Engineer says, the atom has a designer. Trolls disagree.

Jerad/Clavdivs “What about Psittacosaurus? Protoceratops? Chasmosaurus? Monoclonius? Styracosaurus? Pentaceratops? Torosaurus? These are all ceratopsian dinosaurs like Triceratops, one of the largest groups of dinosaurs from the Cretaceous, showing fairly finely graded variations in the rostrum bone, beak, frill and horns – e.g” What about them really? Would you suggest that any two of these are in a direct line of transition, would you have said that any two of these dinosaurs were able to reproduce? What I was saying is that when you look at the fossil record for evidence of gradual change over time, or a direct line of transition as even one creature develops in this manner, you don’t find any. I am therefore suggesting, and I think quite plausibly too, that what you have in the fossil record are complete body forms. I thing KF has summed it up very well in some of his latter posts on this thread. As being someone who never believed in God, and always accepted evolution, no one was more suprised than me to discover that I was wrong on both counts. And how fantsatically liberating that has been. You should try laying aside your Darwinian specs and have a right good look at the evidence. It may just do the same for yo PPeterJ

July 12, 2012

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KF,

You know, or should know that all along, I have been discussing the darwinian tree of life, and its incrementalist framework;

Absolutely, it's your view of that I want you to clarify.

indeed, that is what can be found in the excerpts from Gould I have used repeatedly here and in the linked longer discussion at IOSE. So, the side issue — and notice, having been corrected in more than enough details you went right back to the distractor as though merely repeating a caricature and pretending that an issue has not been clarified puts it back on the table . . . — is and has been from the outset, the transitional forms relative to key cases of such claimed transformation, or in more popular terms, missing links.

It's because I'm not sure how you are using certain terms and that you seems to be at odds with some of what Dr Gould has said.

That, as Gould repeatedly summarised, is that there is an overwhelming absence of the transitional sequences.

But as has been pointed out, Gould himself said that the fossil record is rife with transitional forms. And he pointed out that some of his statements had been misinterpreted. Which is why I'm asking you to clarify your meanings so that we're all clear what you are saying.

The very fact that you have chosen to try to turnabout a burden of proof and pretend that there is an inadequate definition on my part for such transitional sequences, is itself eloquent testimony to the absence. For, had you these in hand, there would obviously have been a triumphant listing

I'm not sure what you are getting at. I just want to know, and I've given a particular sequence for you to work with, what forms you consider transitional and what you consider complete. Not what Gould thought or what I think or what CLAVDIVS thinks. What you think.

The very fact that you have chosen to try to turnabout a burden of proof and pretend that there is an inadequate definition on my part for such transitional sequences, is itself eloquent testimony to the absence.

No attempt at turnaround, I just want you to be specific on what you mean by transitional and complete body plans. And in the case of transitional body plans how your definition compares with Dr Gould's.

Again, where is the lead up to the general body plan, and the lead out to a farther along one, climbing up a branch to an alleged “higher” life form?

Ah, what constitutes a general body plan? You mean like mammals? Or primates? Or . . . .

I trust this makes the pivotal issue sufficiently plain, and why I see no point in further entertaining distractors maintained even after I took a fair amount of time to already address and correct them. After a couple of rounds like that, it becomes evident that side-tracking was the rhetorical object, not clarity.

I just want to know what you consider to be transitional forms/body plans and what are complete forms/body plans. If you answer the question we'll better understand your point of view.Jerad

July 12, 2012

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F/N: I see an attempt to draw us out on a further tangent regarding triceratops and kin. I will simply say, what is the vertical transformational significance of variations beyond say those of the deer family or say the pattern of diversity we may see across mastodons and elephants, or the Finches of the Galapagos? Again, where is the lead up to the general body plan, and the lead out to a farther along one, climbing up a branch to an alleged "higher" life form? I trust this makes the pivotal issue sufficiently plain, and why I see no point in further entertaining distractors maintained even after I took a fair amount of time to already address and correct them. After a couple of rounds like that, it becomes evident that side-tracking was the rhetorical object, not clarity.kairosfocus

July 12, 2012

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Coaudius: Sorry, when Gould makes a plain statement in the per reviewed literature in 1977 and still sustains it 25 years later in his last technical work, two months before he died, this is not something he has retracted or corrected. It is something he has maintained, and it is consistent with his spending the intermediate decades in significant part working on an alternative theory of evo that accounts for the missing transitional sequences. And, to further demonstrate the point that the "vertical," body form transformational transitional sequences -- which we should be tripping over every tie we go out the front door -- are conspicuously absent in the real fossil record, observe the rhetorical pattern of those who have objected to my point. they have not provided us the lists of abundant, unquestionable sequences. Nope, they are trying to resort to Darwin's IOU that the fossil record was but poorly explored and was imperfect. The fossil beds of the past 4 or so By on the conventional timelines have been explored for 150 years. Nay, scoured. Billions of fossils seen in situ, millions in museums, 1/4 million+ fossil species. And the transitionals are simply not there to be seen after all that effort. In short, Gould's summary as I have given it is accurate. His rhetorical retractions once creationists had taken up his writings, are what are suspect, if anything. The evidence is that the cross section is an adequate sample to have captured the general pattern. Just, it is not what we expected on Darwinian models and especially the tree of life with incremental variation without limit to form the full tree across time. the tree is still used, but the plain truth is the connexions between forms are inferred and projected unto the observations, they are not direct from observations. Darwinian gradualism in body plan formation -- never mind the mosaics and the occasionally headlined "missing links" -- is an intellectual construct, not an observational fact. KF PS: Onlookers may want to look at Paul Nelson's presentation here.kairosfocus

July 12, 2012

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Jerad: Pardon, but after a substantial matter has been pointed out and the mischaracterisation has been corrected more than once, it cannot any longer be a mere mistake if stuck with. You know, or should know that all along, I have been discussing the darwinian tree of life, and its incrementalist framework; indeed, that is what can be found in the excerpts from Gould I have used repeatedly here and in the linked longer discussion at IOSE. So, the side issue -- and notice, having been corrected in more than enough details you went right back to the distractor as though merely repeating a caricature and pretending that an issue has not been clarified puts it back on the table . . . -- is and has been from the outset, the transitional forms relative to key cases of such claimed transformation, or in more popular terms, missing links. I have long since pointed out in more than sufficient details why transitional forms should have dominated the history of life, if CV + DRS --> DWM were the driving force behind it. For 150 years, on the contrary, despite the fairly common spectacle of headlined icons (as a rule, backtracked on on further studies, up to cases over the past several years), with 250 k+ fossil species in hand, millions of examples in museums and billions seen in the field, from the major sections of the geologic column and around the world, there is good reason to hold that -- for decades -- we have seen the general pattern of life in the past of origins. That, as Gould repeatedly summarised, is that there is an overwhelming absence of the transitional sequences. The very fact that you have chosen to try to turnabout a burden of proof and pretend that there is an inadequate definition on my part for such transitional sequences, is itself eloquent testimony to the absence. For, had you these in hand, there would obviously have been a triumphant listing.But the horse sequence -- the traditional capital example no 1, is subject to the observations that we have dog-sized mini horses today, three toed horses are still occasionally born, and that three and one toed horses come from the same strata. That is why the sequence that used to [dis?]grace textbooks for generations has fallen out of use in recent years. South Korea is catching up as we speak. The apes to man sequence has fallen on hard times, and the recent whales sequence has a serious problem accounting for perhaps 50,000 transitions from cow-like to whale-like, with relevant population scales and reproduction rates. And so on. Just to underscore what I am talking about, let me excerpt an early ID-friendly peer reviewed paper by Loennig, "Dynamic genomes, morphological stasis, and the origin of irreducible complexity" (2004):

examples like the horseshoe crab are by no means rare exceptions from the rule of gradually evolving life forms . . . In fact, we are literally surrounded by 'living fossils' in the present world of organisms when applying the term more inclusively as "an existing species whose similarity to ancient ancestral species indicates that very few morphological changes have occurred over a long period of geological time" [85] . . . . Now, since all these "old features", morphologically as well as molecularly, are still with us, the basic genetical questions should be addressed in the face of all the dynamic features of ever reshuffling and rearranging, shifting genomes, (a) why are these characters stable at all and (b) how is it possible to derive stable features from any given plant or animal species by mutations in their genomes? . . . . A first hint for answering the questions . . . is perhaps also provided by Charles Darwin himself when he suggested the following sufficiency test for his theory [16]: "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down." . . . Biochemist Michael J. Behe [5] has refined Darwin's statement by introducing and defining his concept of "irreducibly complex systems", specifying: "By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning" . . . [for example] (1) the cilium, (2) the bacterial flagellum with filament, hook and motor embedded in the membranes and cell wall and (3) the biochemistry of blood clotting in humans . . . . One point is clear: granted that there are indeed many systems and/or correlated subsystems in biology, which have to be classified as irreducibly complex and that such systems are essentially involved in the formation of morphological characters of organisms, this would explain both, the regular abrupt appearance of new forms in the fossil record as well as their constancy over enormous periods of time. For, if "several well-matched, interacting parts that contribute to the basic function" are necessary for biochemical and/or anatomical systems to exist as functioning systems at all (because "the removal of any one of the parts causes the system to effectively cease functioning") such systems have to (1) originate in a non-gradual manner and (2) must remain constant as long as they are reproduced and exist. And this could mean no less than the enormous time periods mentioned for all the living fossils hinted at above. Moreover, an additional phenomenon would also be explained: (3) the equally abrupt disappearance of so many life forms in earth history . . . The reason why irreducibly complex systems would also behave in accord with point (3) is also nearly self-evident: if environmental conditions deteriorate so much for certain life forms (defined and specified by systems and/or subsystems of irreducible complexity), so that their very existence be in question, they could only adapt by integrating further correspondingly specified and useful parts into their overall organization, which prima facie could be an improbable process -- or perish . . . . According to Behe and several other authors [5-7, 21-23, 53-60, 68, 86] the only adequate hypothesis so far known for the origin of irreducibly complex systems is intelligent design (ID) . . . in connection with Dembski's criterion of specified complexity . . . . "For something to exhibit specified complexity therefore means that it matches a conditionally independent pattern (i.e., specification) of low specificational complexity, but where the event corresponding to that pattern has a probability less than the universal probability bound and therefore high probabilistic complexity" [23]. For instance, regarding the origin of the bacterial flagellum, Dembski calculated a probability of 10^-234[22].

You will notice that this paper is exploring why the pattern of stasis happens, despite the drifting of genes over the eras of time. And the answer comes down to the irreducible complexity and associated FSCO/I of functional forms. I hardly need to underscore that stasis would not need a serious explanation, if it were not a significant feature of the record of life forms. Similarly, let us note another early peer reviewed ID-supportive paper -- yes, despite many talking points made against it, it passed proper peer review by "renowned" scientists. In it, Meyer tackled the Cambrian life revolution:

The Cambrian explosion represents a remarkable jump in the specified complexity or "complex specified information" (CSI) of the biological world. For over three billions years, the biological realm included little more than bacteria and algae (Brocks et al. 1999). Then, beginning about 570-565 million years ago (mya), the first complex multicellular organisms appeared in the rock strata, including sponges, cnidarians, and the peculiar Ediacaran biota (Grotzinger et al. 1995). Forty million years later, the Cambrian explosion occurred (Bowring et al. 1993) . . . One way to estimate the amount of new CSI that appeared with the Cambrian animals is to count the number of new cell types that emerged with them (Valentine 1995:91-93) . . . the more complex animals that appeared in the Cambrian (e.g., arthropods) would have required fifty or more cell types . . . New cell types require many new and specialized proteins. New proteins, in turn, require new genetic information. Thus an increase in the number of cell types implies (at a minimum) a considerable increase in the amount of specified genetic information. Molecular biologists have recently estimated that a minimally complex single-celled organism would require between 318 and 562 kilobase pairs of DNA to produce the proteins necessary to maintain life (Koonin 2000). More complex single cells might require upward of a million base pairs. Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require orders of magnitude more coding instructions. The genome size of a modern arthropod, the fruitfly Drosophila melanogaster, is approximately 180 million base pairs (Gerhart & Kirschner 1997:121, Adams et al. 2000). Transitions from a single cell to colonies of cells to complex animals represent significant (and, in principle, measurable) increases in CSI . . . . In order to explain the origin of the Cambrian animals, one must account not only for new proteins and cell types, but also for the origin of new body plans . . . Mutations in genes that are expressed late in the development of an organism will not affect the body plan. Mutations expressed early in development, however, could conceivably produce significant morphological change (Arthur 1997:21) . . . [but] processes of development are tightly integrated spatially and temporally such that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream. For this reason, mutations will be much more likely to be deadly if they disrupt a functionally deeply-embedded structure such as a spinal column than if they affect more isolated anatomical features such as fingers (Kauffman 1995:200) . . . McDonald notes that genes that are observed to vary within natural populations do not lead to major adaptive changes, while genes that could cause major changes--the very stuff of macroevolution--apparently do not vary. In other words, mutations of the kind that macroevolution doesn't need (namely, viable genetic mutations in DNA expressed late in development) do occur, but those that it does need (namely, beneficial body plan mutations expressed early in development) apparently don't occur.6

Here, we see the Cambrian revo, which notoriously lacks the transitionals leading up to the dozens of top level forms of animals found. It is in that context that Meyer exerts a calculation of the sort of scale of fresh functionally specific info needed to account for the new life forms, dozens of times over in what is an "eyeblink" on the conventional timeline. He comes up with 100+ million bits as a reasonable estimate. That is where the key absences of transitional forms has significance. We see the issue of the need for the FSCO/I to explain major body plan origination from unicellular forms. That puts us into the 10-100 mn bits FSCO/I ballpark. And that is well beyond the reasonable reach of chance plus necessity, without a trace of the transitional forms towards those dozens of major life forms. Where also the Ediacaran fossils, microfossils etc in preceeding layers removes the credibility of claims that the transitionals were not preserved as the rocks were not adequately fossil forming for soft bodied creatures etc etc. And, you will notice the darwinian tree of life context: LUCA --> Major body forms of the Cambrian. Where are the transitional sequences, from 3.8 to 4.2 BYA to 500 - 600 BYA on the conventional timeline? That is over 3 bn years to play with. It is in that context that we have the report of Gould and of others, that the same pattern of sudden appearances and stasis is a major pattern of the fossil record as collected over these past 150 years. By contrast, if we look at say trilobites, which share a common body plan, we can see all sorts of variations across the span they are seen, to the point where their variation is often used as an index. That is, we do see variations, but not such as transform fundamental forms. Indeed, Wiki, speaking against known ideological interest, says:

The first appearance of trilobites in the fossil record defines the base of the Atdabanian stage of the Early Cambrian period (526 million years ago) . . . . The trilobites were among the most successful of all early animals, roaming the oceans for over 270 million years.[2] When trilobites first appeared in the fossil record they were already highly diverse and geographically dispersed. Because trilobites had wide diversity and an easily fossilized exoskeleton an extensive fossil record was left behind, with some 17,000 known species spanning Paleozoic time.

Of course, just how many of those forms are genuinely different species is an open question, here we can think of red deer and dogs to see the problem of trying to judge species from body form, size etc. But the more basic point is that the record DOES show adaptations and variations, just not trend lines to materially distinct new body plans. In short the required vertical gradation to move from more "primitive" to more "advanced" life forms through incremental variations that are each advantageous enough to be fixed in populations and supplant older ones, is not being seen in the actual record. We see variation within an island of function, but not fundamental transformations of form through unlimited incremental variation driven by chance variation and differential reproductive success. The Darwinian tree of life, then, is an intellectual construct projected unto the actual record, not properly an observational summary of a steady incremental variation from the original unicellular forms to the various branched out forms. Which is what Gould outright stated, and as has been cited. And to top off, the molecular trees that have been constructed in recent years are quite plainly diverse from one another. After all of this, I feel that I have been forced to repeatedly go over a correction to a misperception -- on the most charitable view I can force myself to take -- that should not ever have been made to begin with, which has served to side track discussion and distract from the key issue, that FSCO/I has but one empirically warranted source, and this source is analytically supported, So, the design inference on the sign of FSCO/I is empirically well warranted. That same issue comes back up once we look at the way the cosmos' fine tuned physics sets up a pattern in which the top four atoms, and one of the next to top four, get us from stars to the elements, to water and organic chemistry and proteins. No wonder Sir Fred Hoyle, looking on the resonance that sets up C and O, was moved to remark about how a superintellect had monkeyed with physics. And of course, that too was discussed way upthread. Kindly cf here for a link to a post at UD on the subject. G'day, KFkairosfocus

July 12, 2012

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KF, And, I may be wrong but I didn't see your definition of complete body plans. Dawkins says (and I agree) that ALL fossils represent transitional forms unless they are the last of a line because ALL life forms that left descendants which eventually formed other species could be said to be transitional. Perhaps an example would be helpful, you can tell us what you think of some specific fossilised body plans. Take any proposed fossil record for the development of any modern species. Here's one for whales: http://www.dickrussell.org/graywhale/history_page.html Typically there will be several fossilised extinct life forms with body plans somewhat different from the proposed descendant species and different from the proposed ancestor species. Are those fossilised body plans complete or transitional? For example, in the linked diagram: is Takracetus transitional between Rhodocetus and Gaviocetus? Is Takracetus a complete body plan? Are transitional and complete mutually exclusive? I am not trying to deflect the argument (I have done my best to address your issues and questions a number of times even if I do not come to your conclusions), I am trying to understand a point you brought up: what do you mean by complete body plans and how are they different from transitional body plans? We can return to the design inference later if you wish.Jerad

July 12, 2012

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kairosfocus @ 213, 214 Thank you for engaging with the question on the table, which was (from 183):

How do you know that final forms outnumber transitionals unless you can tell transitional forms apart from final forms? Pray, what is the difference you are basing this statement on?

But for all your rhetorical firepower, you've still not given an answer that bears scrutiny. You claimed the question was a "wrong framing". Yet it could not be more simple nor more logical. You said:

"The extreme rarity of transitional forms [--> notice the term!] in the fossil record persists as the trade secret of paleontology. [--> a famous quote]" [cite] It should be clear that Gould is using the terms here, in the professional literature, in exactly the way I am doing so; ...

But by Gould's own words, this cannot be correct. Gould clarified those remarks - as quoted - explaining that transitionals are only rare at a fine level of granularity, whilst on the whole, across all levels of the fossil record, transitionals are "rife" and "abundant". So by Gould's definition of "transitional form", they are abundant, and by your definition they are exceedingly scarce. Therefore, as a purely logical matter, you must be using a different definition from Gould. What is more, we know what Gould's definition of transitional is, and why by his definition they are undoubtedly abundant: a transitional is an organism that shares traits with two (or more) other groups of organisms. Gould's point was that a form can appear suddenly in the fossil record, remain static for a time, then disappear, and can also be a transitional between other groups. What we want to know is, where precisely do you disagree with Gould's definition of a transitional form? CheersCLAVDIVS

July 12, 2012

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C: Don't forget the observed variability across deer and similar animals. Does this provide a branching, incremental account of the origin of the body plans for these animals, or does it simply show variations and adaptations of a general already existing form? In a case where red deer from Europe (which have quite a range of variants out into Asia, as i recall) and Elk from North America were found freely interfertile when introduced in NZ for hunting, never mind the taxonomic categorisations. KFkairosfocus

July 12, 2012

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Onlookers, Jerad & Claudius: These days I rarely do a point by point excerpt and respond, but I think I need to do so for record now, in addition to the above broader response: 1] Jerad, 206:I don’t think it’s [--> re Gould on the absence of the key transitionals in the fossil record] as big a stumbling block as you do considering all the evidence in favour of universal common descent The first problem here, is that there is one indisputable record of the forms of life in the past, the fossils. Whether or no we accept the conventional timeline (and it has material circularity problems mentioned and linked already), it is that record that has samples of what life was like in the actual past. So, given the now "almost unmanageably rich" record, we should expect to have in hand a reasonable cross section of the dynamics in action. 1/4 million species, millions of samples in museums taken form all relevant geological column levels all around the world, with billions more in situ in known locations. And Gould's testimony as an expert, reviewing the record after it was well known, in the professional literature, is that it is NOT gradualistic. Where the dynamics that would have been involved would imply that transitionals should DOMINATE the record, or at the very least be strongly represented. In short the facts say: islands of function (with relatively minor adaptations within forms), the theory says gradualism. So much the worse for the facts. Which takes us right back to the problem of the Lewontinian a priori imposition of materialism. That is why Philip Johnson highlighted this as the pivotal problem, as already cited. Givent eh a priori, and given the exclusion of realistic alternatives, the evidence will necessarily be seen in a gradualistic frame, and explanations will be used to deflect the inconvenient fact of few or no transitions that show origin of body plans. But there is no good reason to evict serious alternative explanaitons rooted in empirical patterns and known adequate causes of FSCO/I. So, it is not so much that the evidence is in favour of UCD, it is that the imposed ideology that demands UCD and the evidence is viewed from that point of departure. (And that extends to other categories of claimed evidence and icons, across the board. Cf here on for a 101.) 2] I don’t think fossilisation is a good random sample of life forms. Especially for land based critters and plants. I think very, very few lifeforms are preserved in the fossil record. And, like I’ve said, I think the evidence for evolution is great even if we had no fossils. Notice, you have not addressed the range of search, the size and scope of samples, the want of any credible reason to believe that there would be a biasing correlation between fossilisation events and the absence of transitionals to be fossilised, etc. All of which have been raised over and over but simply brushed aside in eagerness to use Darwin's 150 year old claim. Kindly cf Gould on this as already cited. It is not that there is great evidence for -- notice the specifying definition here ("evolution" is a notoriously slippery term with many meanings and a tendency to glide form one tot he other unannounced) -- body plan level incremental blind chance and necessity macroevolution by chance variation and differential reproductive success leading to leading to universal common descent with unlimited modification, but instead that this has been imposed on the evidence by an a priori assumed materialism. Once that has dominated the relevant institutions, often by the back-door route of tendentiously redefining science in the teeth of the requisites of inductive logic and the actual history of science alike. E.g., cf this from the US NSTA as is taken here form the IOSE intro-Summ page:

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. Emphases added.]

By tendentiously injecting the strawman conty5rast, natural vs supernatural, the NSTA, NAS etc avoid dealing wit the real alternative on the table since Plato in The Laws Bk X 2350 years ago: natural (= blind chance + necessity) vs ART-ificial. Where it is long since known that nature and art have characteristic signs that may be used to discern the credible best explanation where we did not directly observe the events in question. Notice, onlookers, Jerad has routinely demanded instead to find separate evidence of a designer, refusing the inference from signs. Which is inconsistent with what s/he would have to do for ever so many important cases of generally accepted knowledge, including history, law courts, many things in pure and applied science, and even statistical inference. This is selective hyperskepticism. We may only instead reasonably ask for adequate and realistic degrees of warrant suitable to the case in question. Where on the origins issues, the deep actual past is unobservable so we are always going to be inferring on best explanation in light of signs and adequate causes for same. To top it all off, ID (think, Behe) as such is not in opposition to evolution with some degree of common descent, all the way up to universal common descent. It objects to a very specific claim that has not been subjected to adequate critical examination: that blind chance and mechanical necessity can account for FSCO/I. The point is that the proposed darwinist mechanism -- and wee may add the range of variant forms too -- is failing the empirical adequacy test and this should be admitted. Then, it should be acknowledged that from OOL on, there is serious reason for informed scientific practitioners and educated people in general alike to hold that FSCO/I in living forms is strong evidence on signs pointing to design as causal process. 3] I just wanted to understand and have some examples of what you considered transitional and final body plans. Examples were given, and the remarks of a major expert were put on the table, repeatedly. That should have been more than enough for a reasonable discussion. In addition, the issue of "missing links" has been a major subject on this matter for the past 150 years. The pretence that all of this is new, and that I need to provide further explanation of a suspect claim from a suspect source, is a patent strawman tactic. 4] You brought up the notion of final body plans, you should be able to define it. Gross and irresponsible misrepresentation, given what has already been laid out. 5] I know you think so [that: "The strong evidence is that [t]he world of life and functional body plans are found in islands of function, with adaptation within the function, but Darwinist gradualism has no cogent answer . . . "], you don’t have to keep reminding me!! I just disagree with you. Mere disagreement is not the issue, warrant is. As has been repeartedly ppinted out. In short, we see here the default assumption of evolutionism at work, with selectively hyperskeptical dismissal rather than grappling with the general evidence on the only observationally known adequate cause for FSCO/I and how from OOL on it applies to the world of life. 6] I’d still like to know what you consider complete and incomplete body plans. Drumbeat repetition of a strawman caricature of the unanswered issue of the missing transitionals. 7] Claudius, 207: I am not a materialist. Just, evidently unduly influenced by their thought on this topic. 8] You know, that might be a good argument, but I can’t say for sure because you still haven’t explained your terms. That you think these are my terms is evidence of the undue influence. The issue is as stated and repeatedly excerpted from Gould. let the darwinist advocates argue with Gould and the fossils, not us. 9] How do you know that final forms outnumber transitionals unless you can tell transitional forms apart from final forms? Wrong framing, and he who succssfully mis-frames can win a debate on persuasiveness in the teeth of the evidence. The issue is, that we have a claimed tree of life. Never mind for the moment how there is the embarrassment that the molecular trees diverge to the point that something is patently wrong with the whole picture. From the root, OOL, we see why -- a current post -- there is excellent reason to infer design as best explanation of the joining of encapsulated metabolism to self-replication with symbolic representation. That is, cell based life as we observe it and infer it from the fossil record of life in the past. So, as discussed already, design is best explanation from the outset. That shifts evaluation thereafter decisively. In particular, it does not allow us to brush aside the absence of the TRANSITIONAL SEQUENCES that should dominate the record were the CV + DRS --> DWM, i.e chance and necessity macro evo picture true. Have you seen the vids of Sternberg and Berlinsky in the IOSE body plan origins page? Do you see why a pattern where 50,000 or even 500 or 50 transitional forms consistently in the record, should leave behind samples that highlight that in "an almost unmanageably rich" fossil record? Transitional sequences should be all over the place, but we find few and far between, with the eye of darwinist faith called on to fill in transitions in place of the abundance of plain sequences. If we can see a sequence for circumpolar gulls, or for different racial characteristics of people, or for finches in the Galapagos [which turned out to be interfertile unexpectedly], why not for the much more important major body plan origins? 10] the pattern of sudden appearance, stasis and disappearance does not entail the absence of transitional forms. According to Gould, the fossil record is “rife” with transitional forms and is also characterised by appearance, stasis and disappearance. Notice, first, the revealing absence of clear lists of examples showing the transitions from chemicals to first life forms, then from unicellular ancestors to major step by step sequences of FOSSILS showing how the main body plans originated, and onward to the myriads of particular forms. If these were there, we would see them proudly displayed in every museum, textbook and major darwinist web site, not clusters of misleading icons and tendentious explanations shaped by the eye of darwinist faith and question-begging historically inapt redefinitions of science. As to assertions of "rife," let the decades long exercise of going out to found a theory of how we can get transitions without seeing them in the fossil record speak volumes. And, observe on this the remarks already cited this morning and previously, especially:

“The extreme rarity of transitional forms [--> notice the term!] in the fossil record persists as the trade secret of paleontology. [--> a famous quote] The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference . . . [Stephen Jay Gould 'Evolution's erratic pace'. Natural History, vol. LXXXVI95), May 1977, p.14.]

It should be clear that Gould is using the terms here, in the professional literature, in exactly the way I am doing so; wedded to the gross structure of the darwinist tree of life interpreted as a frame of macroevo on CV + DRS --> DWM. And, by 2002, 25 years later, in his last technical book (The structure of Evolutionary Theory), he is still saying:

. . . long term stasis following geologically abrupt origin of most fossil morphospecies, has always been recognized by professional paleontologists. [[p. 752.] . . . . The great majority of species do not show any appreciable evolutionary change [--> gradualism in changing body plans is missing in action] at all. These species appear in the section [[first occurrence] without obvious ancestors in the underlying beds, are stable once established and disappear higher up without leaving any descendants." [[p. 753.] . . . . proclamations for the supposed ‘truth’ of gradualism - asserted against every working paleontologist’s knowledge of its rarity - emerged largely from such a restriction of attention to exceedingly rare cases under the false belief that they alone provided a record of evolution at all! The falsification of most ‘textbook classics’ upon restudy only accentuates the fallacy of the ‘case study’ method and its root in prior expectation rather than objective reading of the fossil record. [[p. 773.]

Pardon me, but I missed the dramatic headlines and Nobel prize awards over the past decade for indisputably filling in those gradualistic gaps, and showing that they were filled in on chance variation plus differential reproductive success without intelligent direction, selection or frontloading or guidance. I did see several replacement icons put forth with scare headlines over these years, only to be shot down or retracted or partly retracted on further investigation. Which is exactly the pattern Gould had highlighted long since. 11] Gould is using a different definition of transitional forms than you are. That’s why we’ve been asking you to provide your definitions of transitional forms and final forms all along. Not so at all. Gould and I are discussing the darwinist tree of life and we are both speaking of isolated clusters rather than abundantly and unquestionably evident sequences of transitional forms heavily represented in the "almost unmanageably rich" fossil record. And, I add, all of this is tangential to the empirically credible source of FSCO/I, and to the challenge of the source of such FSCO/I in origin of cell based life, where there is no reasonable possibility of appeal to incremental chance variation of a reproducing population per vNSR to muddy the waters. Design, as of right, is t the table from the root of the tree of life. And that drastically shifts credibility on models of origin of body plan level diversity. PJ, 209: the fossil record is full of complete body forms. I think you only have to look around at the life forms we have on our planet today to see a vast array of complete body forms. What you don’t find are any intermediate steps suggesting otherwise. Take for instance something like Triceratops, an extremely distinguishable life form. There are many fossils of Triceratops, but nothing at all of anything leading up to it. It therefore has in my view what is, without any evidence to suggest otherwise, a complete complete body form. I could suggest many more if you like? Good in- a- nutshell. KFkairosfocus

July 12, 2012

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OOPS: Forgot to fill in a cite from NWE on ID:

Intelligent design (ID) is the view that it is possible to infer from empirical evidence that "certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection" [1] Intelligent design cannot be inferred from complexity alone, since complex patterns often happen by chance. ID focuses on just those sorts of complex patterns that in human experience are produced by a mind that conceives and executes a plan. According to adherents, intelligent design can be detected in the natural laws and structure of the cosmos; it also can be detected in at least some features of living things. Greater clarity on the topic may be gained from a discussion of what ID is not considered to be by its leading theorists. Intelligent design generally is not defined the same as creationism, with proponents maintaining that ID relies on scientific evidence rather than on Scripture or religious doctrines. ID makes no claims about biblical chronology, and technically a person does not have to believe in God to infer intelligent design in nature. As a theory, ID also does not specify the identity or nature of the designer, so it is not the same as natural theology, which reasons from nature to the existence and attributes of God. ID does not claim that all species of living things were created in their present forms, and it does not claim to provide a complete account of the history of the universe or of living things. ID also is not considered by its theorists to be an "argument from ignorance"; that is, intelligent design is not to be inferred simply on the basis that the cause of something is unknown (any more than a person accused of willful intent can be convicted without evidence). According to various adherents, ID does not claim that design must be optimal; something may be intelligently designed even if it is flawed (as are many objects made by humans). ID may be considered to consist only of the minimal assertion that it is possible to infer from empirical evidence that some features of the natural world are best explained by an intelligent agent. It conflicts with views claiming that there is no real design in the cosmos (e.g., materialistic philosophy) or in living things (e.g., Darwinian evolution) or that design, though real, is undetectable (e.g., some forms of theistic evolution). Because of such conflicts, ID has generated considerable controversy.

That, from where I sit, is a reasonable summary of the claims of ID as a scientific enterprise. I -- and many other design thinkers from web discussion level up to those at the coal-face pf active research -- would appreciate it if the issues being discussed reflected this rather than strawman caricatures and distractions routinely put up by objectors. KFkairosfocus

July 12, 2012

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Jerad: FIRST, A NECESSARY NOTE ON YOUR RHETORIC: I find it quite revealing and unfortunate that you have resorted to the tactics of the turnabout, shifting of burden of proof and implicitly assumed default; here compounded by unresponsiveness to cogent reply and drumbeat repetition of talking points. All of these tactics of distraction -- whether knowingly and calculatedly resorted to or not [it is admittedly hard to stick to a main focus] -- are just that, distractions from the pivotal issues on the merits. FYI, each proposed scientific explanation must meet the basic test of empirical, observational support. For itself. And where we deal with origins science and so the unobservable past, we need to examine its traces and signs that per confirmation by observation in the present, give credible indicia on causal processes and forces or factors involved. So where FSCO/I is concerned, it is highly relevant to note that the ONLY observed cause of such is design. And, the threshold of complexity used, 500 - 1,000 bits of explicit or implicit functionally specific information, is such as to preclude chance (the other observed source of high contingency) as a credible cause. In effect, clusters of functional configs are so isolated in the space of possibilities, that a blind walk is maximally unlikely to ever encounter such, on the gamut of atomic resources in the solar system or the observed cosmos. Formerly, you made much of the common resort that life forms reproduce, to dismiss the significance of this point. So, I took time to go to the case that does not allow such muddying the waters. OOL. There, we find that the very self-replication facility itself is a capital example of FSCO/I and that in a context where no appeal may be made to existing capacity to reproduce. Onlookers, cf. here for a post level summary. In short, from the root of the proposed tree, design is sitting at the table as most credible explanation. Thus, evaluation thereafter will need to be in this light. So now, I must again briefly point out, simply for record, as it has been stated several times already but evidently ignored, that it is the neo-darwinian synthesis that has advocated a gradualistic, incremental transitional forms in a tree of life account of the course of life. Thus, per the number of steps implied, there should be an overwhelming number of TRANSITIONAL life forms -- notice your strawman tactic resort to "your assertion that there are complete and non-complete body forms" when more than adequate information was put to show that I am speaking of chains of what have been headlined for 150 years as missing links -- which should therefore on reasonable inferences from sampling theory (notice, how you, by admission trained in statistics have not seriously disputed this as focal point . . . ) be strongly represented in the fossil record. Now, we are not playing high school debate games and clever distractive tricks here, we are about the very serious business of assessing for ourselves by the right to think for ourselves, the warrant for scientific claims that have become a dominant part of institutional science, sci edu and the wider culture. Indeed, of worldviews, especially through the rise of evolutionary materialism and accommodations thereto. With cultural consequences over the past nigh on 150 years as were warned against by Plato, 2350 years ago. But, the very turnabout and distractive rhetorical tactics you resort to are eloquent testimony of the absence in the fossil record of the relevant incremental forms from the record, at body-plan origins level. This, after 150 years of scouring fossil beds across the world from all main sections of the geological column, leading to billions of fossils seen in the field, millions in museums and 1/4 million plus fossil species. The "almost unmanageably rich" record is astonishingly empty of the body-plan level transitional forms that SHOULD be strongly evident or even dominant. We SHOULD be awash in examples of 0.1, 0.2, 0.3 . . . way from cow to whale, or reptile to bird or rat to bat or the like. But instead, these are consistently missing, and indeed the most common transitional sequence since was it 1879, the horses, is being retired from museums and textbooks. The claimed whale transition being substituted is not telling us about the blunder in projecting what turned out to be a quadruped as an early whale as recently as the 1990's, and we simply do not see a discussion of just how many steps, with what degree of vital necessity for function, and how such could be successively fixed per population genetics, etc. (Onlookers, cf IOSE on body plan origins to see the real issue in outline at 101 level, not the rhetorical strawman being set up to be knocked over, mostly elsewhere in the usual hostile fora. Both of my interlocutors know or should know that I have that discussion as well as a similar one in my always linked briefing note. That is why I am concluding that I am here dealing with more of irresponsible rhetorical game-playing rather than serious discussion.) Such transitionals, BTW, do occur at minor adaptation level as may be observed in the current world, e.g. among types of birds (as I noted). We can argue that variations among men of different climes also in significant part show adaptive radiation at the small scale within common body plan level that is warranted. In short, Jerad (and Claudius), it seems you have not seriously read or engaged with what has already been put in this thread or elsewhere and linked just a click or two away. And, again, the issue is claimed incremental origin of body plans, bauplane. The linked question -- which you must be familiar with (despite the rhetorical tactic of passing over in silence) -- has been discussed for decades under terms like transitional forms, and in popular circles as missing links. Let me again cite Gould on the key matter on this side track, noting that in that context he and others set out to construct an entire alternative evolutionary theory to account for the missing incremental transitionals:

"The extreme rarity of transitional forms [--> notice the term!] in the fossil record persists as the trade secret of paleontology. [--> a famous quote] The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, . . .

[--> recall, Lewontin's cat out of the bag comment about how a priori evolutionary materialism controls that reasoning: >> . . . 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.]>> NB: cf here on for response to the all too common "quote-mining" talking point]

. . . not the evidence of fossils. Yet Darwin was so wedded to gradualism that he wagered his entire theory on a denial of this literal record:

The geological record is extremely imperfect and this fact will to a large extent explain why we do not find intermediate varieties, connecting together all the extinct and existing forms of life by the finest graduated steps [[ . . . . ] He who rejects these views on the nature of the geological record will rightly reject my whole theory.[[Cf. Origin, Ch 10, "Summary of the preceding and present Chapters," also see similar remarks in Chs 6 and 9.]

Darwin's argument still persists as the favored escape of most paleontologists from the embarrassment of a record that seems to show so little of evolution. In exposing its cultural and methodological roots, I wish in no way to impugn the potential validity of gradualism (for all general views have similar roots). I wish only to point out that it was never "seen" in the rocks. Paleontologists have paid an exorbitant price for Darwin's argument. We fancy ourselves as the only true students of life's history, yet to preserve our favored account of evolution by natural selection we view our data as so bad that we never see the very process we profess to study." [[Stephen Jay Gould 'Evolution's erratic pace'. Natural History, vol. LXXXVI95), May 1977, p.14.]

Notice the highlighted. Starting with the term: TRANSITIONAL FORMS. And, onlookers, notice, this is all a rhetorically convenient side track. The central question is whether it is reasonable to infer cause on characteristic observed signs. The answer from logic and common sense alike, is that it is, indeed in dealing with what we cannot directly inspect and observe, it is the only empirically grounded analytical tool we have. We therefore routinely reconstruct the inferred causal process from signs left behind per abductive inference to best explanation. Now, design theory is an application of such reasoning regarding the unobservable actual past of origins of life (and the cosmos). As the NWE introductory article -- as opposed to the Wikipedia ideological hatchet job -- notes:

In particular, functionally specific, complex organisation and associated information are put forth as a case in point. The only observed cause for FSCO/I is design. Per million monkeys at keyboards failing to type coherent text at random at sufficient length and hard to find needle in haystack analyses, we see why that is analytically plausible. We see that 500 - 1,000 bits is adequate complexity for these issues to kick in. We compare that first cell based, metabolising and self replicating life will have credibly been 100,000 - 1 mn bits of digital info. And without both capabilities, reproducing life is not extant, so there is no reasonable resort to claiming incremental origin. Notice, the vNSR has to code for the metabolic automaton to replicate it, as well as for itself. This case puts design firmly at the table of alternatives, and there simply is no sufficiently solid alternative to compete. The very fact that in exchanges supporters of the dominant evolutionary school of thought routinely insist that OOL is separate from evolution of extant life is eloquent on this. But, without a viable, empirically well grounded account here, the tree of life has no root on evo mat accounts. Where also, once design is at the table here, it is at the table as a serious alternative across the whole world of life. Going on, we now observe that, contrary to the imagined, hoped for incremental branching and diversification through myriads of transitional forms, we see instead clear and consistent evidence of discrete islands of functional forms. This, right back to the Cambrian fossil layers, where the top level taxonomic domains by the dozens appear at the point where diversification of multicellular forms that continue to today, comes in. This is consistent with the observation that we credibly require 10 - 100+ mn bits of bio info to create such forms, well beyond the needle in the haystack threshold. So, we see a good part of why Gould spoke and acted as he did. He was facing the evidence of isolated islands as opposed to the hoped for raftloads of cases of incremental transitional forms. And so, we see that a major problem is that evidence that is highly relevant to why design is a good explanation is being force-fitted into a gradualistic model. Because of a dominant school of thought that a priori locks out alternatives. That is why, Jerad, I mark up your just above comment as follows:

I’m sorry you have chosen not to answer CLAVDIVS and my question regarding your assertion that there are complete and non-complete body forms. a --> Gross, strawman tactic misrepresentation As stated we think it is fair to ask you to address this issue b --> You ignore how it has been repeatedly addressed in this thread, and at length in linked materials since a) you brought it up and b) it would help us to evaluate some of your arguments. c --> In fact, the matter of incrementally modified body forms as part of the gradualistic evolution of life forms was put on the table by the founders of evolutionary theory d --> The tactic of suggesting that I have just now raised it is intended to shift burden of proof improperly, and to insinuate that I have suggested dubious claims e --> Where you know, or full well should know that the topic comes from the leading proponents of evolutionary theory, and has done so for 150 years. f --> This is irresponsible on your part. g --> the proper matter, given the actual history of ideas on the matter, is not evaluating of implicitly dubious claims by a "nobody" but the assessment of evidence on the longstanding claim of gradualism. h --> So also, that places OOL front and centre, given the need to account for the origin of cellularly encapsulated metabolism and integrated vNSR. i --> The best explanation in light of the origin of FSCO/I challenge, is design. j --> That then utterly transforms the view of the credibility of alternatives thereafter as we look at the elaboration of the forms of life. k --> In this context, pace force-fitting the OBSERVED systematic discontinuities in life forms into a gradualistic account, the evidence actually points to islands of functional forms, that are indeed adapted, but we do not see the sort of progressions that should be there in a fossil record of this magnitude, if the suggested incremental formation of diverse body plans happened. l --> so in fact, we are seeing turnabout burden of proof shifting, rather than actual evidence of the incremental transitions. m --> That is itself highly revealing on the balance on the merits. That is, the empirical evidence comports far better with design than with the chance and necessity gradualistic model. n --> even such adaptations within body plans as we see are consistent with adaptability as a built in capacity that makes for robustness. (One way to do this, as is discussed at popular level in the recent Nat Geog with a dog cover story, is through multiple genes involved in phenotype traits. That way, blends, filtered out extrema and mods are possible.)

I hope that we can now return to a proportionate focus on the main issue. KFkairosfocus

July 12, 2012

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PeterJ @ 209

Personally I think the fosil record is full of complete body forms.

But we remain unable to assess the soundness of your thinking unless you define for us the difference between "complete body forms" and transitional forms. What's the difference you are thinking of?

Take for instance something like Triceratops, an extremly distinguishable life form. There are many fossils of Triceratops, but nothing at all of anything leading up to it.

What about Psittacosaurus? Protoceratops? Chasmosaurus? Monoclonius? Styracosaurus? Pentaceratops? Torosaurus? These are all ceratopsian dinosaurs like Triceratops, one of the largest groups of dinosaurs from the Cretaceous, showing fairly finely graded variations in the rostrum bone, beak, frill and horns - e.g. see here. What definition of "complete body form" are you thinking of that makes all these variations "complete" and not "transitional"? CheersCLAVDIVS

July 12, 2012

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Jerad, Personally I think the fosil record is full of complete body forms. I think you only have to look around at the life forms we have on our planet today to see a vast array of complete body forms. What you don't find ar any itermediate steps suggesting otherwise. Take for instance something like Triceratops, an extremly distinguishable life form. There are many fossils of Triceratops, but nothing at all of anything leading up to it. It thereforehas in my view what is, without any evidence to suggest otherwise, a complete complete body form. I could suggest many more if you like? PPeterJ

July 12, 2012

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KF, I'm sorry you have chosen not to answer CLAVDIVS and my question regarding your assertion that there are complete and non-complete body forms. As stated we think it is fair to ask you to address this issue since a) you brought it up and b) it would help us to evaluate some of your arguments.Jerad

July 11, 2012

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Kairosfocus @ 205

Pardon directness, but I tire of turnabout rhetoric, real fast. It is the evo mat side that has to get to a first metabolising, self-replicating unicellular body plan through thermodynamic processes and chemistry in a warm little pond or otherwise. (Cf the new post on this here, particularly noting the diagrams and discussion of requisites.)

I am not a materialist.

K @ 182: There is every reason to believe that transitionals would have vastly outnumbered final forms. K @ 205: That means, as I pointed out, that if the scheme is to be scientific not ideologically imposed metaphysical speculation, there has to be observed evidence of transitional sequences, in sufficient numbers to make a difference. Where, using the cow-whale thought exercise as a pivot, I pointed out WHY there would be an overwhelmingly larger number of transitional forms than final ones.

You know, that might be a good argument, but I can't say for sure because you still haven't explained your terms. Here is the question again (@ 183): "How do you know that final forms outnumber transitionals unless you can tell transitional forms apart from final forms? Pray, what is the difference you are basing this statement on?" Jerad also wants to know the answer to this question (@ 184): "You have not spelled out what you mean by ‘fully formed body plans’ so I shall defer answering this until you have done so as I think it might influence my argument."

K @ 105: And, that is exactly why Gould, et al went out and worked to found a new theory that pivoted in part on providing a rationale for why the fossil record was characterised by sudden appearances, stasis and disappearance. So, we should revert tot he principle that actions speak louder and far less ambiguously on words in a controversial context. If such people set out to find an alternative theory, there was and is a real problem.

This all sounds fine. However, the pattern of sudden appearance, stasis and disappearance does not entail the absence of transitional forms. According to Gould, the fossil record is "rife" with transitional forms and is also characterised by appearance, stasis and disappearance. Obviously, then, Gould is using a different definition of transitional forms than you are. That's why we've been asking you to provide your definitions of transitional forms and final forms all along. CheersCLAVDIVS

July 11, 2012

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KF,

Please, don’t pretend that you have not seen the issue I have presented, starting with Gould, that there is a significant challenge to move by increments from an initial unicellular form to main body plans, a la Cambrian revo, and onward to various specialist types.

I see your point but I don't think it's as big a stumbling block as you do considering all the evidence in favour of universal common descent.

Further, please don’t pretend that there is a good excuse on sparseness of the fossil record, to infer that we should not expect to be overwhelmed with examples of incremental transitions, if that were the actual history of life. Not after 150 years, an exploration of the world’s fossil beds, billions of fossils in situ, millions in museum back rooms, and 250,000 fossil species.

I don't think fossilisation is a good random sample of life forms. Especially for land based critters and plants. I think very, very few lifeforms are preserved in the fossil record. And, like I've said, I think the evidence for evolution is great even if we had no fossils.

In short, please, don’t pretend that you can turn about the issue and pretend that I am ducking a question. Not, after the thread above.

I just wanted to understand and have some examples of what you considered transitional and final body plans. What's wrong with that? You brought up the notion of final body plans, you should be able to define it.

The strong evidence is that he world of life and functional body plans are found in islands of function, with adaptation within the function, but Darwinist gradualism has no cogent answer — one that is empirically warranted — to get to the range of body plans. And, that is after it already has no answer on the root of the tree of life.

I know you think so, you don't have to keep reminding me!! I just disagree with you.

The macroevo, body plan origin challenge is to get to body plans, not to adapt existing ones.

l I'd still like to know what you consider complete and incomplete body plans.Jerad

July 11, 2012

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Claudius: Pardon directness, but I tire of turnabout rhetoric, real fast. It is the evo mat side that has to get to a first metabolising, self-replicating unicellular body plan through thermodynamic processes and chemistry in a warm little pond or otherwise. (Cf the new post on this here, particularly noting the diagrams and discussion of requisites.) Complete with digitally coded algorithms and credibly involving 100 k - 1 m bits of coded info. Where also, until the vNSR is in place complete with code and controls for creating the metabolic automaton that is attached to the self-replicator, evolution by the proposed mechanism of chance variation and differential reproductive success cannot start. Since the 1920's, unsolved, and in effect lopped off and isolated under a separate label. Net effect, the incrementalist, chance + necessity tree of life proposed is rootless. More importantly, the functional specificity, complexity, code, algorithms and system integration all point strongly to design, which transforms the whole view of the process beyond that line. Next, it is the darwinist school of thought that has been searching for and headlining claimed "missing links" since 1861. The whole tree of life scheme requires incremental transitional forms, from unicellular common ancestral forms, to the dozens of main body plans, and myriads of specific forms with complex features, including of course our own linguistic ability. That means, as I pointed out, that if the scheme is to be scientific not ideologically imposed metaphysical speculation, there has to be observed evidence of transitional sequences, in sufficient numbers to make a difference. Where, using the cow-whale thought exercise as a pivot, I pointed out WHY there would be an overwhelmingly larger number of transitional forms than final ones. As the IOSE course body plan unit discussion excerpts and gives vid clips on from Sternberg [knowledgeable on evolution and pop genetics] and Berlinsky [a mathematician], this transition will require a great number of forms, estimated by the latter at 50,000+. Even if it were 50 or 100, the point would be plain: transitionals should have dominated the history of life. So, we should expect to find 0.1, 0.2. 0.3 . . . bats, birds, whales, flowering plants, insects, lobsters and shrimp or comparable forms, etc etc etc. And, these should be absolutely dominant in the fossil record, as per sampling theory the uncorrelated sampling through fossilisation events should provide a cross section of the bulk of the record. Where also, there are linked issues on reproduction rates and population sizes to get the transformations in the windows of time available on the conventional timeline, if the claimed mechanisms are the ones at work. As I pointed out above, but which has been clearly lost in the swarm of talking points since. That is exactly what we do not find. And, that is exactly why Gould, et al went out and worked to found a new theory that pivoted in part on providing a rationale for why the fossil record was characterised by sudden appearances, stasis and disappearance. So, we should revert tot he principle that actions speak louder and far less ambiguously on words in a controversial context. If such people set out to find an alternative theory, there was and is a real problem. Worse, as I pointed out already, there is a lot of history on headlined missing links allegedly found, and the later backtracking of the headlines and museum and textbook displays and illustrations. Where also, oddly enough we DO have clear transitional sequences, of say the circumpolar gulls. This now admitted to not be a neat linear trend as even Denton presented in the mid 80's, but it does show diversification of populations radiating and branching out from a plausible core. (For that matter, the ground doves I am familiar with across the Caribbean have distinctive variations from island to island, and someone familiar with the populations of people in the islands can often make a successful guess as to island of origin from physical appearance.) Is that a proof of body plan origin by incrementalism? No. Why? Because of the obvious problem: these are all gulls or ground doves or people. There is adaptation and variation, but not the innovation of the leap in complexity to go to a major body plan or a major mod to a basic plan such as wings or echolocation etc. Blind cave fish are similar, as are wingless insects on islands or the like, or of course white/black moths -- insofar as the investigations and presentations can be justified against the challenges on methods. The macroevo, body plan origin challenge is to get to body plans, not to adapt existing ones. Which should be a no-brainer. And, Gould's words in justification of being on the incrementalist side do not resolve the issue of observations of fact that he has made. Where is the credible information and algorithm source to move to novel body plans incrementally? Nowhere. The observed sequences of transitional forms that show emergence of the major body plans and key features of specialised forms? Again, nowhere. Where also, speculation uncontrolled by key empirical observed data and facts is ideology, not science. In short, it is entirely in order to cite Gould's key remarks on the subject, to show that there is a major and unanswered problem. Let me remind:

"The absence of fossil evidence for intermediary stages between major transitions in organic design, indeed our inability, even in our imagination, to construct functional intermediates in many cases, has been a persistent and nagging problem for gradualistic accounts of evolution." [[Stephen Jay Gould (Professor of Geology and Paleontology, Harvard University), 'Is a new and general theory of evolution emerging?' Paleobiology, vol.6(1), January 1980,p. 127.] "All paleontologists know that the fossil record contains precious little in the way of intermediate forms; transitions between the major groups are characteristically abrupt." [[Stephen Jay Gould 'The return of hopeful monsters'. Natural History, vol. LXXXVI(6), June-July 1977, p. 24.] "The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils. Yet Darwin was so wedded to gradualism that he wagered his entire theory on a denial of this literal record:

The geological record is extremely imperfect and this fact will to a large extent explain why we do not find intermediate varieties, connecting together all the extinct and existing forms of life by the finest graduated steps [[ . . . . ] He who rejects these views on the nature of the geological record will rightly reject my whole theory.[[Cf. Origin, Ch 10, "Summary of the preceding and present Chapters," also see similar remarks in Chs 6 and 9.]

Darwin's argument still persists as the favored escape of most paleontologists from the embarrassment of a record that seems to show so little of evolution. In exposing its cultural and methodological roots, I wish in no way to impugn the potential validity of gradualism (for all general views have similar roots). I wish only to point out that it was never "seen" in the rocks. Paleontologists have paid an exorbitant price for Darwin's argument. We fancy ourselves as the only true students of life's history, yet to preserve our favored account of evolution by natural selection we view our data as so bad that we never see the very process we profess to study." [[Stephen Jay Gould 'Evolution's erratic pace'. Natural History, vol. LXXXVI95), May 1977, p.14.]

Where also, as alate as in his last book, The Structure of Evolutionary Theory, 2002, he stated:

. . . long term stasis following geologically abrupt origin of most fossil morphospecies, has always been recognized by professional paleontologists. [[p. 752.] . . . . The great majority of species do not show any appreciable evolutionary change at all. These species appear in the section [[first occurrence] without obvious ancestors in the underlying beds, are stable once established and disappear higher up without leaving any descendants." [[p. 753.] . . . . proclamations for the supposed ‘truth’ of gradualism - asserted against every working paleontologist’s knowledge of its rarity - emerged largely from such a restriction of attention to exceedingly rare cases under the false belief that they alone provided a record of evolution at all! The falsification of most ‘textbook classics’ upon restudy only accentuates the fallacy of the ‘case study’ method and its root in prior expectation rather than objective reading of the fossil record. [[p. 773.]

Notice, here how Australian paleontologist Tim Flannery reviewed it in NYRB:

Niles Eldredge and Gould first coined the term "punctuated equilibrium" in 1971 and published it the following year. The theory seeks to explain a persistent pattern in the fossil record whereby a species suddenly appears, then persists unchanged for a very long time before going extinct. This pattern is seen in a wide variety of contexts, from marine creatures such as shellfish and sea urchins to mammals and birds. Punctuated equilibrium posits that these species come into existence relatively rapidly (over tens of thousands of years), though just how (and indeed if) this happens is hotly debated. An opposing explanation is that these species have evolved much more slowly somewhere else, and their "sudden" appearance is the result of migration. While, as Galton's polyhedron suggests, the concept of punctuated equilibrium was not entirely new to paleontology, Eldredge and Gould's formulation of it was timely and coherent. Even among its supporters, however, argument has raged over its significance, with many questioning whether it really challenges Darwin's concept of gradualism. (After all, tens of thousands of years is sufficient time for species to evolve "gradually.") Most researchers, though, recognize that the concept has been invaluable in encouraging paleontologists to examine the fossil record with a rigor and attention to detail that previously was largely lacking. Punctuated equilibrium has forced paleontologists to focus not only on the origin of species, but also on their often long, unchanged persistence in the fossil record . . . [["A New Darwinism?," The New York Review of Books, 49 (May 23, 2002): pp. 52–54.]

This is a real problem, not a pretend one made up on out of context citations, as is too often pretended. Deal with it fairly and squarely, kindly. KFkairosfocus

July 11, 2012

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Jerad: Please, don't pretend that you have not seen the issue I have presented, starting with Gould, that there is a significant challenge to move by increments from an initial unicellular form to main body plans, a la Cambrian revo, and onward to various specialist types. Further, please don't pretend that there is a good excuse on sparseness of the fossil record, to infer that we should not expect to be overwhelmed with examples of incremental transitions, if that were the actual history of life. Not after 150 years, an exploration of the world's fossil beds, billions of fossils in situ, millions in museum back rooms, and 250,000 fossil species. In short, please, don't pretend that you can turn about the issue and pretend that I am ducking a question. Not, after the thread above. The strong evidence is that he world of life and functional body plans are found in islands of function, with adaptation within the function, but Darwinist gradualism has no cogent answer -- one that is empirically warranted -- to get to the range of body plans. And, that is after it already has no answer on the root of the tree of life. KFkairosfocus

July 11, 2012

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PeterJ,

I have enjoyed discussing this with you, and appreciate the time you have taken. Although I can’t help but feel we have very sadly reached an end. Like Dawkins and Coyne et al, you see evolution and can’t see past it. A few posts back you almost accused me, it seemed, of ‘having made my mind up’, but do you not think this is the case with you?

Well, I don't think so. Firstly, while I haven't changed my mind participating in this forum, listening to the podcast ID: the Future and various other ID friendly activities has made me look at the evidence again several times and think more deeply about it. Secondly all the new evidence that comes out practically everyday continues to uphold the modern evolutionary synthesis. Unlike some of the moderators and commentators on this site I do not think evolution is on it's last legs. I think it's getting stronger all the time as the gaps in our knowledge get smaller and smaller. I'll skip Dr Cornelius' post. I do read them on a regular basis and I find him mostly bluster with little real understanding of science.

“All scientists agree that evolution has occurred,” the University of Massachusetts professor goes on to explain that natural selection “eliminates and maybe maintains, but it doesn’t create,” that she believed the textbook orthodoxy that random mutations lead to evolutionary change and new species “until I looked for evidence,” and that “There is no gradualism in the fossil record.”

Thank goodness there's a lot more evidence than the fossil record. Peter, you haven't discussed the other lines of data but I hoped you've considered them, on their own and in conjunction with the fossil record. It's the combination of all the evidence that really makes the case for evolution.

Why don’t you try doing the same. Look at the evidence for yourself instead of relying on sources such as Dawkins and Coyne. Perhaps then you will learn something. Ah, but there lies the problem: you don’t want to

Well, as I've just indicated, I have looked at the evidence from both sides. And I continue to do so on a daily basis.

Thanks again. And all the best

Thanks! Best to you as well!!Jerad

July 11, 2012

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Jerad “Well, I’d recommend several books: Only a Theory by Miller is quite good. I like The Greatest Show on Earth by Dawkins but he does rub some people the wrong way. Why Evolution is True by Coyne is a very good summary as well and he spends time talking about the geographic distribution of species which I hadn’t really considered before.” It is books such as you have sited that actually turned my attention to this site. Dawkins, Miller, Coyne, they are all very clever people, but they are strict with their agenda. Which I shouldn’t need to describe, as it is plainly obvious to anyone who has read their material. I have enjoyed discussing this with you, and appreciate the time you have taken. Although I can’t help but feel we have very sadly reached an end. Like Dawkins and Coyne et al, you see evolution and can’t see past it. A few posts back you almost accused me, it seemed, of ‘having made my mind up’, but do you not think this is the case with you? There is an in article on this very point http://darwins-god.blogspot.co.uk/2012/07/evolutionist-speaks-savor-irony.html “All scientists agree that evolution has occurred,” the University of Massachusetts professor goes on to explain that natural selection “eliminates and maybe maintains, but it doesn’t create,” that she believed the textbook orthodoxy that random mutations lead to evolutionary change and new species “until I looked for evidence,” and that “There is no gradualism in the fossil record.” Regardless of this womans ideas in the past she makes a very good point, and it’s one that I have been pursuing for some time now: what does the evidence actually say? Why don’t you try doing the same. Look at the evidence for yourself instead of relying on sources such as Dawkins and Coyne. Perhaps then you will learn something. Ah, but there lies the problem: you don’t want to ;) Thanks again. And all the best PPeterJ

July 10, 2012

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Kairosfocus @ 191

KAIROSFOCUS: There is every reason to believe that transitionals would have vastly outnumbered final forms. CLAVDIVS: You made the claim that the final forms outnumber the transitionals. What I want to know is: How are you distringuishing between final forms and transitional forms? If we do not know this then we cannot assess the soundness of your argument. KAIROSFOCUS: Pardon me but 150 years worth of looking for “missing links” and of headlining and highlighting links and icons in museums that then had to be taken back and similar, says very different to your talking points.

No talking points, Kairosfocus, just assessing the soundness of your argument that final forms outnumber transitional forms in the fossil record. You have not backed it up by explaining your definition of final forms vs transitional forms, despite being asked to do so a number of times. Until you do so, your argument about the relative paucity of transitional forms is irrelevant, because nobody knows exactly what it is. This is a purely logical point that has nothing to do with burden shifting. You have argued there are more Xs than Ys. It behooves you to define what you mean by X and Y.

KAIROSFOCUS: finally, I have cited Gould as exactly a case of an expert giving a key admission against known interest. You know what that is, or you SHOULD know what that is, and its evidentiary value. Gould went out and tried to develop a theory of evo, to account for the missing transitionals. That too is telling, so your attempted turnabout is itself revealing.

Actually, the turnabout comes straight from your own cited authority, Gould, so don't blame me for the own goal. Here is what you said @ 187 about Gould:

KAIROSFOCUS: So, where are the overwhelming numbers of missing [found] links? Gould tells us, they are not there, period. Indeed, he spent decades advancing an alternative theory to provide an explanation after the fact that would make it seem plausible that his would be the case.

Did Gould say anything like "there are no transitional forms, period"? No he did not, and I quoted him for you on that very question. Are you suggesting Gould did not know what Gould himself meant? Not only that, Gould went on to complain, on a number of occasions, that his words were being taken out of context, and he pointed out specifically and in detail how his views on transitional fossil sequences were being misrepresented:

Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again ... as admitting that the fossil record includes no transitional forms. The punctuations occur at the level of species; directional trends (on the staircase model) are rife at the higher level of transitions within major groups. [Gould S.J., "Evolution as Fact and Theory," Hens Teeth and Horse's Toes: Further Reflections in Natural History, New York: W. W. Norton & Co., 1983, pp. 258-260] Creationists, with their usual skill in the art of phony rhetoric, cynically distorted punctuated equilibrium for their own ends, claiming that we had virtually thrown in the towel and admitted that the fossil record contains no intermediate forms. (Punctuated equilibrium, on the other hand, is a different theory of intermediacy for evolutionary trends-pushing a ball up an inclined plane for gradualism, climbing a staircase for punctuated euilibrium.) [Gould S.J., "Opus 200," Natural History, Aug. 1991] Punctuated equilibrium is neither a creationist idea nor even a non-Darwinian evolutionary theory about sudden change that produces a new species all at once in a single generation. Punctuated equilibrium accepts the conventional idea that new species form over hundreds or thousands of generations and through an extensive series of intermediate stages. But geological time is so long that even a few thousand years may appear as a mere "moment" relative to the several million years of existence for most species. Thus, rates of evolution vary enormously and new species may appear to arise "suddenly" in geological time, even though the time involved would seem long, and the change very slow, when compared to a human lifetime. [Gould S.J., quoted in Teaching About Evolution and the Nature of Science (1998), National Academy of Sciences] Gould could not have been more clear that transitional forms are "rife" in the fossil record. Cheers

CLAVDIVS

July 10, 2012

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KF, Does that mean you're not going to answer my questions about fully and not fully formed body types?Jerad

July 10, 2012

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KF,

Do me the favour of identifying an observed case where blind chance and mechanical necessity sufficed to produce digital symbolic codes and algorithms [both of which reflect purpose, intentionality and logical-linguistic ability], storage media loaded with same, organised executing machines and associated, co-ordinated material flows. Then work your way through the presentation here on what a “simplest” self replicator requires.

I cant do an observed case but I think the evidence points to DNA being created via non-directed processes.

Failing that, do us all the basic respect of acknowledging why we think inference from sign to signified is warranted.

I certainly acknowledge why you think inference to design is warranted. I just disagree with you.

Failing both, sad to say, it is clear that no mere evidence that is reasonably accessible will move you.

I didn't ask to be moved. I only wanted to make sure I didn't misrepresent the arguments for ID. I understand them much better now, thanks!!

I have addressed the requisites of a self-replicating constructor automaton here, building on Mignea’s presentation.

Interesting. Of course DNA doesn't have a blueprint (a one-to-one mapping) of the structure it creates but interesting. How would it look in a biological situation? If all the machine did was self-replication and if it had no other function except that I would think it could be pretty small.

the 1,000 bit FSCI threshold is based on all the 10^80 or so atoms of the observed cosmos, and changing state every 10^-45s, for the thermodynamic lifespan of the cosmos. All of those resources could not search 1 in 10^150 of the possible states for just 1,000 bits. That is why, per sampling theory, a blind, chance plus necessity walk in the config space is maximally unlikely to hit on ANY FSCI zone in such a space. And the minimally complex range for living systems, is 100,000 bits. That is 9.99 *10^30,102 possibilities. Your hoped for billions and billions of double goldilocks zone (water-zone orbit, terrestrial planet in the habitable zone of a well behaved spiral galaxy), terrestrial planets are just a drop in that bucket. Nope, that is nowhere near enough space to seriously sample something like that with any hope of hitting on FSCI zones.

How do you know the minimally complex range for living systems is 100,000 bits? And if the first self replicator was only a self replicator, nothing else, then surely it would be smaller than that? Let's see . . . 4 bases: A, C, T, G . . . that's 2 bits per base. 100,000 bits means possibly 50,000 bases. That's more than lots of viruses. I'm thinking that 100,000 may be too high. The smallest non-viral genome is a bacterium with about 160,000 base pairs so that clearly is over the 100,000 bit threshold. I'd like to see more work done on a minimal biological self replicator before I make a call on this. I see what you're getting at and I'd be very, very interested to see it all translated into a biological context given that some viruses are well under the 100,000 bit limit.Jerad

July 10, 2012

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PPS: See what the relevant threshold looks like per requisites of a self-replicating automaton?kairosfocus

July 10, 2012

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PS: Jerad, the 1,000 bit FSCI threshold is based on all the 10^80 or so atoms of the observed cosmos, and changing state every 10^-45s, for the thermodynamic lifespan of the cosmos. All of those resources could not search 1 in 10^150 of the possible states for just 1,000 bits. That is why, per sampling theory, a blind, chance plus necessity walk in the config space is maximally unlikely to hit on ANY FSCI zone in such a space. And the minimally complex range for living systems, is 100,000 bits. That is 9.99 *10^30,102 possibilities. Your hoped for billions and billions of double goldilocks zone (water-zone orbit, terrestrial planet in the habitable zone of a well behaved spiral galaxy), terrestrial planets are just a drop in that bucket. Nope, that is nowhere near enough space to seriously sample something like that with any hope of hitting on FSCI zones.kairosfocus

July 10, 2012

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F/N: I have addressed the requisites of a self-replicating constructor automaton here, building on Mignea's presentation.kairosfocus

July 10, 2012

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Jerad: Do me the favour of identifying an observed case where blind chance and mechanical necessity sufficed to produce digital symbolic codes and algorithms [both of which reflect purpose, intentionality and logical-linguistic ability], storage media loaded with same, organised executing machines and associated, co-ordinated material flows. Then work your way through the presentation here on what a "simplest" self replicator requires. Failing that, do us all the basic respect of acknowledging why we think inference from sign to signified is warranted. Failing both, sad to say, it is clear that no mere evidence that is reasonably accessible will move you. G'day KFkairosfocus

July 10, 2012

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kuartus,

erad, who or what is this designer which you repeatedly claim there is no evidence for?

The one KF keeps inferring when he asserts some biological features could only come about via intelligent design. No evidence except the 'designed' object in question that is. And if you use the object you're trying to establish is designed in your argument then it begins to sound like a circular argument. To me anyway.Jerad

July 10, 2012

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Jerad, who or what is this designer which you repeatedly claim there is no evidence for?kuartus

July 10, 2012

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KF,

I of course point you tot he just above on the subject of fully formed body plans, as though that is really a mystery in context. When pine trees appear they are pine trees. Ants are ants. When bats appear, they are bats. Lobsters are lobsters, shrimp are shrimp. The missing links are missing, and Gould et al tell us not to expect them to be found. Appearance, stasis, disappearance or continutity into the modern era.

I'm still not quite sure what you're saying . . . are penguins incomplete forms? (Not having 'functional' wings) Or flying squirrels? (Being somewhere between regular squirrels and bats) Or the proposed precursors to whales? Since dogs descended from wolves are wolves incomplete forms? And, in 500 years, if dogs and wolves are no longer able to interbreed would that change your mind? What about the plant brussels sprouts came from? What about Neanderthals? Homo Erectus?

I guess that should make me less than surprised to see how you try to deflect the force of the implications of the requisites of a von Neumann replicator joined to a constructor and controlled by digital code by making a sloppy half-quote. For, von Neumann — as you cited and as I pointed out when you wanted to skip over this key point — believed that such a replicator could get more complex ONCE ABOVE A CERTAIN THRESHOLD of complexity. The problem of course is to get to that threshold, which is well past the FSCO/I limit.

No, I noticed the reference to a threshold. What did von Neumann say the threshold was? Did he agree with your threshold?

That is why it is a safe conclusion that he origin of a metabolising, self-replicating entity is not a credible product of spontaneous processes in some warm little pond or the like.

Well, lots of people disagree with you. And, no matter how improbable, it only had to happen once on at least one of the billions and billions of planets in the Goldilock's Zone where billions and billions of molecules were colliding and combining. Life MAY be exceedingly rare. Maybe it has only happened once. But without evidence of a suitable agent what other inference can we make? We can't just magic an agent out of nothing.

Kindly explain to us on empirical evidence, the origin of digital symbolic codes, algorithms, control tapes storing the object codes, properly arranged execution machines and associated component and energy source machines, etc, by spontaneous, chance and necessity processes in that warm little pond or equivalent, again. this has been repeatedly put t6o you, but has just as repeatedly been ducked.

I assume it came about by non-directed processes. You infer a designer agent which, in my mind, there is no evidence for. I find my assumption more parsimonious.

And yet, it is the issue at the root of the whole tree of life proposed by Darwin. Without a sound, empirically based answer here, the whole scheme is literally rootless. And, the only empirically warranted source for such FSCO/I is design. Which, puts design as a credible causal candidate at the root of the whole world of life.

I'm still not willing to infer an agent for which there is no evidence aside from the phenomena in question.

Save, of course, to those who have long since made up their minds before the evidence is allowed to speak, that design is strictly verbotten, tut tut!

I never, ever claimed I was agnostic about evolutionary theory. I am here to find out what ID proponents think. I'm not trying to convert or convince anyone. Just to make sure I understand the arguments being wielded.

In other cases, small-scale variations well within the body plan limit — e.g. moth colouration, or insecticide or antibiotic resistance — are being grossly extrapolated into a grand, metaphysically driven narrative sold to us under the label, “science,” presented as practically certain knowledge.

Extrapolating from breeding information might be less warranted without all the other lines of evidence. It's the convergence of all the data that makes the case.

The real issue at stake is that a modest set of mechanisms that covers minor population adaptation has been grossly extrapolated into an account of body plan diversity, and presented to us under the false colours of being as well supported as the view that the planets orbit the Sun.

You are free to disagree of course. I've read a lot of Dr Gould's writings and I agree with CLAVDIVS: I don't think he's saying what you think he's saying. Here's a quote from one of his last books, The Structure of Evolutionary Theory "In this crucial sense, the theory of punctuated equilibrium adopts a very conservative position. The theory asserts no novel claim about modes or mechanisms of speciation; punctuated equilibrium merely takes a standard microevolutionary model and elucidates its expected expression when properly scaled into geological time."Jerad

July 10, 2012

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