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

Onlookers: CH seems to have captured a relevant case in point here:
Venema reviews a recent paper by other evolutionists who say they have found evidence of natural selection acting on random mutations to help change a population of small primates into humans. Venema tells us that such findings are “elegant and powerful” and that they “powerfully support the common ancestry of humans with other forms of life, such as chimpanzees and other great apes" . . . . [T]he paper’s explanation for how it made such an amazing discovery is fairly technical and not accessible to the non specialist. This is where Venema, a specialist writing for a broad audience, could have helped. Instead he further obfuscated the implications of the study. Very simply put, while there are many ways evolutionists test for positive selection, they all take evolution as a given. It is not possible simply to measure objectively the selection in DNA as one would, for instance, measure the voltage or current in a circuit using a multimeter. For example, one strategy evolutionists use to test for selection is to (i) compare the DNA sequences from several species including humans, (ii) derive the corresponding DNA sequence of the common ancestor of those species, (iii) find the changes in the human DNA compared to the common ancestor, (iv) conclude that those human DNA regions with relatively large change are under positive selection and that those regions with relatively little change are under negative, or purifying, selection. Notice that the second step implicitly assumes there is a common ancestor. And likewise the third step assumes the species evolved from that common ancestor. And so consequently the fourth step concludes that DNA regions with greater differences probably underwent positive selection. The conclusion is based on the presupposition that evolution occurred. Venema, as a specialist, knows all this. He knows the entire project presupposes evolution . . .
See the pattern in action, on a related front? KFkairosfocus_{July 29, 2012
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PM: 1: It should be clear (the beavers provide a direct and striking counter example, albeit a limited and non-linguistic one) that you have no good grounds for asserting or implying that humans exhaust the set of possibly intelligent beings. 2: This means that we are left to infer intelligence based on an ostensive definition, with credible cases forming a set of key exemplars against which further cases are assessed on reasonable comparison. 3: The creation of functionally specific, complex organisation (and associated or implied information) seems to be a good candidate for that. 4: In the particular case of coded symbolic linguistic and/or algorithmic info, we are looking at a parallel with the case of humans, and the origin of life. 5; As for the latest attempt to brush aside the implications of the exaggerated claims of "shown," "history," "record," "demonstrate" etc and what hey mean in the known context of the "assumptions" of "evolutionary biology" -- i.e. evidently Lewontinian a priori evolutionary materialism [and I gave these cases to illustrate just how widespread and publicly documented the system is that I am pointing to -- that is this is not a claim that does not have a wider context of warrant, i.e. what is happening here is what we should EXPECT, given what is going on in the wider context . . . your attempt to imply red herrings and strawmen fails, and does so in a way that brings your own thinking under question . . . ], I can leave the judgement on circularity to the same basis I did with the Marxists: the informed, concerned onlooker who has to deal with the potential consequences of such ideological factions gaining and holding power. 6: In short, your collective behaviour as an institutionalised school of thought has forfeited the benefit of the doubt. Those who would play politics to radically redefine science in the teeth of common good sense, the logic of induction and history, then use political pressure to force feed such to children in school under penalty of failure and threats of exclusion from employment and access to higher education do not have any reasonable benefit of the doubt. The linked specifically indicts the US NAS and NSTA, and the silence (= implied consent) for several years in wider circles carries a much more serious import. (IP, see some of what I mean about some very familiar partyline conformity tactics?) 7: FYI, what I did was to compare a good case of a conservative timeline model (star clusters in light of the HR diagram and the physical models of stellar dynamics) with the track record (KNM ER 1470 is a case that is particularly relevant) and problems of geodating that show institutionalised question-begging and ideological conformity to a party line. 8: Recall, the problems -- as I discussed in linked materials you have never referenced in your discussions go up to and include the "star" technique, concordant isochrons. And such points of concern appear in the relevant technical literature. In short, we must never confuse the model timelines of the past of origins with the actual but unobserved past regarded as factually known or practically so. 9: In light of the problems with such dating, I have reasons to distrust claimed concordant climate timeline reconstructions. 10: Further to all this, you have never proffered dynamics and empirically warranting observations adequate to show the origin of language-using, credibly reasoning humans from some chimp-like ancestor in 6 - 10 MY, through in effect CV + DRS --> DWM = evo, in light of challenges on ability to create information that is specifically functional and complex, and to fix same in populations in the relevant window given reasonable mutation rates, limits, and generation times, with population levels that are reasonable. (I have used the whale several times as a relevant parallel.) 11: instead, what has consistently come across is that the institutionalised assumption of evolutionary materialism sets a context in which something like the darwinian mechanism in effect must have happened, and so any evidence in hand (which does not amount to something adequate to answer the issues just summarised) has been read in light of the system. Through the eye of Darwinian faith, so to speak. 12: All of this, in a context, where we cannot observe the remote past. And indeed your attempt to compare the jury is still out case of the Higgs boson, simply showed the gap in observability and firm grasp of relevant dynamics between the two cases. KFkairosfocus_{July 29, 2012
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KF - re 85 above: You made specific claims about circularity in Schultz et al., and now do not appear to be able to support them - or at least you have not addressed these in #85. Instead you opted to discuss Richard Lewontin, Wikipedia and a definition of circularity. Everything except Schultz et al., you might say. Let me remind you that claimed: a) it is circular to use dated hominin fossils to estimate a timeline for evolutionary change in the hominin lineage b) it is circular to use palaeoclimatic reconstructions to infer a role for climate in any of the major changes on this timeline. You have not claimed that any such estimations should be taken with a grain or two of salt because of the potential for error in them (which they should), but that they are decidedly circular.paulmc_{July 28, 2012
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KF -> is that a yes?paulmc_{July 28, 2012
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Indium, You're confused. An argument is circular when the conclusion itself appears as one of the premises. I think what you mean to say that the argument begs the question. For example you say that the premise that all FCSI is a result of design is not known when it comes to biology. It would be a case of begging the question when the premise is presented without arguing for it when it is that premise which is in question. But thats what the whole ID movement is about. To show that material processes are incapable either in principle or in the time available to account for the FCSI in question. Yet the FCSI is there. So if not natural processes then what else can account for it? Thats what the whole ID program is about. It doesnt beg the question since its been arguing its premises from the very beginning. Whether it has been successful or not is a whole nother question.kuartus_{July 28, 2012
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PM: 1] How many cases of digitally coded algorithmic or linguistic information of beyond 500 bits or the equivalent have been observed to have been caused by unintelligent causes tracing to undirected forces of chance and/or mechanical necessity? 2] How many such cases have been observed to be produced by intelligent causes? 3] Have you or any other party got an empirically warranted, defensible explanation that on such non-intelligent forces, successfully accounts per a detailed explanation for the spontaneous origin of gated, encapsulated metabolic automata using von Neumann self replicators (and thus digitally coded information), i.e. the living cell? KFkairosfocus_{July 28, 2012
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KF:
It is the conclusion from the real investigation, and grounds a provisional but empirically reliable (per, billions of test cases) generalisation. Namely, that such FSCO/I is a reliable sign of intelligent design.
I haven't been following this part of thread very closely - when you say billions of test cases do you mean the billions of items that humans have designed (plus beaver dams)?paulmc_{July 28, 2012
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F/N: let's make the matter a bit more specific. Taking in the scope of our solar system (our practical universe so far as significant chemical interactions are concerned), with 10^57 atoms, and about 10^17 s as time available, with the fastest chemical interactions being about 10^-14 s (and organic ones far slower as a rule), then:
a --> The number of configurations for 500 bits [2^500 ~ 3.27*10^150] is such that, at chemical interaction rates, the maximum sample size is comparable to a one straw sized sample of a cubical hay bale 1,000 LY across; the thickness of our galaxy. b --> If we were to set such up centred on the earth and pull a straw-sized sample at random just once, with maximum likelihood, we would get a sample of the overwhelming bulk of the distribution, straw. c --> This is the needle in the haystack problem. d --> Now, functionally specific and complex objects require well-matched components organised in specific was to work. That is, they depend on particular and special configs, that are identifiable by the criterion of whether or not they are workable. e --> They come from special, unrepresentative, narrow zones of configuration spaces. (NB: By reducing an complex entity to a nodes and arcs diagram, it can be represented by a digital string, similar to what say drawing software does.) f --> That is why the needle in the haystack analysis is relevant. g --> this may be represented in an expression: Chi_500 = I*S - 500, bits beyond the solar system threshold. h --> I is an information content metric deducible from a nodes and arcs representation, and S is a dummy variable that defaults to 0 [not functionally specific, and only where there is a positive objective reason for holding otherwise would it trip to 1]. (NB: Going to 1,000 bits would address the observed cosmos as a whole.) i --> In effect the FSCO/I inference is that where Chi_500 goes to 1 we may comfortably infer that an object was designed, on its complex functional specificity.
I give this summary, to highlight the reasoning for the above. I trust we may now return tot he main focus for this thread. KFkairosfocus_{July 28, 2012
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Indium: Why are you insisting on erecting a willful misrepresentation, in the teeth of having been corrected several times? You say:
In the logic used by kf, he starts with the premise that all objects we know that show FSCI (or whatever) are designed.
You know or full well should know (and it has been repeatedly said here in this thread and before) that there is an inductive inference from the commonplace OBSERVATION that functionally specific, complex organisation and associated information are routinely and only observed to be the product of designers. Yes, that includes humans, and beavers [as in designers and builders of site-specific gravity and arch-dams), and probably others too. This is multiplied by the ANALYSIS on searching for needles in haystacks on limited resources, i.e. the sampling theory result that shows why chance based random samples normally capture the bulk of a distribution not special, separately describable and rare members or clusters thereof. (As in, the analytical basis of the theory of hypothesis testing.) Such an inductive conclusion is NOT a premise -- a start-point for an argument. It is the conclusion from the real investigation, and grounds a provisional but empirically reliable (per, billions of test cases) generalisation. Namely, that such FSCO/I is a reliable sign of intelligent design. It is on this basis of examining the divergent characteristic patterns produced by mechanical necessity (natural regularities AKA laws of nature), chance circumstances (chance bases stochastically distributed contingencies), and designers, that we use FSCO/I as a sign that points to design as cause, even in cases we are interested in where we did not or could not separately observe the actual causal event. Such cases include those of origins science, where once we see credible traces form that causal processes and tha these include FSCO/I, we have good grounds to infer inductively that these are designed. You have willfully suppressed the underlying investigatory work, and present an inductively warranted conclusion as though it were an unwarranted question-begging premise. That is, at this stage intellectually irresponsible and dishonest. For, you are speaking in willful disregard of the truth, in the hope that that which is untrue would be perceived as true to your advantage. There is a name for that, and it is not a pretty word. Kindly, stop it. If you disagree with the inductive process, or have a good case where in our observation chance -- the other source of high contingency outcomes -- by itself or with mechanical necessity without intelligent guidance or intervention routinely produces FSCO/I that would be a different story. Plainly, you and others like you do not -- or this would be trumpeted all over the Internet. (Onlookers, many attempts have been made, from canals on Mars as sketched to simulations of pendulums, levers and gears that magicaslly turn into time-keeping clocks. Only, in each case, design is involved. If canals had been seen on Mars that would have been a sign of a Martian civilisation, as it was, the drawings were obviously designed to represent what the astronomers THOUGHT they saw. Similarly, the begged questions of the source of the simulation world and what is required to say make an accurate gear -- a 3-d very complex object not a convenient 2-d simulation, and even the required base plate that would have to be a precision object, were overlooked. And so on. In that context of not being able to throw over the induction on evidence, your resort to a willfully false strawman misrepresentation in the teeth of repeated correction speaks volumes, and none of it to your advantage. Please stop it. KFkairosfocus_{July 28, 2012
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Indium- If you do not like what KF says nor the design inference well please, step up and demonstrate that blind and undirected processes (not "evolution" whatever that is) can produce what either a biological organism or a multi-protein machine that requires more than two protein-to-protein binding sites. Ya see it is the failure of your position plus our knowledge of cause and effect relationships that allows us to reach a design inference wrt the universe and biological organisms. The criteria for inferring design in biology is, as Michael J. Behe, Professor of Biochemistry at Leheigh University, puts it in his book Darwin ' s Black Box: "Our ability to be confident of the design of the cilium or intracellular transport rests on the same principles to be confident of the design of anything: the ordering of separate components to achieve an identifiable function that depends sharply on the components.” He goes on to say: ” Might there be some as-yet-undiscovered natural process that would explain biochemical complexity? No one would be foolish enough to categorically deny the possibility. Nonetheless, we can say that if there is such a process, no one has a clue how it would work. Further, it would go against all human experience, like postulating that a natural process might explain computers.” So there ya go, have at it...Joe_{July 28, 2012
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kuartus: In the logic used by kf, he starts with the premise that all objects we know that show FSCI (or whatever) are designed. He bases this analysis on stuff that has been build by humans (and beavers! :-)). He never proves that this also true for biological objects that have a completely different history and for which no designer is known or even plausible. So he assumes his conclusion in form of an extremely weak inductive argument. Therefore it´s circular. By the way, there are other instances that might show that kfs premise is not valid and which therefore require additional checks (for example ev and avida). That does not mean that all inductions/deductions are wrong. But in the real work you have to be careful and you need to be able to support your inductive argument with evidence. If, for example, kf could prove that FCSI must *necessarily* always be introduced by a designer, then yes, he would have a case and the circularity is broken. But again, this is exactly the question we are discussing: Can evolution lead to FCSI (whatever that is)? If he would have additiional evidence for his designer, maybe a time, a method, specific predictions, or whatever else, his inductive argument would be strengthened. He has almost nothing to support his theory, just very weak attacks of evolutionary biology. Therefore, kfs reasoning remains circular. He begs the question. And I think your logic is wrong, not mine. For a start, you may look up the difference between deductive and inductive reasoning.Indium_{July 28, 2012
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BT: In your haste to label and dismiss, with the neat little dismissive Dawkins pigeonholes -- ignorant, stupid, insane or wicked -- it has evidently not dawned on you that I am not a Young Earth Creationist, but a design thinker on origins -- i.e. my evaluations are not constrained by debates and views over exegesis of scripture? (Did you see or pay attention to the contrasted case of dating our galaxy per the HR plot and the H-ball model for star physics? As in branch points of stellar cluster HR diagrams that give reasonable age estimates with a minimum of questionable assumptions. I have a lot of respect for those dates. They may be wrong, as there are factors we do not know, and we were not there to see the actual past, but to accept these provisionally on IBE is very reasonable. I just emphasise that all of these are model not actual past timelines. In fact, if last Thursday the cosmos were created in an instant complete with our memories of the past, it would be empirically indistinguishable. We have to make a worldview level choice -- best, per comparative difficulties -- to accept a worldview. So, instead of begging big questions, face them.) I am fully capable of seeing the difference between cautious and provisional models on stellar life cycles and exaggerated claims or implications of factual status on a circular geodating process riddled with subjectivity and institutional ideology. I have repeatedly pointed to the case of KNM ER 1470, which now that I know the behind the scenes story that was not reported in the Sci mags and newsmags with the lavish displays in my days as a 6th former and college student, leave me with a distinctly sour taste in my mouth. Kindly, take time to work through the serious concerns that are there on reconstructions of the remote past before trying to label and dismiss in future. I suggest here on in context for a start, noting the contrast with cosmology and astrophysics. (I do note that as an inadvertent testimony to what I am highlighting there are YEC physicists who propose a young earth in a 15 BY cosmos model pivoting on a time freeze.) KFkairosfocus_{July 28, 2012
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Mr. Focus, Why don't you just come out and say you're a Young Earth Creationist? Seriously, all this (verbose) dancing around! You sound like Ken Ham; except Ham manages to ask "were you there?" in three words - you take 3000. Don't worry Mr. Focus, there's room under ID's big tent.Bartax_{July 28, 2012
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paulmc:
You seem surprised that people working within an evolutionary paradigm use evolutionary assumptions.
But if you keep assuming the very things that need to be tested, what good is that?Joe_{July 28, 2012
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PM: Blandly dismissive "who are you going to believe, me or your lyin' eyes" declarations do not remove the facts on the table as already given. Look, again, at the language used in the abstract cited by you as decisive. Then, contrast how we inherently cannot observe the remote past of origins, and the use of language that implies that we have such in hand as facts, i.e. "show," "history," "demonstrate," "record" etc is inherently question begging -- only fools dispute facts, so if something is effectively decreed and [improperly] accepted as a fact . . . -- and a case of the fallacy most blatantly expressed in the all too common assertion that equates the degree of confidence in such to that in the observed orbiting of the planets around the sun. Your attempt above to try to compare to the CERN provisional -- and cautiously stated -- results on the Higgs boson only served to underscore how there is a ladder of empirically accountable dynamics that gives us high confidence in the CERN results (the issue is WHAT was there, not if it was there at a pretty well identified window of time). By contrast, neither the ladder of genetic mutations fixed in sewquence in pops, nor the full chain of fossils alleged to show human ancetry are t5here. And in particular, we do not have the ladder of changes and the pop genetics that allow duly cautious conclusions that we have a transitional sequence that shows the actual origin of human language and reasoning capacity. In short, we have exaggerations, pivoted on a clear a priori assumption or assertion of evolutionary materialism as dominant frame of thought. That way, there HAS to be some sort of darwinism-like process so one is in reality only looking for indicators of what it was. Lewontin put the matter this way:
. . . It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated . . . [["Billions and billions of demons," NYRB, Jan 1997. (cf. here on for a longer, annotated cite that shows that I am not "quote mining," the usual, too often dishonest deflective accusation.]
This massive begging of questions has literally been written into the very definition of science and its methods as taught to students in recent cases, e.g. here is the US science teachers association board, 2000; NSTA (from the same place as just linked):
The principal product of science is knowledge in the form of naturalistic concepts and the laws and theories related to those concepts . . . . Although no single universal step-by-step scientific method captures the complexity of doing science, a number of shared values and perspectives characterize a scientific approach to understanding nature. Among these are a demand for naturalistic explanations supported by empirical evidence that are, at least in principle, testable against the natural world. Other shared elements include observations, rational argument, inference, skepticism, peer review and replicability of work . . . . Science, by definition, is limited to naturalistic methods and explanations and, as such, is precluded from using supernatural elements in the production of scientific knowledge. [[NSTA, Board of Directors, July 2000.]
Naturalism, of course is a philosophy that embeds evolutionary materialism as its origins narrative. So, the very definition of science is being distorted, in the teeth of history, reason and common good sense. Then, the predetermined materialist circle of argument on origins is presented as fact. Indeed, Wikipedia as at August 2010 had a clanger on that point:
. . . When scientists say "evolution is a fact" they are using one of two meanings of the word "fact". One meaning is empirical, and when this is what scientists mean, then "evolution" is used to mean observed changes in allele frequencies or traits of a population over successive generations. Another way "fact" is used is to refer to a certain kind of theory, one that has been so powerful and productive for such a long time that it is universally accepted by scientists. When scientists say evolution is a fact in this sense, they mean it is a fact that all living organisms have descended from a common ancestor (or ancestral gene pool) [8] even though this cannot be directly observed. [["Evolution as theory and fact," coloured emphasis added. Acc: Aug. 7, 2010.]
In case there is need to clarify what circular argument and begging the question mean, here is the Fallacies page IEP:
Begging the Question A form of circular reasoning in which a conclusion is derived from premises that presuppose the conclusion. Normally, the point of good reasoning is to start out at one place and end up somewhere new, namely having reached the goal of increasing the degree of reasonable belief in the conclusion. The point is to make progress, but in cases of begging the question there is no progress . . . Circular Reasoning Circular reasoning occurs when the reasoner begins with what he or she is trying to end up with [and moves in an uninformatively small circle of reasoning]. The most well known examples are cases of the fallacy of begging the question . . .
By contrast to this, a case of inference to the best explanation, the underlying form of inductive logic in scientific reasoning, seeks to unify a cluster of otherwise puzzling facts (Things directly known to be so, typically by observation, experience or credible record) by comparing the difficulties of alternative possible explanations and then based on reasonable criteria may conclude that one is best on factual adequacy, coherence and balance of explanatory elegance -- neither ad hoc nor simplistic. All, being provisional, as Newton so aptly summarised. Such a process is not compatible with stacking the deck by cherry picking facts [i.e. the lack of observationally warranted CV + DRS --> DWM dynamics to account for origin of body plans etc is significant, as is the lack of population genetics to support such, cf. here again on the whale example, which is similar to the problem for origin of human language and rational faculties) or improperly injecting a priori constraints on otherwise reasonable explanations [such as evolutionary materialism as we see with Lewontin, US NAS, NSTA, NCSE etc etc], or exaggerating the degree of warrant attaching to a proffered candidate, such as we see with the text of the abstract for the paper you have cited. In short, what we have is the a priori imposition of a materialist circle of thought that immediately implies that here must have been an evolutionary process for origin of life from chemicals in some warm little pond or comparable environment somewhere. In such a circle, the degree of warrant acceptable to the high priesthood of the system is of course constrained by the underlying a prioris. And of course they can then plead longstanding consensus as though that warrants conclusions tot he point where they can suggest that they can call these things facts. All that tells us who look on with a critically aware eye is that the system is under ideological thralldom to a priori evolutionary materialism, a system of thought that is by reduction to self referential absurdity, inherently and necessarily false. (Cf., here.) And inescapably amoral also. (I link these for the onlooker primarily, as it is obvious from what has already transpired that you are not going to do more than glance at a linked discussion then brush it aside.) Philip Johnson, in his reply to Lewontin, aptly stated the bottom-line:
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." . . . . 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.]
There is no tyranny of the mind more effective at selling a circular system of thought than that of an unconsciously absorbed, social or institutional consciousness backed, a priori system. And that is what evolutionary materialism demonstrably is. KFkairosfocus_{July 28, 2012
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All I was referring to was the use of the word 'observation'. Back to the main issue, neither of your responses address the circularity you claim to have identified.paulmc_{July 27, 2012
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PM: You are now resorting to an attempted turnabout. Can you show me the instruments and observations that on known physics etc, captured a record of the past 3 mn years of human origins? You cannot, the deep past of origins is unobservable. The Higgs boson has been recorded by that standard, here and now. Similarly, the circularity in constructing a model past comes out strongly in exaggerated language of warrant -- the onlooker can see for himself [what do show, demonstrate history and record normally mean], and in a pattern of inference on claimed dynamics allegedly capable of creating the transformation of a chimp like animal into a human in 6 MY, where the dynamics do not have empirical warrant for that and the pop genetics is highly dubious. KFkairosfocus_{July 27, 2012
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F/N: Regarding CERN and a not quite certain "catch" of a Higgs Boson in the predicted 125 MeV energy range:
When CERN announced that they had observed a boson consistent with the Higgs boson, was your first reaction “what do they mean, observed?” Really, all they did was use detectors to record a signal from the putative decay of something. Layers upon layers of assumptions.
1 --> Notice, the implicit promotion of an origins science on a deep, remote, non-repeatable past, with repeatable observations made in the present, with instruments and observers in hand. This is the "it's a FACT like the orbits of the planets" fallacy. 2 --> The trick here of course is that a boson is not directly observed, we are relying on rather elaborate clusters of instruments and software programmed on various operational science theories. 3 --> For just one instance, particle physics often relies on the Lorentz force to set a magnetic field, and then look at particle traces across the field as they curl, which gives a charge/mass ratio on the laws of centripetal force. 4 --> Where also the actual particles are invisible, but they can trigger local effects such as condensation trails in a cloud chamber or bubbles in a bubble chamber or precipitation in a stack of films, down to modern electronic detectors. The physics behind these effects is well known to be empirically reliable. And, the observations are repeatable. 5 --> For instance to teach how a squirrel cage induction motor works, I used to use a sacrificial analogue CRO, and set it to XY mode. The physics of the deflected beam and the screen phosphor that makes its point of impact visible are well tested and reliable. Then I would bring up a bar magnet sideways -- the field is easy to plot or outline with iron filings. 6 --> Lo and behold, it would push it in the way the cross product equation indicated. Then, I would rotate the magnet, showing how the little deflected dot of light is "pulled" along in a circle. The predictions are confirmed, reliably and routinely so. The impact is clear enough that I am willing to risk calibration of a US$ 400 instrument (preferably an obsolete one) to get the point through to students who are otherwise often mystified by the way the induction motor works. and of course, I teach young Physics students the Lorentz force, as the basic law. Then, I teach them how to draw their hands high-noon style with the hand rules and remember that we crank the generator right-handed. Maybe, one of these days, someone ought to make a youtube vid out of it. And the consequences of the insights extend all the way to what is going on at CERN. 7 --> Observe something else: they are NOT yet saying, this is it, as there are some possibilities that need to be further investigated. That essential conservativeness is itself a salutary lesson. 8 --> By contrast, no-one has developed the reliable, repeatable consistent dynamics of darwinian evolutionary change at body-plan emergence level. Including, on the emergence of language. We have no reliable, demonstrated causal mechanism that routinely delivers the level of change required, with the scale of population, on the timeline, with the genetics and reasonable mutation rates. All is inference, loaded up with a priori materialism that predetermines the conclusion that something like this MUST have happened. 9 --> See why I contrasted the estimates of the age of our galaxy in light of the HR diagram, the physics of giant balls of H, and the clusters with breakaways from the main sequence headed for the giants branch? (Note geochronology concerns on institutionalised circularities here on in context.) 10 --> Now, go back above to the issues with the abstract. This is essentially non-conservative, and wants to promote speculative reconstructions to the status of fact. We did not observe the past 3 mn years, we did not have a RECORD of this, we have not SHOWN such, nor have we DEMONSTRATED. And consensus of a school of thought on its assumptions and models and stories are not to be confused with facts. What is truly astonishing and revealing of the damage being done to science, is that we have to go through such in so much detail over and over. Notice, it seems, some are struggling with inductive reasoning. We need to wake up and see what is going on. Finally, notice, we see nowhere in sight a straightforward, properly empirically warranted, epistemologically cautious evolutionary account of human origins, including of language and logic. And meanwhile the self same object ever so strenuously to inferring design on well tested routinely demonstrated signs such as FSCO/I. Sadly revealing. KF KFkairosfocus_{July 27, 2012
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One more time: You haven't demonstrated circularity. All you have done is been hypersceptical about their methods and their word choice. To your 12 points about the abstract: 1 --> beyond that point, facts have gone out the window . . . They didn't claim anything about facts. 2 --> abuse of a word, history properly denotes reconstruction of the OBSERVED past based on credible record and supplemented by other investigations Rubbish. History, like many words in English, has multiple meanings. It is clear what they mean. 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 They didn't say observation they said understanding; they didn't refer to a mechanism. 4 --> inadvertently key word There was nothing inadvertent about their use of 'estimate'. They understand they are making estimates here. 5 --> Just what, per the basic limitations of your ability to observe the remote past beyond record, you could not do Are you seriously claiming we cannot 'show' (all they mean is infer) anything that uses palaeoclimatic or fossil records? 6 --> the t-line is reflective of all sorts of circularities and is a theory-dependent model framework not a factual observation They did not say 'factual observation'. Asserting that the timeline is circular is not sufficient as an argument. 7 --> Ditto Ditto. 8 --> You have no such capability to demonstrate anything 'Demonstrate' again has a clear meaning in the circumstances. 9 --> Yet more circles of inference within the system Palaeoclimatic reconstructions are independent of the hominin fossil record. I fail to see the circularity and you have done nothing to demonstrate it. 10 --> i.e. "consensus" an appeal to collective authority not a fact Actually, very much the opposite in the context. 10#2 --> assertion, not fact, and mechanism is nowhere to be seen They didn't unpack this in the abstract, and they assume the reader has some familiarity with the literature. 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 assumption is yours. Putting these things in the same sentence does not make them all the same.paulmc_{July 27, 2012
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PM: The problem is not with assumptions being present in all arguments, but with circularity and assertions that cannot be so. We cannot show the remote past of origins, we cannot speak of records put up on the shelf with historical records, and the like. Let me clip 41 above again, for those who came in late (the links and emphases are there): ______ >>[PM] actually touches on the case of origin of human language [which I had pointed to]:
[PM:} 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 [from a Royal Society paper] 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 points where a theoretical scheme has been inserted and improperly assigned a degree of warrant that it cannot have is astonishing. >> ______ See the problem, and notice how you are lining up next to another objector who evidently does not understand the inductive logic of science? I'll let that stand for now. That is what you have to face. KFkairosfocus_{July 27, 2012
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KF:
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.
You seem surprised that people working within an evolutionary paradigm use evolutionary assumptions.
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.
Indeed - conclusions in science are always provisional. The best current explanation for a series of fossils that palaeontologists consider part of the hominin lineage that show a progression in cranial capacity over time (the progression being indicated by dating of those fossils) is that the hominin lineage experienced a cranial expansion, with a corresponding increase in brain size. Because of the correspondence with archaeological records at the end of this period of expansion, the conclusion is that our large, metabolically expensive brain was implicated in the emergence of modern language. Other interpretations might be possible, but their one is the simplest conclusion that is consistent with the hominin fossil record and a larger body of theory. Again, they're working within a paradigm, as happens in every single field of science and is necessary to make and test predictions. That they don't restate the whole paradigm in their abstract is not something sinister even if you, the outsider, see it differently. When CERN announced that they had observed a boson consistent with the Higgs boson, was your first reaction "what do they mean, observed?" Really, all they did was use detectors to record a signal from the putative decay of something. Layers upon layers of assumptions. Of course, following their model they could make the prediction that if the Higgs exists it would occur and then decay under certain circumstances within a certain mass range, which they recreated and then detected.paulmc_{July 27, 2012
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F/N: Newton's rules of scientific reasoning from Principia:
Rule I [[--> adequacy and simplicity] We are to admit no more causes of natural things than such as are both true and sufficient to explain their appearances. To this purpose the philosophers say that Nature does nothing in vain, and more is in vain when less will serve; for Nature is pleased with simplicity, and affects not the pomp of superfluous causes. Rule II [[--> uniformity of causes: "like forces cause like effects"] Therefore to the same natural effects we must, as far as possible, assign the same causes. As to respiration in a man and in a beast; the descent of stones in Europe and in America; the light of our culinary fire and of the sun; the reflection of light in the earth, and in the planets. Rule III [[--> confident universality] The qualities of bodies, which admit neither intensification nor remission of degrees, and which are found to belong to all bodies within the reach of our experiments, are to be esteemed the universal qualities of all bodies whatsoever. For since the qualities of bodies are only known to us by experiments, we are to hold for universal all such as universally agree with experiments; and such as are not liable to diminution can never be quite taken away. We are certainly not to relinquish the evidence of experiments for the sake of dreams and vain fictions of our own devising; nor are we to recede from the analogy of Nature, which is wont to be simple, and always consonant to [398/399] itself . . . . Rule IV [[--> provisionality and primacy of induction] In experimental philosophy we are to look upon propositions inferred by general induction from phenomena as accurately or very nearly true, notwithstanding any contrary hypotheses that may be imagined, till such time as other phenomena occur, by which they may either be made more accurate, or liable to exceptions. This rule we must follow, that the arguments of induction may not be evaded by [[speculative] hypotheses.
Of course, this is the same sense of hypotheses in Opticks, query 31. The interested onlooker may wish to see here in the ongoing ID foundations series, and ponder the comparative case of deer tracks. It seems some fur-pants wearing ancestors wish to have a word or two with Indium.kairosfocus_{July 27, 2012
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Indium: First, please read the primer on basic sci methods and logic, here. Maybe this on the underlying epistemology will help too. If you are objecting to the logic I am using as circular, you are objecting to the logic of science -- especially origins science -- as circular. FYI, it is based on broad and reliable observations backed up by the needle in haystack analysis that we have a right to infer (provisionally, as in all of science) that functionally specific, complex organisation and associated information are signatures of design. Just as, on repeated, reliable observations we know that water boils at 100 degrees under certain conditions, or that energy is conserved or that the second law of thermodynamics is so. I have already pointed out that we are dealing with an induction that is empirically based. Let me cite Newton en bloc, this time from Opticks, Query 31, as you plainly have not looked him up when I linked a cite from Principia, putting in paragraphing to make it easier to follow:
As in Mathematicks, so in Natural Philosophy [~ Physics], the Investigation of difficult Things by the Method of Analysis, ought ever to precede the Method of Composition.
This Analysis consists in making Experiments and Observations, and in drawing general Conclusions from them by Induction, and admitting of no Objections against the Conclusions, but such as are taken from Experiments, or other certain Truths.
For Hypotheses are not to be regarded in experimental Philosophy. And although the arguing from Experiments and Observations by Induction be no Demonstration of general Conclusions; yet it is the best way of arguing which the Nature of Things admits of, and may be looked upon as so much the stronger, by how much the Induction is more general. And if no Exception occur from Phaenomena, the Conclusion may be pronounced generally. But if at any time afterwards any Exception shall occur from Experiments, it may then begin to be pronounced with such Exceptions as occur. By this way of Analysis we may proceed from Compounds to Ingredients, and from Motions to the Forces producing them; and in general, from Effects to their Causes, and from particular Causes to more general ones, till the Argument end in the most general . . .
This is probably the root source for the "method" you would have been taught in primary school, and would have been further trained in in High School and College. So, recognise: FSCO/I is observed routinely and reliably to trace to intelligent cause, human and otherwise. In addition, we have needle in haystack analysis reasons to see why this should be so, similar to the statistical arguments that ground the second law of thermodynamics. On that double ground of inductive generalisation and related needle in haystack analysis, we have reason to infer that FSCO/I is a reliable sign of design as cause. So, when we observe this in cases that we do not have direct access to the causal events, we trust the sign. Where also as in all cases, such an inference to best explanation inductive conclusion (yes, IBE is a form of inductive argument) we follow Newton in his provisionality. If you want to dismiss such a provisional but empirically reliable inference on reliable signs, then if you are consistent you will cast away a great deal of science, management, forensic procedure and day to day common sense analysis. But of course, you don't, it is only in this case that you do not like that you object. And in a case where there is REAL circularity, as I pointed out from the Royal Society paper, you have been silent. This is selective hyperskepticism. I think this has been pointed out to you over and over. As for beavers, have you so soon forgotten that above you said: "Your billions of testcases have all been build by humans"? The beavers are a direct factual counter to that. With illustrated cases in point of building arch and gravity dams based on circumstances in a stream. (And in case you missed my AI leanings, I take them as a model for building reasonably autonomous construction robots. Or at least a beginning. Remember, across this century I want us to build self-replicating industrial networks capable of supporting in the first instance third world development then onwards solar system colonisation. And after that . . . ) I trust you will take time to think this through before coming back for more. KFkairosfocus_{July 27, 2012
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Indium, obviously logic isn't your strong suit. Entailment doesn't count as circular reasoning. If that was the case then every valid deductive argument would be a fallacy. A circular argument occurs only when the conclusion is identical with a premise. The design argument you call circular is not circular since the conclusion is not one of the premises of the argument. But since the argument is logically valid, the conclusion is entailed by the premises. Go study up on your logic.kuartus_{July 27, 2012
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kf: How do beavers get you out of the circular reasoning? Or do you think they change the fact that we have a large class of objects (the biological world), for which you can´t assume design in our premise? How so? Beavers inventing DNA billions of years ago? But my original question was: How are dating techniques circular? Could you sum it up in a few sentences? Just a very short summary would be enough, thanks.Indium_{July 27, 2012
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F/N: On scientific fights in paleontology:
SVANTE PÄÄBO: As an outsider to paleontologists, I'm often rather surprised about how much scientists fight in paleontology. And I am thinking about why that is the case. Why do we have less vicious fights in molecular biology, for example? I suppose the reason is that paleontology is a rather data-poor science. There are probably more paleontologists than there are important fossils in the world. To make a name for yourself is to find a new interpretation for those fossils that are extant. This always goes against some earlier person's interpretation, who will not like it very much. There are many other areas of science where we can agree to disagree, but at least we often generally agree on what data we need to go out and collect to resolve the issue and no one wants to come out too strongly on one side or the other because the data could, in a year or two, prove you are wrong. But in paleontology you can't decide what you will find. You can not in most cases go out and test your hypothesis in a directed way. It's almost like social anthropology or politics — you can only win by somehow yelling louder than the other person or sounding more convincing. That's perhaps the reason why paleontologists get so heated in these fights.
kairosfocus_{July 27, 2012
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Larry Moran is using gene duplications- gene duplication followed by function changing mutations is evidence for ID- read "Not By Chance" by Dr Lee SpetnerJoe_{July 27, 2012
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Indium: You are wrong. The test cases have been built by intelligent beings (not all of whom are human, cf here as was discussed at UD some time ago and which I believe was brought to your attention previously but ignored), and generally speaking we have no good reason to infer or assume that humans exhaust the possibilities for intelligence. In short, you are injecting an irrelevant criterion to object. Indeed, in the case of OOl, as was also discussed and objected to on relevance [which it here shows in spades!], we have encapsulated, metabolic automata with von Neumann self replicators making explicit use of digitally coded symbolic information. Right at the foundation of cell based life.) Sorry, this predictable talking point fails. KFkairosfocus_{July 27, 2012
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Your billions of testcases have all been build by humans. You can´t assume that all FCSI systems that we know of have been designed when we know of another set of billions of things (biology) where it is unclear if they have been designed.Indium_{July 27, 2012
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F/N: This is a bit of what Luskin may be talking about.kairosfocus_{July 27, 2012
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