in view above] will see these built in circularities and will call stop. That is not a matter of word choices that could be simply edited out. It is central. And inadvertently revealing of the controlling mindset. At he highest level, as this is a Royal Society paper, in its abstract, which will be seen and consulted far more often than the body of the paper itself. So, if it passed peer review, and was published by the relevant editors, that is telling on the circularities of the system. Nor, is this an isolated case, it is unfortunately typical. And your further go to lunch on Luskin, whilst a retraction on the invidious associations you made above are still missing in action, are further telling. In that context, I think you do not have credibility to remark on others, as your own judgements are patently inaccurate and biased. As to problems of disputes, there are serious case studies, and I linked one such above. Your brush-aside and passing over the major logical problems then going on to beat up on what seems to be a strawman Luskin, therefore fall under the context of willful atmosphere poisoning by the trifecta fallacy: red herrings that distract, led away to strawman caricatures soaked in overt or implicit ad hominems and ignited by snide or enraged words that trigger a conflagration, confusing poisonous clouds of rhetor5ical and emotional smoke, and polarisation. Not good enough, and all too reminiscent of the tactics of subversive extremists I know ever so well from 30 years ago that did so much harm to my homeland and to that of IP. You need to stop the distractive, denigrarory and divisive tactics, and deal with a significant problem of the logic of the methods being used by practitioners of "mainstream evolutionary biology." (Onlookers, read here: evolutionary materialism dominated scientism applied to the life sciences on matters of origins.) I trust that you will now take a serious look at the issues of circularity undermining the work in question. yes, all arguments have assumptions, but some assumptions have a problem of being tendentious and question-begging. One such is to assert or imply facts in the deep past projected where there are and can be no facts other than traces we observe in the present. Kindly contrast the outline case of dating our galaxy that I have already given. Notice, how carefully observations and inferences and models are separated, and how the conclusions are presented as a model of the past. Then, think about how the following will look to an informed outsider to the system, who is concerned about empirical warrant and inductive logic: the projection of a model past as if it were fact, in a context where there has been no empirical warrant for the claimed driving dynamic to work at body-plan origin or major adaptation level (here, upright biped and language-using mind are particularly in view); instead, an extrapolation form minor cases often dealing with loss of genetic information, to a wholly different level. I think you would find it useful to take a second look at the origin of the human systems that equip us to use language and to think, know and reason, and the resulting warrant for the results of investigations. (Onlookers, cf, here again on the implications of the self-referentiality implied.) KFkairosfocus_{July 27, 2012
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Indium: First, did you notice, that I linked a discussion of the dating problems, and took time to link a particularly clear example of the way the dating issue can break down behind the scenes in the specific context of human origins? As well as the contrast with a case that is much less subjective? It seems not. That makes your remarks come across as willfully ill-informed burden of proof shifting and defiance of duties of care to truth and fairness. Next, you seem to be suffering a breakdown of basic inductive logic (in the context of scientific reasoning) here:
- All things we know that show FSCI (or whatever your current acronym is) are designed [a --> Missing in the rhetoric: per an observational base of billions of test cases, with no significant exceptions, leading to an inductive scientific generalisation that, though inevitably provisional is empirically reliable. Actually the root problem is that in the teeth of such a base of observations, you wish to imply that there is no such pattern. If you wish to overturn it, kindly show cases within our observation that reliably show the origin of functionally specific, complex organisation of multiple well-matched parts to form a working whole, and associated information by blind chance and mechanical necessity, without intelligent guidance on the stage or behind the curtains. Where, said cases are such that Chi_500 = I*S - 500 exceeds 1.] - biological objects show FSCI [b --> Per observation of what has been identified at a as an empirically reliable, credible sign; e.g. cf DNA and RNA, proteins, and the mechanism that step by step creates proteins from the digitally coded information stored in DNA, and the related von Neumann self replicating facility, all in an encapsulated entity with gated interactions with the outside world.] - biological objects are designed [c --> Per reliable, tested sign and signified, and with the Newtonian proviso of provisionality subject to further empirical tests that is standard for science. This last being similar to the basis on which the laws of thermodynamics stand, and is the context in which quantum theory and relativity showed the limitations of Newtonian dynamics.] See? Circular reasoning. [d --> Not at all, reasonable inductive generalisation and inference to best explanation for cases where we did not observe the causal process, and which exhibit the same sign] You are assuming your conclusion in the premise. [e --> That is what you wish were the case. But in fact, the one projecting an unwarranted assertion at the first step is the objector (as in: show the reliable cases of blind chance and necessity spontaneously creating FSCO/I without intelligent guidance or intervention . . . ], who then twists the matter about to pretend that there is not a serious observation and induction basis for the generalisation given.]
Do you see that it is you who by your remarks patently do not understand the nature and limitations of the scientific method in general? Did you take time to observe not only the discussion of Newton's rules of scientific reasoning here in the IOSE intro-summary, but the unit on scientific methods in light of relevant considerations here, also? In short, your objections fail, and fail in a way that does not reflect well on the way you have approached the matter. Please, do better next time. KF PS: Onlookers, if there were a reliable observed pattern of chance and necessity giving rise to FSCO/I spontaneously without involvement of design on stage or behind the curtains, there simply would be no design theory movement.kairosfocus_{July 27, 2012
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Nice one kuartus. But, I hope you agree that your premise can be supported by much more evidence and is not at all relying on checking if Sokrates is really mortal. There always will be the limits of induction. But while indeed all men we know are mortal, there is a class of objects (biological objects) where we don´t know if they are designed. Still, funny comment, thanks for the laugh in the morning. :-)Indium_{July 27, 2012
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Well if that is circular then so is this: 1.All men are mortal 2.Socrates is a man 3.Therefore Socrates is mortal Its so circular that Im getting dizzy!kuartus_{July 27, 2012
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kf, please show how dating methods are all in the end circular. They are not. I give you an example of circular reasoning: - All things we know that show FSCI (or whatever your current acronym is) are designed - biological objects show FSCI - biological objects are designed See? Circular reasoning. You are assuming your conclusion in the premise. Now show the same for the dating methods.Indium_{July 26, 2012
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Larry Moran latest post: some notes on the evolution of enzyme families, and enzyme specificity. He also mentions he will be addressing Gauger and Axe from a biochemistry stance.paulmc_{July 26, 2012
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KF:
Did you expect that the article could be seen in a very different way, as inadvertently listing ever so many potentially disputable assumptions
Yes, I see the point you are trying to make. Obviously there are assumptions, and they are unlikely to justify them in an abstract. Basically you take issue with a few word choices like 'history' and 'show'. You present no reasons to doubt their timeline, you only assert that it is circular.
In short, I think you may have read Gauger et al, but from so alien a perspective that they have reason to feel that you have not fairly read them with genuine understanding. This is the impression I get from your multi-part review.
My 'alien' perspective is that of mainstream evolutionary biology. If I haven't read with genuine understanding, I'd expect that there'd be matters of science you could be addressing here rather than simply suggesting I'm missing the point.
Luskin is not in their class but he is insisting on thinking for himself, is obviously intelligent and has investigated the matter. Gauger is a researcher publishing in the peer reviewed literature and Axe is a more senior researcher. Show the modicum of respect that deals with matters on the merits rather than people.
Luskin might be very intelligent indeed. For all I know he might also be charming and personable and a great guy to have a beer with. But you talk about people showing a modicum of respect? Luskin accuses the entire field of palaeoanthropology of being driven by personal disputes, that its practitioners are dishonest to the public, and he speculates about sinister motives with no evidence. These are massively disrepectful things to say. He later directs a personal attack at Francis Collins. And then there's his treatment of the literature. I was sarcastic but there is a context. Gauger and Axe repeatedly demonstrate misunderstandings of the population genetic processes - look at what Axe claims towards the end of his response to me. In science, respecting their work does not mean ignoring these mistakes.
Do you see why someone outside the circle will see such as reflecting circularity rather than solid warrant?
I assume you are suggesting that there is circularity regarding my interpretation of the fossil record. The fossil record is what it is. It'd be convenient if better, more regular, and more representative preservation happened but it isn't. My interpretation isn't circular simply because it occurs within the evolutionary paradigm. Finally - and back to the point - none of this addresses my criticisms of Axe and Gauger, which should test an adequate model of evolution if they are to provide evidence for ID.paulmc_{July 26, 2012
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And that is the problem- correctly and fairly testing the null model. Even after 150+ years no one has a clue of how to do so. Strange, that...Joe_{July 26, 2012
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I'd like to make a few points, addressing what lpadron said above. First, thanks for laying out a calm version of events from the ID side. I do have to disagree, and I'd like to explain exactly why. You're right that I do want to stay focused on one issue, because this is the comments thread on a blog, and it is impossible to focus on many things at once and do them justice. I disagree about the claims on metaphysics and circular reasoning - here's why. I was discussing the reaches of evolution as argued by Gauger and Axe. If it turns out that they are entirely wrong, this should not be considered evidence against intelligent design as a whole. That there are certain things within the reach of evolution does not mean that other things are not. Everyone these days seems to accept 'microevolution' so this should be uncontroversial. If you want to test the intelligent design as a scientific hypothesis, you should have a null model to test it against. The null model is that there is no designer. Fortunately for you guys there has been 150 years of development of such a null model. This may sound like I am saying evolution is 'true' until you prove otherwise, but actually I am not because testing the alternative does not provide positive evidence for evolution. You could also conceive a different no-designer null model if evolution is inadequate. However, it is essential that the null model is correctly and fairly tested. If not, you have exactly no evidence of anything. What I have suggested is that the expectations of evolution were unreasonable and rejecting them tells you nothing about it or the alternative. There is nothing circular about this.paulmc_{July 26, 2012
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Indium: Do you understand that in the citation from a Royal Society paper, PM used a deep past timeline, perceived as fact? Do you understand that it is pivotal to his argument and that there are serious and longstanding circularities involved in geochronology, especially the reconstructed timeline for origin of man, as say the mess with KNM ER 1470 -- a "hot" fossil human case in my youth and student days -- showed? Do you therefore see why I took time to outline a different approach, one that (with reference to dynamics of known physics) provides age estimates for our galaxy with much less of circularity, though there is an inescapable degree of assumptions? Do you notice how I explicitly highlighted the way the approach lays out models and compares model with observation in this case of star clusters? Did you see how I used this to draw out the inference to best current (and provisional) explanation logical basis for scientific reconstructions of the remote and unobservable deep past? Did you notice how I contrasted this to the tendency to suggest "facts," that things have been "shown," and the claim that one has "demonstrated" on "records"? Do you see how this is an illustration of the circularity problem I am identifying in PM's arguments and in those of the authorities he cited as decisive on the specific subject which I raised earlier in the thread and which in his quite hostile review part 3 he used in rebutting and dismissing Gauger et al? Do you see why I am heavily underscoring the circularity problem and the importance of an inference to best explanation [IBE] anchored by adequate empirical observation basis as the way forward? Do you understand that the pivot of the design inference is an IBE argument on empirically well warranted signs, in a scientific context? In that light why not go back up to 41 and 46 and reread my comments? KFkairosfocus_{July 26, 2012
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IP: Ah, boy. I understand. I hope you did not lose family or friends of family. (I just did a revision to a key doc and stakeholder discussion, took a break.) I suggest you make acquaintance of the Alinsky tactics, summarised here. Also cf Phillips here -- the book looks like a must-read. PM et al flipped some serious warning flags. A lot of what is breaking down in our time is that the techniques that were created by communist subversives have now become "standard" pressure group tactics. The underlying nihilism traces to the evolutionary materialism Plato deplored 2350 years ago, cf here. KFkairosfocus_{July 26, 2012
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Indium, If paulmc is arguing in a circle then his argument is altogether invalid no matter what paulmc points to as evidence. KF has argued that paulmc is doing just that.lpadron_{July 26, 2012
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KF, 1. Good post. 2. As I mentioned at CZ's site, Luskin has a degree in law and a Masters in earth science. Zimmerman holds only a BA in english. That hasn't stopped anyone from claiming Zimmerman is something of an authority. Of the two and given their academic backgrounds, who's more likely to have had some training in critical thinking? 3. As the son of parents who fled Castro's cuban revolution I'm familiar with the communist tactics you mentioned. I don't know that paulmc is guilty of them or even aware that they may be perceived as such. But I'm extremely grateful for whatever you've done to stomp them out in the past.lpadron_{July 26, 2012
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kf: Which specific point (!) of paulmcs review do you think your post 54 is adressing? I can´t find anything about cosmology (of all things...) in paulmcs review, nor is there anything about the evolution of language. Hydrogen ball model??? I will tell you something: Even if you are correct and all your cosmological arguments are right and your islands of functionality idea is relevant (it isn´t) and so on, all of this would not make paulmcs argument any less valid. So, why do you bring all these distracting tangents up?Indium_{July 26, 2012
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PM: I have changed my mind on a point, and apologise for a misunderstanding coloured by the context with Zimmer and a triggering remark on your part. I now believe that you have made a sincere attempt to read and respond to Gauger et al. However, I believe -- and the case with the alleged origin of language was pivotal here in my revised thought -- the circle of thought you are in has drastically coloured how you read. Pause and look at my response on what you clearly believed was a decisive citation from credible source on the origin of human language in 41 above. Look closely at my comments on and surrounding the source. I don't care just now if you agree with them, I am simply concerned to know if you were aware of how such a cite would look to someone like me who is decidedly outside the evolutionary materialist paradigm and who is trained to think in terms of logical and empirical warrant for claims. Did you expect that the article could be seen in a very different way, as inadvertently listing ever so many potentially disputable assumptions, or that it is giving the impression of an access to the remote past of origins that is not in our gift? Do you see why it will look ever so different to one who does not share that circle of assumptions? And, why such a person will have reason to see the whole as an ideologically driven circle of thought? By contrast, cf here on, a simple survey of astronomical and cosmological themes with special emphasis on the HR diagram and its significance. Notice how I speak in terms of a hydrogen ball MODEL, as distinct from actual stars. Then notice how I use the HR diagrams of clusters. Notice the inferences that because they are gravitationally linked local groups of stars they are about the same distance away so relative magnitudes link to absolute ones. Similarly, they plausibly share a common origin. From this and the H-ball model, we see age estimates based on branch-off points that look like they are heading for the giants branch, the later life of a star per the model. Do you see the inferences that are laid out and the reasoning behind the "best explanation"? Do you notice how I refrain from announcing such as though they were record or pretty certain facts? Which do you think is more likely to persuade an outsider that the process of thought involved is reasonable and conservative in conclusions? Why? Now, turn back to how you seem to have read Gauger's argument and her response of July 19, in 46 above, on enzyme functions. Do you notice the gap between how you have looked at the evidence, what Gauger says in response and what I highlighted and amplified? I think you have inadvertently stumbled on the verge of seeing the isolated islands of function challenge, but are blocked by your circle of thought. In short, I think you may have read Gauger et al, but from so alien a perspective that they have reason to feel that you have not fairly read them with genuine understanding. This is the impression I get from your multi-part review. (And BTW, please lose the annoying tab that comes up on the RHS of your blog pane, it interferes with scrolling at least on my machine.) Your responses may feel good to those on your side of the divide, but come across as very unfair and even denigratory to those of us on this side. For instance, observe how you introduce Luskin:
In walks Casey Luskin, armed with a law degree and a Masters in earth science, ready to take on the idea of our shared common ancestor with chimpanzees in a chapter entitled 'Human origins and the fossil record'. Luskin must be something of a polymath, for here he takes on the world's palaeoanthropologists on the hominin fossil record and in the next chapter he tackles the existence of junk DNA . . .
This is denigratory, AND commits the fallacy of appealing to modesty in the face of the presumed authority of the deans of your school of thought. Einstein was a nobody when he came up with relativity and was not exactly a celebrity for years thereafter. Newton was a student when he came up with his pivotal insights. Luskin is not in their class but he is insisting on thinking for himself, is obviously intelligent and has investigated the matter. Gauger is a researcher publishing in the peer reviewed literature and Axe is a more senior researcher. Show the modicum of respect that deals with matters on the merits rather than people. (NB: Your invidious comparisons above did much to poison this thread, and frankly, I am trying hard to see through your eyes instead of taking you for what such tactics point to, now and 30 years ago when I had communist agitators dealing with. Kindly, turn down the voltage, and understand that science is inherently provisional so learned schools can be wrong.) in closing, I really have to get moving, notice your:
Luskin is right to point out that the hominin fossil record is imperfect, and that at times the completeness of that record have been overstated. But he goes further, and channels Lewontin to make a strange claim: 'so “fragmentary” and “disconnected” is the data that in the judgment of Harvard zoologist Richard Lewontin, “no fossil hominid species can be established as our direct ancestor.”' It is not a sign of the poverty of a fossil record that extant species lack directly fossilised ancestors, but rather evidence that there were various, diverse lineages that mostly led to evolutionary dead ends. This is the case for hominini as it is in other lineages. We have no particular reason to expect to find direct ancestors of living species in the fossil record, and of course there will be appropriate controversy for any given fossil because of how different characters will be interpreted.
Do you see why someone outside the circle will see such as reflecting circularity rather than solid warrant? Now, think again on your update and onward link as cited in 41. Think about how the authority you cite goes around the circle. Then, look again at why I am raising the concerns I have raised. And no, this is not hyperactivity or attention deficit on my part. That was outright rude on your part. Maybe the matter can be addressed on a more reasonable basis now. KFkairosfocus_{July 26, 2012
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kf: Now, I will make a comment to PM directly, for I have changed my mind somewhat.
Great news. This is going to be interesting.Indium_{July 26, 2012
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IP: Before heading off I decided to pass by. You have understood what I have been raising on a crucial facet. In addition, standing on their own empirical observation merits, there is a need to warrant the claim that CV + DRS --> DWM, thence macro-evo etc. The two are directly connected as the injected a priori seems to make claimed evidences carry far more weight than is reasonably warranted. This is because once such an a priori is locked in, something pretty much like that MUST follow. But, "every tub must stand on its own bottom." That is, PM et al cannot properly demand a default, in which it is just a matter of solving a few puzzles on HOW what MUST have happened did so. There are fundamental gaps. That is why I am highlighting the closed question-begging circle that reminds me ever so strongly of the Marxist system, and the linked want of grounding warrant. It is why I am calling for the kind of warrant I am, from the root of the Darwinist tree of life up. I am not just tossing out scatter-shot obstacles and objections to make it impossible to answer. And it is why I am drawing a very direct parallel between digital codes and algorithms in the original cells, and the rise of language-logic capacity in humans. Now, I will make a comment to PM directly, for I have changed my mind somewhat. KF PS: Indium, I think you are having a very similar problem to what I have just discussed, and am about to discuss.kairosfocus_{July 26, 2012
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lpradon: Without wanting to speak for paulmc, I would like to remark that of course kf can invent millions of questions that paulmc has to answer to defend his materialistic worldview or whatever. But that is not the point of the argument. Paulmc has made very specific arguments regarding a very specific ID paper in an "ID-friendly" journal. kf does not seem to be able to address these arguments, so in my mind his walls of text are just a distraction. Paulmc is not arguing that the materialistic worldview is correct, that there is a working model of the OOL or that all population genetics questions kf might think of have been answered. And even if paulmc answered every one of kfs questions (and he has answered some), kf would invent new ones (and he already did, in this very thread). Do you really think this is an acceptable debating style?Indium_{July 26, 2012
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"you"=kf, in my last post, not lpadron.Indium_{July 26, 2012
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This onlooker and long time dismissive objecter notes that despite another 1000 hypersceptical and just plain distracting words you still don´t answer paulmcs simple and relevant arguments. Because you can´t. And you won´t. Which would be a lot less amusing if you wouldn´t try to hide this fact behind such large walls of text, so keep it up.Indium_{July 26, 2012
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paulmc, Thanks for taking the time to post here. I appreciate your efforts to explain your position and critique of Axe & Gauger's book. I also appreciate that unlike others you *have* taken the time to read and critique the book chapter by chapter. I think the disagreement between you and Kairosfocus boils down to two things: 1.your desire to stay focused on particulars (enzyme functions, chromosome fusions, etc.) 2. and KF's desire to bringing attention to how your own views are shaped not by science but by, as he put it, "a materialistic metaphysical system" with its own a priori truths. If I understand KF is correctly then your critique of Axe & Gauger and their testing methods is as biased in favor of the reigning view of evolution, pop. genetics, etc. as you'd say theirs is against it. I think that's what he was getting at back in post #14: "Let’s see the dynamics, the play-out that credibly led to us in reasonably available time [incl. pop genetics], and warranting empirical evidence that does not go in a priori materialist circles or depend unduly on extrapolations accepted through the eye of Darwinist faith." If true, then appealing to studies and published papers with results from the latest research by others committed to the same metaphysical view is of little help. The particulars you want to focus on will, and more importantly, *can* do one thing only: confirm the reigning view. Since all evidence is first subject to that metaphysical stance (even before peer review!) it can only be interpreted in such a way that it will either fit the reigning view or be considered a mystery to be resolved later. But the one thing no amount of evidence can do is this: disprove the theory. Nothing can. If I've got this right then KF's requests aren't unreasonable. In fact, I'd say they require answering. Of course, I could be completely wrong which isn't unusual. I apologize to both you and KF if that's the case. Finally, here's hoping you both tone it down a bit and that you address only the questions without attribute ulterior motives to each other. This is a great opportunity for both of you to teach those of us on the low end of the IQ scale. Again, thanks!lpadron_{July 26, 2012
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tl;drStarbuck_{July 26, 2012
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F/N: Since there is a tendency on the part of evolutionary materialist objectors to design to simply repeat talking points and ignore cogent replies, first, I will again excerpt the issues highlighted by Gauger that appear at 11 above, I will follow with 33 above. This is with particular reference to 36 just above, which is of course unresponsive to the pivotal issues, never mind the wider "every tub must stand on its own bottom" point: ______ >>Getting a feature that requires six neutral mutations is the limit of what bacteria can produce. [1 --> per the empirical work put on the table by Gauger et al, observe absence of work that demonstrates that such a limit or a similar one is not so, is conspicuously absent, and the population genetics pop size and generation time issues are not resolved, so the transformations to make a whale out of a cow or something similar, run into serious problems, as do the changes to make a chimp like animal into a human. Note, bacteria have the pop size and short generation span to produce observable results in a reasonable lab span] For primates (e.g., monkeys, apes and humans) the limit is much more severe. Because of much smaller effective population sizes (an estimated ten thousand for humans instead of a billion for bacteria) and longer generation times (fifteen to twenty years per generation for humans vs. a thousand generations per year for bacteria), it would take a very long time for even a single beneficial mutation to appear and become fixed in a human population. [2 --> Notice the contrast on population genetics relevant points] You don’t have to take my word for it. In 2007, Durrett and Schmidt estimated in the journal Genetics that for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years. The same authors later estimated it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect. [3 --> Notice this report from a separate study] Facing Facts But six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. [4 --> hence the 6 - 10 MY window] Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes— sixteen anatomical features—in the time available. At most, a new binding site might affect the regulation of one or two genes. [5 --> So, where are the resources to do the transformation in the window of time available?]>> _____ Next, we have the issue of the enzyme transformation, so I clip from 33 above, Gauger again, which directly anticipates what we see in 36 (and I hope Indium learns a lesson about commenting adversely late in a thread's life): ______ >> Those who follow the evolution intelligent/design are probably familiar with one accusation that we often face — that we do not do peer-reviewed research. In fact, we have published a number of peer-reviewed articles and one of them in particular, called “The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway,” contributed to the argument we made in the new book published by Discovery Institute Press, Science and Human Origins. That paper was critiqued last November by Paul McBride. [a --> This was published July 19, i.e. before the exchanges above] He has now extended that critique in his review of our book, available here. McBride’s main complaint is that we picked an unnatural evolutionary transition to test. We chose to examine how hard it would be to get a modern-day enzyme to switch to the chemistry of a closely related modern-day enzyme, with very similar structures and catalytic mechanisms. The reason for our choice was not ignorance. We knew that the enzymes we tested were modern, and that one was not the ancestor of the other. (They are, however, among the most structurally similar members of their family, and share many aspects of their reaction mechanism, but their chemistry itself is different.) [b --> Notice the reasons] We also knew that in order for a Darwinian process to generate the mechanistically and chemically diverse families of enzymes that are present in modern organisms, something like the functional conversion of one of these enzyme to the other must be possible. We reasoned that if these two enzymes could not be reconfigured through a gradual process of mutation and selection, then the Darwinian explanation of gene duplication and gradual divergence to new functions was called into question. [c --> Notice the reasons] Our results indicated that a minimum of seven mutations would be required to convert or reconfigure one enzyme toward the other’s function. No one disputes that part of our research. [d --> Observe the results] What Paul McBride and others claim is that because we didn’t start from an “ancestral” enzyme, our results mean nothing. They say something like, “Of course transitions to new chemistries between modern enzymes are difficult. What you should have done is to reconstruct the ancestral form and use it as a starting point.” [e --> Observe the built in default to the a priori on ancestral forms, i.e we see a circle of argument without empirical warrant on specific observations] Have you noticed the assumption underlying this critique? [f --> indeed] The assumption is that genuine conversions can be achieved only if you start from just the right ancestral protein. Why is that? Because conversions are hard [g --> Notice, that is an implicit admission that complex, multipart function dependent on proper arrangement of well chosen well matched parts strongly comes in islands, which is a key reason why the needle in haystack challenge applies to FSCO/I and why it is an empirically reliable sign of design]. . . . The problem then becomes, where did the diverse families of enzymes come from, if transitions are so hard, evolution is so constrained, and selection is so weak? [h --> this is based on a direct quote from PM, and it again points to the isolated islands of function issue. You have to have just the right sort of starting config or no dice] Were the ur-proteins from which present families sprang so different from modern ones, so elastic that they could be easily molded to perform multiple functions? [i --> On what empirical warrant per observations? or, are we simply back in the circle of a priori evolutionism] If so, how did they accomplish the specific necessary tasks for metabolism, transcription, and replication? [j --> Notice the link back to OOL] More than that, how did the proteins necessary for replication, transcription, translation, and metabolism arrive at all, if evolution is so constrained? [k --> How do you get to the shores of islands of complex function in vast seas of non-functional configs, by chance based random walks without a differential performance filter because until you get tot he start point you have no function; it gets tiring to have to point out what should be obvious over and over and over . . . ] Those processes are much more complicated that a cellulase enzyme. We have ribosomes, spliceosomes, photosynthesis, and respiration. We have hummingbirds and carnivorous plants and even cows who make use of cellulose-degrading symbionts. The things that have not arrived or arrived very rarely, like cellulases, seem trivial by comparison to the things we see around us. [l --> responsive to particular points] Our results argue that only guided evolution, or intelligent design, can produce genuine innovations from a starting point of zero target activity [m --> Notice, the island of function issue, if you beg the question by starting in an island of function, you are (maybe unconsciously) ducking the key issue.] . . . . Life is inherently teleological [n --> We are seeing complex things that have to be put together in well matched properly organised ways to achieve function], and the needs of an organism cannot be met by whatever happens to show up. [o --> There is no good observational evidence to warrant an assumption of continents of function such that we have vast "fitness landscapes" that reward incremental change from arbitrary initial points, and this extends to cases where we have random drift to jiggle around and allow the landscape to shift too] I would say, rather, that his faith in the unending creativity of evolution, in spite of the limitations of natural selection, the rarity of paths, and the functional needs of organisms, is itself a form of religion. [p --> Cf Johnson as repeatedly cited] This is an interesting turn in evolutionary thinking. People have been saying for years, “Of course evolution isn’t random, it’s directed by natural selection. It’s not chance, it’s chance and necessity.” [q --> Yup] But in recent years the rhetoric [r --> that's the right word] has changed. Now evolution is constrained. Not all options are open, and natural selection is not the major player, it’s the happenstance of genetic drift that drives change. But somehow it all happens anyway, and evolution gets the credit. All around us we see marvelous examples of successful, even optimal design. [s --> I.e. we see complex, specific function that depends on correct arrangements of matched parts, and these work very well in ever so many cases, never mind the distractors that point to some dubious cases of allegedly sub-optimal design; though the point is that optimisation can be detrimental long term (the robustness issue) if it locks out flexibility] If evolution is constrained to just a few paths, and you have to start with the right ancestral form to get anywhere, and fixation of useful new traits happens by accident, how did anything ever happen at all? [t --> Other than by design that put you down on the islands of function implied by such] Were the paths of adaptation “preordained”? Paul’s choice of words, not mine. If there are only a few ways to solve any problem set by the needs of the organism because transitions are hard, then either the deck was stacked in our favor, or the process was guided, or we are incredibly lucky. [u --> Design is on the table . . . ] >> ______ I trust these notes will help onlookers who really want to find out what is going on and what is on the table. I have long since given up hope -- save by blatant system collapse a la 1989 - 91 -- for those locked up in the closed circle a priori materialistic metaphysical system, or carried along as fellow travellers. KFkairosfocus_{July 26, 2012
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F/N: Just remember, onlookers, the evolutionary materialist paradigm for OOL and for body plan origins has to "stand on its own bottom," rooted in empirical evidence, not mere appeals to a consensus of the reigning orthodoxy. Let us note:
1 --> Absent a cogent account of the origin of cell based life -- encapsulated metabolic automata that self replicate using a von Neumann self replicator requiring a considerable amount of coded (thus, language based!) information -- has no root and no starting point, the Darwinist tree of life is rootless. 2 --> Similarly, absent an empirically warranted mechanism accounting for the origin of major body plans and key adaptations such as in birds, bats and language using reasoning humans, per CV + DRS --> DWM, thence novel body plans, the Darwinist (including derived) macro-evolutionary scheme is a tissue of gaps papered over with speculative reconstructions, not a proper scientific account. 3 --> In particular, since it is self-referential, absent an adequately empirical observation backed account of human origins that grounds our language, intelligence and reasoning and knowing, the system collapses in self referential absurdity. Similarly, the system had better have in it a well warranted IS that objectively grounds OUGHT, or it is amoral and opens the door to might and manipulation makes right nihilism. [Cf. here on for first details.]
By contrast, we know that FSCO/I is routinely observed as the product of intelligent, purposeful and skilled design, and we ONLY observe it as so. We can show per empirically backed up analysis on needles in sufficiently big haystacks (here 1,000 ly on the side, the thickness of our galaxy)that blind chance and mechanical necessity is maximally unlikely to create such from an arbitrary starting point in a config space. And we therefore have excellent reason to infer that such FSCO/I is an empirically reliable sign of design. KFkairosfocus_{July 26, 2012
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F/N: If the onlooker wants to follow up this point, cf here in brief and onward here for some first details, noting:
So long as [[Neo-]Darwinian macro-evolutionary theory lacks an empirically credible, tested and well-supported explanation of the origin and validity of human intelligence, language and associated reasoning powers, the very need to use these same human faculties to propose, discuss and analyse a theory that should but cannot account for them, turns every presentation of (or argument for) the theory into an unintended but eloquent illustration of the major and un-answered weaknesses of the theory.
There are of course many, many other gaps in the warrant for the case that is usually so confidently presented, sometimes in terms that compare it favourably to the orbiting of the planets around the sun.kairosfocus_{July 26, 2012
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Onlookers: Indium is a long term distractive, dismissive objector. It is quite clear that the substantial issue has been put on the table, and that the basic problem is that the evolutionary materialist scheme cannot stand on its own bottom. I have taken time just above to take a slice of PM's attempted review (notice, how this is a specific point I had raised as a test case: origin of language ability among humans) and I have shown -- on a pivotal point of human origins -- just how the question has been massively and evidently unconsciously been begged in an a priori materialist circle. We do not see the empirically warranted step by step justification of the Darwinian mechanism, or of the population patterns, etc. but instead a presumed default backed up by an implicit appeal to consensus and collective authority. I do not know if PM (a) did not read what I wrote earlier enough to see this, or (b) lacked confidence in his own case at a key self-referential point or (c) thought it rhetorically advantageous to attack the man rather than address the issue, or what combination of the 6three, but the just above speaks for itself on the "every tub must stand on its own bottom" problem. Especially the Royal Society paper's argument. KFkairosfocus_{July 26, 2012
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So many words. Still no answer to paulmcs questions. How surprising. This onlooker thinks your're just distracting here.Indium_{July 25, 2012
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Onlookers: Maybe there is a slice of the cake that has in it sufficient of the ingredients that we can understand the phenomenon we are dealing with: failure to recognise that every tub must stand on its own bottom, leading to thinking in a closed circle such that we have the sort of ideological lock-in that I used to see with some Marxists. In the update to the third ~~review~~/ ~~noview~~/ dip, denigrate and dismiss -- I have had to find a best description (and I know it will be painful; however, PM needs to learn that something is very wrong with how he has handled those whom he would brush aside as irritating insects . . . ) -- articles on Gauger et al, he actually touches on the case of origin of human language:
There has just been a themed issue of Philosophical Transactions of the Royal Society B that deals with the evolution of cognition in humans. A paper in this issue by Schultz, Nelson and Dunbar elegantly summarises hominin cognitive evolution, showing a series of progressive and punctuated changes that culminate in the emergence of modern human language within the last 100,000 years. Brain size evolution over more than 3 million years is summarised . . .
The pivotal problem is, no such thing has been SHOWN. This is rather like how in a recent biology textbook, the 5th Edn of the Johnson and Losos text, The Living World (McGraw Hill, 2008), in which there was a figure that laid out a series of mammal reconstructions on an equally reconstructed timeline and presented it as an OBSERVATION of macroevolution. The deep past is never observed, it is reconstructed. That means there is an inherent limitation on degree of warrant attaching to any scientific investigation of the past of origins. And, the timeline projected -- here, across three million years (as though someone was ticking off on a diary) -- is riddled with all sorts of circularities. And this is not just a matter of those despised silly Young Earth Creationists -- note the "{typical" adjectives that show another problem of projection of a programmed dismissal talking point string -- who cannot accept the all but certain findings of "science." If you cannot see and understand the circularities in geo-dating systems, you have a problem with basic inductive logic. (I have a lot more respect for say the dating of star clusters based on the physics of H-balls leading to the HR plot and the observed branch-points heading to the Giants branch. There are some assumptions in this, but there is nowhere near as much circularity in the system.) Next, the circularity extends to the inference that origin of language has been SHOWN. What has been actually done is a bunch of skulls have been reconstructed [with some degree of circularity attaching in cases where the skulls are sufficiently incomplete that subjectivity is involved in the reconstruction, similar to the notorious case of KNM ER 1470), and lined up on a projected -- essentially, assumed -- evolutionary timeline. At no point has there been an actual empirical demonstration with actual direct observations and measurements of the actual facts. The abstract PM linked shows this sufficiently for our purposes:
As only limited insight into behaviour is available from the archaeological record [1 --> beyond that point, facts have gone out the window . . . ], much of our understanding of historical changes [2 --> abuse of a word, history properly denotes reconstruction of the OBSERVED past based on credible record and supplemented by other investigations] in human cognition is restricted to identifying changes in brain size and architecture. [3 --> There is no actual observation, and there certainly is no observation of mecahnism in action to identify that CV + DRS --> DWM, hence origin of key major feature has occurred, much less on a given timeline] Using both absolute and residual brain size estimates [4 --> inadvertently key word], we show [5 --> Just what, per the basic limitations of your ability to observe the remote past beyond record, you could not do] that hominin brain evolution was likely to be the result of a mix of processes; punctuated changes at approximately 100 kya, 1 Mya and 1.8 Mya [6 --> the t-line is reflective of all sorts of circularities and is a theory-dependent model framework not a factual observation] are supplemented by gradual within-lineage changes in Homo erectus and Homo sapiens sensu lato. While brain size increase in Homo in Africa is a gradual process, migration of hominins into Eurasia is associated with step changes at approximately 400 kya and approximately 100 kya. [7 --> Ditto] We then demonstrate [8 --> You have no such capability to demonstrate anything] that periods of rapid change in hominin brain size are not temporally associated with changes in environmental unpredictability or with long-term palaeoclimate trends. [9 --> Yet more circles of inference within the system] Thus, we argue that commonly used [10 --> i.e. "consensus" an appeal to collective authority not a fact] global sea level or Indian Ocean dust palaeoclimate records provide little evidence for either the variability selection or aridity hypotheses explaining changes in hominin brain size. Brain size change at approximately 100 kya is coincident with demographic change and the appearance of fully modern language. [10 --> assertion, not fact, and mechanism is nowhere to be seen] However, gaps remain in our understanding of the external pressures driving encephalization, which will only be filled by novel applications of the fossil, palaeoclimatic and archaeological records. [11 --> Observe how the only actual factual record is put in a list of theory dependent, circularity-riddled reconstructions as though these are on the same level of warrant]
The list of point6s where a theoretical scheme has been inserted and improperly assigned a degree of r=warrant that it cannot have is astonishing. Moreover, at no point have we seen any sound presentation on empirical observation of the incremental chance genetic changes fixed in populations by differential reproductive success, and then leading to origin of the human linguistic-logical capacity. Don't even ask, how such a process could deliver a reliable cognitive function capable of good reasoning and well-warranted knowledge. The population and genetics issues on fixing incremental changes within the alleged window of available time is simply missing. The notion is simply implied that there is a Mt Improbale slope running up the backside of the peak is assumed. Don't even mention the notion of a random walk across a smoothly connected fitness landscape [oh yes you can jiggle around a bit and you can have the fitness jiggle too that is irrelevant and a sidetrack led off to a strawman used by PM . . . ] that gets us there without any problems of needing to span search space challenges linked to the issue that complex specific multipart functionality based on proper arrangement of well matched parts leads to islands not a continent of function. And as for the way nature is assumed to nicely constrain variation so that the sort of EMPIRICALLY OBSERVED difficulties Gauger raised on moving from one enzyme to another can just be brushed aside, we just note it in passing. Epicycles upon epicycles. It is OBVIOUS that the sun, moon and stars go around the earth! So, we have to find a way to fit those funny back-loops into the system. Forty cycles? Eighty? Never mind it has to work out somehow. And see, we pretty nearly save the phenomena, look we are predicting eclipses. Just ask Columbus about how he got those Arawaks to feed him when he was stranded in Jamaica! That is why we all need to stop and seriously ponder Philip Johnson's retort to Lewontin:
For scientific materialists the materialism comes first; the science comes thereafter. [[Emphasis original] We might more accurately term them "materialists employing science." And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) "give the appearance of having been designed for a purpose." [Emphasis added] . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [[Emphasis added.] [[The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]
I doubt that this or any far more lengthy evaluation of the scheme will be sufficient to open the eyes of a PM to see the problem. But that does not mean that we who look on cannot take note for ourselves and see what has gone wrong. I am pretty well convinced that established systems, never mind flaws that are gaping, have to crash and burn to change. As happened 1980 - 92 with Marxism. So, t5he key thin is that we just have to stop giving our consent to the system and have to stop allowing its overlords and high priests in the holy lab coats to tell us what to think or do. But, the Emperor doesn't have on any clothes daddy . . . Shush, sonny . . . KFkairosfocus_{July 25, 2012
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PM has of course brought up his attempt to overthrow and dismiss the recent book by Gauger et al, which seems to be by a dismissive focus on one particular point
Once again, KF, this is demonstrably untrue. One particular point? My review addresses the major points of every chapter in the book. It is not my fault that you haven't read the review, but there is no point in your continued dishonesty about it. As you so often like to tell others, you have been repeatedly corrected on this. So, once more, this: I have made a series of specific comments on Gauger and Axe's work in comment 36 above with a link to a fuller discussion, and you have replied only with generalities, once again bringing up everything from OoL to body plans to human evolution. You have now added to your list the origin of DNA. There is little value in yet another long post from you talking about everything except the evolutionary relevance of taking two highly diverged sequences and expecting to bridge their functional difference by way of sequential nucleotide substitutions.paulmc_{July 25, 2012
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