Francisco Ayala: “You’re a heretic and blasphemer, but don’t ask me what I am.”

_{William Dembski

May 17, 2010

Intelligent Design}

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Darwin's Gift to Science and Religion Francisco Ayala has taken an aggressive theological stance against intelligent design, even using words like “blasphemy” and “atrocity” to characterize it (go here). But if Ayala feels entitled to make such strong accusations against ID, one might wonder what Ayala’s own theological views are. I therefore emailed him and copied Michael Ruse:

Dear Prof. Ayala,

I’m writing to inquire whether in any of your writings you lay out your present religious faith (and, if so, where?). I’m copying my friend Michael Ruse because I find his criticisms of ID parallel your own, and yet he makes clear that he himself is an atheist. You, on the other hand, regularly cite your background in the Roman Catholic Church as a priest. Yet you left the priesthood and it’s not clear what aspects of the Christian faith you retain. Do you, for instance, believe in a personal God who created the world? Do you believe that humans experience continued conscious existence after they die? Do you believe that Jesus was God incarnate? I would appreciate any clarifications you can provide. Thank you.

Blessings,
Bill Dembski

Ruse got back to me first and suggested that Ayala would not be forthcoming about his religious views, whereupon Ayala got back to me, agreeing with Ruse: “What Michael Ruse told you about my not asserting publicly my religious convictions is correct. I have stated that on numerous occasions, quoted in all sorts of publications from The New York Times and Scientific American to religious journals and periodicals.”

Interesting that Ayala is willing publicly to acknowledge his former theological views as a Roman Catholic priest (presumably he embraced RCC dogma). And yet his present theological views are off limits. Perhaps when Dover II rolls around, Ayala will be an expert witness and under deposition be required to state his theological views. In the mean time, Ayala’s reticence about his present religious faith (or lack thereof) is at best a convenient ploy.

Comments

Petruska begins by telling Timaeus that no evidence against materialism is sufficient, and with these last comments, is now telling Kairos and BA that no evidence for it is necessary. Garden variety scientism.Upright BiPed_{May 31, 2010
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Petruska you seem fairly confident in all this,, Do you mind falsifying Abel's null hypothesis? The Capabilities of Chaos and Complexity: David L. Abel - Null Hypothesis For Information Generation - 2009 To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: "Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration." A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis. http://www.mdpi.com/1422-0067/10/1/247/pdf http://mdpi.com/1422-0067/10/1/247/agbornagain77_{May 31, 2010
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At any rate, the Weasel algorithm does not require a fixed target. It only requires an oracle that ranks individuals. If the oracle shifts criteria, the population shifts accordingly. It is rather easy to write an oracle that ranks the population by its conformity to another population, rather than to a fixed target. For example, the criterion could be nearness to words in general, rather than to a particular word. It doesn't matter to the algorithm if the oracle switches languages. The algorithm will follow.Petrushka_{May 31, 2010
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Petruska you state: "The important question is not how the oracle works, or what specific information it contains. The question is whether random (non-foresightful) variation can supply changes which survive selection." Neglecting the fact that Weasel drives the variation to a predetermined "goal", it seems to you that "random variation" is the "god" that creates everything in your worldview. Thus Petruska, why does it not fascinate you in the least when conscious intention is shown to influence random number generators? Scientific Evidence That Mind Effects Matter - Random Number Generators - video http://www.metacafe.com/watch/4198007 Come on Petruska, if random (non-foresightful) variation is the be all, end all, "creator god" in your worldview, what in the heck is pushing your "creator god" around in the random number generator experiments?bornagain77_{May 31, 2010
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P: An oracle is an intelligent signaler, like in the case of Weasel, where NONFUNCTIONAL strings are evaluated on increments of proximity to a target [Hamming Distance], and are rewarded on proximity through an intelligently designed warmer/colder algorithm.. In the bio-world, the problem is not whether one may move around within an island of function through minor random variation of an already existing population, but the justification on adequate empirical evidence of the claimed chance plus blind mechanism origin of body plans requiring 100's of thousands to tens or more of millions of bits worth of information; starting from the first one. Until that is answered decisively by darwinists, assertions and declarations of the wonderful power of darwinian mechanisms to create novel body plans are simply empty statements of belief backed up by a priori commitments to evolutionary materialism. GEM of TKIkairosfocus_{May 31, 2010
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Do you not see that by Dawkins’ own admission, Weasel works by comparing variations with the defined target and keeping whatever makes an increment to target, regardless of the fact that it is non-functional?
The important question is not how the oracle works, or what specific information it contains. The question is whether random (non-foresightful) variation can supply changes which survive selection. From the point of view of the variation generator, the oracle is arbitrary. And in biology the oracle is sometimes arbitrary. There are some absolute selection criteria -- biochemistry is not arbitrary -- but there are thousands or millions of details that differentiate one individual from another. It strikes me that the discussion of Weasel tends to ignore the real issue -- not where the information comes from, but where variation comes from. What Weasel does do is demonstrate that an algorithm using a completely random variation generator can accumulate information from any arbitrary oracle.Petrushka_{May 31, 2010
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KF remarks:
...islands of function...
This paper suggests there may be more than a few additional islands of function that reduce the odds a bit!Zach Bailey_{May 31, 2010
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P: Do you not see that by Dawkins' own admission, Weasel works by comparing variations with the defined target and keeping whatever makes an increment to target, regardless of the fact that it is non-functional? [Which means that nothing remotely analogous to NS is a part of the situation in Weasel.] That he also acknowledges that this rewarding of non functional variations on increment to a preloaded target is what makes Weasel work with reasonable resources and time? Do you not see how this implies that the real problem is to get TO the shorelines of islands o function in the space of possible configs? And, that the way Dawkins did that was to implement a targetting procedure and cumulative selection process that are intelligent? And so, when you say:
Whether or not a variation in the genome results in a viable organism is determined by biochemistry, not an outside agent. The list of viable organisms is not in the mind of an agent, but is an attribute of physical laws. It really makes little difference how variations are generated, as long as the the rate of variation does not produce an entire generation of non-viable individuals.
. . . that rather gives the game away: 1 --> You are begging the question of the amount of integrated, functional information and organisation to effect a body plan, starting with the first. (And when the observed quantity of information has been brought to your attention explicitly, you have glided over it in a telling silence.) 2 --> You are begging the question of the observed structure of the space of known viable organisms: islands of function on distinct body plans that appear suddenly without the overwhelming number of transitionals that should be there on gradualist hypotheses. 3 --> Similarly, you are ducking the question of origin of complex, embryologically sound, functional organisation and associated coded information by chance processes. 4 --> We must note, again, that "natural selection" is little more than a label for the fact that if an organism is embryologically unsound, or is otherwise crippled from function in its environment, or cannot find viable mates etc, it will not have descendants. 5 --> That is, the NS part of the darwinist expression CV + NS --> Evo is a REMOVER of information, not a SOURCE. And chance --the implied source of information -- has strict limits to what it can credibly do as an information source, on the gamut of our observed cosmos. 6 --> So, you have not bridged the gap between 1,000 bits as a generous upper limit on functional by happenstance, chance based variations in data strings, and observed simplest life forms with 100+ k bases in their DNA, or that complex life forms have counts in the 10's - 100's of millions of bases or more. [Not to mention, you have nor accounted for the credible origin of language as the framework of codes, of algorithms and data structures or implementing machinery, apart from the implication of materialistic statistical miracles by the warehouse- full.]
(If you want to believe in statistical miracles, that's fine; but please don't then turn around and dismiss those who would believe that intelligence is a more credible account for the origin of complex functional organisation and information, in light of our experience of the routine source of such; especially not by making acid comments about inferring to the supernatural or Divine Feet in doors. That would show that materialistic ideological bigotry not reason would be driving the process; while hiding under the credibility of the lab coat functioning as the moral equivalent to evil masking itself in the ecclesiastical robes of yore. For, in every age, evil sneaks in by hiding in the robes of the most respected institutions and falsely claiming to act in the name of the good. Thankfully, we can always spott he woldf in sheep's clothing by seeing the presence of the wolfish tactics of trying to promote "truth" by suppressing fair examination of evidence, and resorting to the tactics of doing evils in the name of promoting good. Sadly, resemblance to recent trends with appealing to "consensus" of the power brokers of key institutions, and backing this up by expelling dissenting scientists and thinkers is not coincidental.)
7 --> In saying that viability of a variation "is determined by biochemistry" you have begged the question of how that biochemistry works. 8 --> Namely, it is based on an information system that uses a definite digital code, step by step finite procedures with halting [i.e. algorithms], string based data structures, and associated implementing namomachinery.
(And that is no mere "analogy" that one can airily dismiss without properly reckoning with how central reasoning by apt analogy is to inductive logic. For, as we can see in commonly available animations [or harder to understand detailed descriptions], DNA stores 4-state per base digital data, the mRNA transfers that data to the ribosome, in which with the aid of tRNA that uses key-lock matching anticodons and a nudged arm with active tip procedure to chain amino acids step by step, terminating with a stop codon and thus making the protein workhorse machines for the cell.)
9 --> Thus, while the various machines and processes are indeed using the power of "physical laws," those laws do not account for the organisation. Information bases systems and complex functional organisation do. (Back to Leibniz: when we see the wheels of a mill grinding away and with wheat coming in one end, flour going out the other, we do not explain the functionality of the organisation on the laws and forces and materials that are used as means to effect a purposefully organised, information-rich, onward useful and valuable end.) 10 --> By utter contrast, we routinely see that intelligence produces complex functional organisation by design, and that functionally specific, complex information is a routine empirically recognisable signature of that effort. 11 --> In short, it is plainly evident tha the reason why you refuse to allow a serious diswcussion o9n inference to best explanation with all the relevant possible causes of "variation" on the table is a priori materialism by the back door. Namely, imposition of so called methodological naturalism by which the only admitted sources of variation are chance and mechanical necessity; those that happen to sit well with evolutionary materialism as a dogma. 12 --> Indeed, this set of materialistic blinkers plainly blinds you to the obvious -- and author-admitted -- facts on Weasel. ============ P, please think again. G'day GEM of TKIkairosfocus_{May 31, 2010
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Mr Timaeus, KF-san, Thank you for your kind wishes. Having just returned recently from Malaysia, I won't be heading off to Tahiti! My strategy is to dodge all the people I'd rather not deal with by saying that the wedding is in Budapest, when it is in fact in Prague. The happy but exhausted couple will be going no further than a spa in the Czech countryside. (Sorry, VMartin, not hiking the High Tatras this year.) Oh, and I downloaded "Trilobites: Eyewitness to Evolution" to my nook for those brief moments.Nakashima_{May 31, 2010
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Petruska, seeing as the coding found in simplest life on earth greatly exceeds what man has done so far,,,,,,,,,,, "No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms' genomes programmed?" - David L. Abel and Jack T. Trevors, “Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information,” Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8 http://www.biomedcentral.com/content/pdf/1742-4682-2-29.pdf Stephen Meyer is interviewed about the "information problem" in DNA, Signature in the Cell - video http://downloads.cbn.com/cbnnewsplayer/cbnplayer.swf?aid=8497 The Cell - A World Of Complexity Darwin Never Dreamed Of - Donald E. Johnson - video http://www.metacafe.com/watch/4139390 Cells Are Like Robust Computational Systems, - June 2009 Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,"We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail." http://www.sciencedaily.com/releases/2009/06/090616103205.htm ,,,,,,,, and you are convinced that random variation and natural selection can produce what teams of software engineers can't, Please tell me exactly why Bill Gates does not employ millions of random number generators and selection software programs to produce staggering levels of computer coding? Maybe Bill Gates wants computers to do more than spit out "Me Thinks Its Like A Weasel? and better antennas? Just a thought petruska,,, I can tell you one thing that Random Number generators did that I found interesting: The Global Consciousness Project http://www.youtube.com/watch?v=GPUTA1a6KHkbornagain77_{May 30, 2010
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Information is not "smuggled in." The information about the relative value of variants is in the oracle, the selector. The algorithm merely accumulates or preserves information. Whether or not a variation in the genome results in a viable organism is determined by biochemistry, not an outside agent. The list of viable organisms is not in the mind of an agent, but is an attribute of physical laws. It really makes little difference how variations are generated, as long as the the rate of variation does not produce an entire generation of non-viable individuals.Petrushka_{May 30, 2010
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P: First, a corrective: Weasel is a classic example of design by smuggled in active information in the name of a non-designed process. It rewards nonsense -- non-functional -- strings on mere increments in proximity to target, which is thus shown to be pre-loaded and designed. As Dawkins says in so many words, but if you are not primed to spot the significance of that, you will miss it:
It . . . begins by choosing a random sequence of 28 letters ... it duplicates it repeatedly, but with a certain chance of random error – 'mutation' – in the copying. The computer examines the mutant nonsense phrases, the 'progeny' of the original phrase, and chooses the one which, however slightly, most resembles the target phrase, METHINKS IT IS LIKE A WEASEL . . . . What matters is the difference between the time taken by cumulative selection, and the time which the same computer, working flat out at the same rate, would take to reach the target phrase if it were forced to use the other procedure of single-step selection: about a million million million million million years. This is more than a million million million times as long as the universe has so far existed . . . . [TBW, Ch 3]
He needs to openly acknowledge the blunder, and correct himself on this. On the bigger question, observe carefully that what has been pointed out is that complex bio-function is based on codes and implementation of coded algorithms and data in the cell, which is thus shown to rest in islands of function in the space of possible configurations of the data storage elements, here the GCAT elements of DNA. Putative blind chance plus necessity evolutionary mechanisms will have to start from an arbitrary config and plausibly get to shores of islands of function, starting with origin of life. That, in a context where observed life starts in the 100's of k bases. (Autocatalytic molecules that do not code for associated metabolic functions and machines need not apply.) For the first life, that means implementing a version of a von Neumann self-replicator, which requires:
(i) an underlying storable code to record the required information to create not only (a) the primary functional machine [here, a metabolic entity] but also (b) the self-replicating facility; and, that (c) can express step by step finite procedures for using the facility; (ii) a coded blueprint/tape record of such specifications and (explicit or implicit) instructions, together with (iii) a tape reader [[called “the constructor” by von Neumann] that reads and interprets the coded specifications and associated instructions; thus controlling: (iv) position-arm implementing machines with “tool tips” controlled by the tape reader and used to carry out the action-steps for the specified replication (including replication of the constructor itself); backed up by (v) either: (1) a pre-existing reservoir of required parts and energy sources, or (2) associated “metabolic” machines carrying out activities that as a part of their function, can provide required specific materials/parts and forms of energy for the replication facility, by using the generic resources in the surrounding environment.
That such codes, algorithms and machines are spontaneously producable by chance molecular interactions and chemical forces in credible pre-life soups is highly dubious; for reasons already identified. And, by comparison with simplest observed life forms, we are looking at 100+ k bases, or over 100 times the threshold for information spaces that the whole cosmos we observe cannot credibly walk through enough of by blind chance and associated mechanical necessity to make happening on an island of function reasonable. Then, to create novel body plans, we are looking at increments of 10's or more of millions of bases, for the sort of level of complexity implied by say the Cambrian fossils. And, the developments will have to be embryologically feasible and integrated, starting from early systems and structures unfolding from the initial cells of a new life form. The idea that by tiny increments this can be surmounted -- the easy back way up Mt Improbable hypothesis -- founders on the organisation and informational requisites to get to minimum functionality for say a wing. ESPECIALLY AS WE HAVE YET TO SEE OBSERVATIONALLY THAT CHANCE VARIATIONS IN A DATA STRINGS HAVE CAPABILITY TO GENERATE FUNCTIONAL CODE BEYOND A REASONABLE THRESHOLD. Of course, chance in principle can do any configuration. But beyond a point you are producing the materialistic equivalent of magic. E.g. as I have discussed here, the notion that by chance rocks falling down a hillside on the Welsh border would spontaneously form "Welcome to Wales" is strictly possible but so overwhelmingly beyond reasonable plausibility on the sea of possible configs that if we were to see an avalanche doing that we would suspect a trick. Your side is asserting that you can provide an easy back path up Mt Improbable. You need to show it, and on something a bit more credible than Weasel. In particular, as a frst step, you need to provide us a web of missing links that would turn the tree of life into a gradually evolving pattern of incrementally formed novel body plans. (Pleas about the paucity of the fossil record are wearing thin after 150+ years and 1/4+ millions of species with multiplied millions of individuals. And, with many or the "right" type and strata of rocks preserving soft bodied animals etc, just not the ones expected by Darwinists. For decades now it has been an open secret of paleontology that the fossil record pattern of gaps and stasis then disappearance or continuation into today's world, is real. That's why punctuated equlibria models were invented -- to try to explain the systematic absence of desired and expected evidence.) What has been observed is minor variations within existing body plans, and not a mechanism that on the information challenge can credibly account for origin of body plans starting with the very first one. Overgenerous extrapolation from well inside the FSCI threshold to well beyond it is an implicit admission of want of a solid case. In that context, Behe's observations on the limits with malaria parasites shows microevo and limits on it per observations in a context of more reproductions than the vertebrates can have had. 1,000 bits -- which is far within the scope of DNA for the first body plan, and for observed DNA increments to move to complex multicellular body plans -- is a threshold that identifies where the search capacity of the cosmos acting on a random walk till it can get a reproducing population going on an island of function so that incremental changes can move up the hill to optimality through differential reproductive success -- becomes utterly inadequate for a plausible chance based information innovation mechanism. (Recall, natural selection works by culling out less successful sub populations in relevant environments, i.e by REMOVING information from the population. It is not and cannot be the source of the information.) So, please stop playing at burden of proof shifting and start showing that blind chance plus mechanical necessity acting on happenstance initial conditions can produce algorithmically functional, code based information beyond the FSCI limit. Posts in this thread are ample enough demonstration that intelligence is a routinely observed source of such FSCI as we are interested in. I have already shown the inference to best explanation on empirically known routine causes of FSCI and associated reasons why FSCI is not a credible product of chance + necessity. So, if there is a burden of proof for the design side, it has already been met in the relevant form: warrant on empirical and analytical evidence to best explanation. GEM of TKIkairosfocus_{May 30, 2010
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Petruska you state: "I think it would bee interesting if ID proponents could demonstrate that all functional structures and objects are the result of intentionality." That is the whole point Petruska all functional structures (and information) that we do know the origination of have always arisen from intelligence (intention) and not from material processes. Including the post which you just posted which I can somewhat safely surmise arose from an intelligent being and not from a non-intelligent one and which exceeds the,,, The Universal Plausibility Metric (UPM) & Principle (UPP) - Abel - Dec. 2009 Excerpt: Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified. But can something so seemingly relative and subjective as plausibility ever be quantified? Amazingly, the answer is, "Yes.",,, c?u = Universe = 10^13 reactions/sec X 10^17 secs X 10^78 atoms = 10^108 c?g = Galaxy = 10^13 X 10^17 X 10^66 atoms = 10^96 c?s = Solar System = 10^13 X 10^17 X 10^55 atoms = 10^85 c?e = Earth = 10^13 X 10^17 X 10^40 atoms = 10^70 http://www.tbiomed.com/content/6/1/27 Petruska Instead of ID proponents having to prove every single functional structure arose by intelligence, as you are asking, the burden is on you to provide just one example of purely material processes doing as such: Petruska the materialistic argument essentially appears to be like this: Premise One: No materialistic cause of specified complex information is known. Conclusion: Therefore, it must arise from some unknown materialistic cause. On the other hand, Stephen Meyer describes the intelligent design argument as follows: “Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information. “Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information. “Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.” As for you nonchalantly saying there are multiple paths to the bacterial flagellum that don't involve intelligence all I can say is , Fine, Prove It!!! Michael Behe on Falsifying Intelligent Design - video http://www.youtube.com/watch?v=N8jXXJN4o_A Bacterial Flagellum - A Sheer Wonder Of Intelligent Design - video http://www.metacafe.com/watch/3994630 Genetic Entropy Refutation of Nick Matzke's TTSS (type III secretion system) to Flagellum Evolutionary Narrative: Excerpt: Comparative genomic analysis show that flagellar genes have been differentially lost in endosymbiotic bacteria of insects. Only proteins involved in protein export within the flagella assembly pathway (type III secretion system and the basal-body) have been kept... http://mbe.oxfordjournals.org/cgi/content/abstract/msn153v1 "One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. ‘The most parsimonious explanation is that the T3SS arose later," Howard Ochman - Biochemist - New Scientist (Feb 16, 2008) Genetic analysis of coordinate flagellar and type III - Scott Minnich and Stephen Meyer Molecular machines display a key signature or hallmark of design, namely, irreducible complexity. In all irreducibly complex systems in which the cause of the system is known by experience or observation, intelligent design or engineering played a role the origin of the system. http://www.discovery.org/scripts/viewDB/filesDB-download.php?id=389 Bacterial Flagella: A Paradigm for Design - Scott Minnich - Video http://www.vimeo.com/9032112bornagain77_{May 30, 2010
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Nakashima-San: Congrats, mon. Best wishes! (And, don't forget, you are now under new management!) GEM of TKIkairosfocus_{May 30, 2010
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First, the basic design inference is in principle quite easy to overthrow: provide a specific, credibly observed case where 125 bytes of functional information originated by chance and blind mechanical necessity.
In principle, Weasel is an example of chance and selection. I can see no rational argument demonstrating that Weasel's algorithm for accumulating information is mathematically different from biological evolution. In both cases, the algorithm captures and accumulates information that exists independently of the operation of the algorithm. It would be an error though, to argue that biological evolution seeks a specific target or targets. All that is necessary for change to accumulate is that some changes are not so detrimental as to prevent reproduction. Other that that, it makes no difference whether the changes are trivial, such as hair color, or metabolically significant. I think it would bee interesting if ID proponents could demonstrate that all functional structures and objects are the result of intentionality. Is leishmaniasis the result of intentionality, or is it the result of chance and selection? Biological evolution may not provide a videotape of every point of change, but it does provide an observed mechanism of change, a mechanism that has been routinely exploited by human plant and animal breeders for thousands of years. I think it would be interesting for some ID advocate to demonstrate conclusively, that change cannot, in principle, accumulate -- indefinitely, to use Wallace's word. As for 125 Bytes, that is a bit of an escalation. Behe set the limit at approximately two bits. There are only a couple pf proteins that are bot essential to all flagella like structures and common to all known organisms that have such structures. There are, in fact, numerous pathways to similar functionality, and no cases where an exact sequence of data must be specified in advance.Petrushka_{May 30, 2010
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Nakashima: Congratulations on your upcoming marriage. Yes, now would be a good time to leave web debates aside for a while. Your new spouse will not appreciate sharing you with the computer on your honeymoon. And while I relish the image of you reading one of Behe's or Denton's books on the plane to Tahiti, I wouldn't advise bringing along any ID literature, either. You perhaps have already heard the joke: "I can't tonight, dear -- someone on the Internet is wrong." Best wishes for your new life, Nakashima. T.Timaeus_{May 30, 2010
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PS: Darwinists do not like to hear me cite Lewontin on the point, but he makes the matter plain: ______________ >>. . . To Sagan, as to all but a few other scientists, it is self-evident that the practices of science provide the surest method of putting us in contact with physical reality, and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test . . . . Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. 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. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. >> ________________ That is what you need to show us you are not falling into. Whether for the whale [and the Pakicetus blunder is a telling issue, one that happened within 20 years] or the inner ear or the Cambrian revolution or something else, you need to show us how it is credible t6hat chance variation plus natural selection, etc gave rise to novel and significant body plans. Including accounting for information, and the organization that emerges incrementally in competing populations that then allow for superior performing varieties to dominate. And remember, computer simulations do not count: we need real world data not someone's fancy multimedia just so story.kairosfocus_{May 30, 2010
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Petrushka First, the basic design inference is in principle quite easy to overthrow: provide a specific, credibly observed case where 125 bytes of functional information originated by chance and blind mechanical necessity. We can show 2 Zettabytes worth of cases in point on intelligent design, in the Internet. After years of asking, objectors cannot provide a single case where chance + necessity without intelligence give rise to a relevant case of FSCI. Also, factoring in:
a: what we can easily see about the configuration space of 1,000 bits [2^1,000 => ~ 1.07 * 10^301 configurations] and b: the search capacity of the observed cosmos [~ 10^150 Planck time states for 10^80 atoms in 50 mn times the usual timeline since the Big bang], we see that: c: the cosmos acting as a search engine could not credibly sample 1 in 10^150th of the configs, thus d: the reason for chance + blind necessity not being able to access functional configs of a relevant degree of complexity is the swamping out of even a universe full of resources by the config space for just 1,000 bits.
So, we have good empirical and analytic grounds for inferring that FSCI is an empirically reliable sign of design. In that context, on observing that cell based life rests on the DNA based information system, and that both the original and novel body plans will easily exceed the 1,000 bit threshold [500 base pairs, what a few reasonable proteins would take up], we have good reason to infer from FSCI to design as its best explanation. In the case of the evidence and claims usually cited to substantiate darwinist claims, we find that often the empirical evidence is well below the relevant threshold of complexity -- point mutations and micro-evolution more generally. And when evidence is brought out to claim body plan level evolution by Darwinist mechanisms, we find that even if we accept the evidence as being explicable in terms of ancestry and descent, it fits at least as well with an intelligently guided process. Moreover, too often, when evidence is interpreted in Darwinist terms, it is by a priori, ideological, institutional or philosophical exclusion of otherwise relevant alternatives. So, we are asking for evidence that would truly substantiate the claim. But obviously from your dismissive reference to the usual darwinist claim of "incredulity" on our part, you do not have real evidence that can discriminate between Darwinist and non-darwinist mechanisms, including intelligence. Going further, you plainly do not have the chain of evidence that should be all over the animal and plant kingdoms: gradual development form unicellular to multicellular organisms and various forms. Instead we see islands of forms, which fit with the design insight that functional coded algorithmic information is going to come in islands. And, when we turn to the origin of the first life forms, we see that observed life is based on coded information interpreted and carried out by namomachinery that uses information to guide its actions step by step, e.g. in protein synthesis. Worse, we find nowhere the faintest trace of a credible account of how codes, algorithms and implem4enting machinery could credibly originate in a pre-biotic world by chance plus blind necessity. Indeed, we can see how the RNA and metabolism first views are mutually destructive, as say the recent Shapiro-Orgel exchange shows. So, if you are going to claim a demonstrative case of macro-evo by darwinist mechanisms, you need to give solid answers to serious challenges. A priori materialism that makes just so stories seem plausible by mere logical implication do not count. GEM of TKIkairosfocus_{May 30, 2010
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There is absolutely nothing in the fossil record that supports a Darwinian mechanism. Yes, there is the appearance of new forms but nothing points to a gradual mechanism as its driver. The fact that one points to the inner ear is an admission of weakness. There must have been millions of transitions and this is all one has. There is no obvious mechanism for these changes. In the whales there are large gaps and no evidence of all the side branches that must exist in a Darwinian scenario. Every step is viable (and there are theoretically thousands of steps) and then each step can theoretically branch in many directions and we should thus witness branches that are several levels of magnitude greater in number than exist in the fossil record and also in the current suite of organisms on the earth. The absence of these branches indicates that the process did not work this way or that there was something within the organism that propelled it in specific directions. Either finding disproves Darwinian processes and most likely any naturalistic process. Micro evolution operates to refine species in small ways but there is nothing in the fossil record to indicate it can build complex novel characteristics nor is there anything in the current species on earth today to indicate such a capability. The fact that no one can provide it is telling and I often ask where does Richard Dawkins and Jerry Coyne do so in their books. These are two of the modern disciples of Darwin and they cannot do it.jerry_{May 30, 2010
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A claimed ancestral sequence of fossils is laid out, and loss of function joined to emergence of new function is woven as the standard just so story. But at no point do we hear of a detailed genetic, developmental and biochemical pathway that credibly competently creates the new function based on the claimed dynamic principles.
I'm thinking the demand for transitional fossils is somewhat less than sincere. When a nearly perfect transitional series is available, it is unconvincing because it doesn't include the complete sequence of DNA changes that produced it. When whale transitionals were entirely missing, creationists pointed to this gap as evidence against evolution. As transitionals have been found, the demand switches to DNA sequences, which must be complete -- no gaps at all. I can only point out out that if this tactic were persuasive in courtrooms, where people's lives and liberty were at stake, no one would be convicted. We know from animal breeding that the shape of facial bones is quite malleable and selection alone can take us from the long snout of sighthounds to the squished face of the Pekingese. But you guys are a tough jury. The prisoner will go free.Petrushka_{May 30, 2010
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PS: Dr Hunter's remarks on Horizontal Gene Transfer amplify the force of the point on the need to account for origin of complex functional information and implementing mechanisms in biological life forms.kairosfocus_{May 30, 2010
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Petrushka: Timaeus at 132 has raised some specific challenges that Darwinian theories of macro-level, body plan origins need to answer. In 128, I raised the point that once one talks about chance variation plus natural selection -- which last is simply a culler not a source of information -- as being able to move from a microbe with a genome ~ 1 mn bases, to body plans with ~ 10's - 100's+ mns of bases, we are running orders of magnitude past the credible information-generating capacity of random walks in genome space. (Indeed, we can add from Behe that in several decades, with more reproductive events than the vertebrate line can have had, malaria parasites responding to the severe pressure of antimalarial drugs, have only gone as far as 2 - 3 base pairs worth of more or less co-ordinated variation.) Your further points are therefore looking highly illustrative of a point made by Johnson, responding to Lewontin's a priori evolutionary materialism:
For scientific materialists the materialism comes first; the science comes thereafter. [Emphasis original]We might more accurately term them "materialists employing science." And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) "give the appearance of having been designed for a purpose." [Emphasis added.] . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses.[Emphasis added.] [The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]
So, I will comment on a few points: 1] P,134: If underperforming individuals are culled, one might ask where their underperforming genes came from. The answer would be, from the same source that all variation comes from. What we generally observe is that existing, functioning organisms on a viable body plan reproduce, and sometimes there is relatively minor variation. Too often, that variation is inconsistent with life or with reproduction. In many other cases, we see loss of function or garbling of genes that may attract the eye of the artificial selector [e.g. with so-called fancy goldfish], or in the face of an unusual pressure like drugs or insecticides. Minor variation happens, and can be traced to actual mutations in some cases, in others to selecting out of existing varieties. (E.g. examination of bodies of arctic explorers from before the antibiotic era turned up antibiotic-resistant strains.] None of this addresses the issue of origin of novel body plans, and accounts for the origin of functional information in viable organisms well beyond 1,000 bits to achieve that. (And by the way, please notice I have discussed islands of function within which variations and selections can happily proceed; the issue is to get to the islands of function, or else to show beyond reasonable doubt on empirical data that the functional subset of the genomic config space is an interconnected tree. So far, after 150 years of trying and 1/4+ mn fossil species and millions more in the existing world, we still see the pattern of appearance, stasis and disappearance or continuation into today's world. That is, the observations fit with islands of function, and that starts with the Cambrian revolution.) 2] A changed allele can result in the individual failing to reproduce, or it can affect the probability of the individual reproducing. The effect can be statistical rather than absolute, as you have indicated. Given time, this algorithm can produce any genome. The evidence is that most variations are neutral to increasingly adverse, as would be expected from the requisites of an integrated, intricate functional basis for life. In short, the pattern supports the islands of function view. The proposed algorithm can explain the tendency of populations to remain stable in form -- Blythian natural selection: the sports usually do not work so well as a rule and get weeded out. In other cases, it can explain minor variations, like relative dominance of light/dark moths [noting the problems with how observations were made and reported] or the switching off of a regulator on penicillinase production, or variation of an enzyme to eat a fairly closely related chemical to proteins, nylon, or the oscillating variation in finch beak sizes that were so celebrated a few decades back. It may explain specialisaiton and loss of variability to fit into a new ecological niche. But, it does not begin to explain and empirically substantiate the origin of relevant body plans by darwinian mechanisms. For, no plausible mechanism for origin of substantial quanta of functional information has been provided, nor has there been justification for the idea that the overall set of major body plans come in a continuum that can be incrementally scanned by a tree starting from its roots. 3] For evolution to be true, all existing genomes must be placeable in a nested hierarchy A nested hierarchy antedates the creation of macroevolutionary theory [Linnaeus was in fact a Creationist], and fits in with say creation in an orderly pattern, or imposition of forms that serve as attractors for variations, or guidance of variation by intelligent direction through front-loading or even use of a library of parts. In this regard we should reflect on mosaics like the Platypus that has not only gross features from all across the animal kingdom, but genes and proteins etc too. In short, this is not a point that discriminates across relevant theories. It is only a priori ruling out of otherwise relevant alternatives that makes it seem to especially support the Darwinian model. 4] and historically, every individual must have exact or nearly exact copies of its parents genes This is simply to say that variation must be incremental, to preserve viability. It begs the question of how then do we bridge the gaps between body plans, starting with unicellular organisms and ending with dozens of phyla [and equivalent in other kingdoms] worth. And this, in the teeth of strong evidence that complex functional information is not easily transformed incrementally from one form to another that is significantly different. Designers of course routinely adapt existing information to create novel systems. 5] 135, Biologists since the 1930s have been quantifying the frequency of mutations and the mutational distance between species. This activity has been near the top of the priority list since we have been able to study biology at the molecular level. It’s a good question. It occupies the center. That is for 50 - 80 years, the question has remained stubbornly resistant to answers in a Darwinian frame. Especially when we move to the relevant level, not origin of species [which is often an arbitrary construct as say the inter-specific breeding of Finches in Galapagos showed], but instead the origin of body plans. 6] Why not look at a well preserved sequence, such as the evolution of the mammalian inner ear? Let's use Wiki's summary to show the problem with this and other similar show and tell on the bones cases:
The evolution of mammalian auditory ossicles is one of the most well-documented[1] and important evolutionary events, demonstrating both numerous transitional forms as well as an excellent example of exaptation, the re-purposing of existing structures during evolution. In reptiles, the eardrum is connected to the inner ear via a single bone, the stapes or stirrup, while the upper and lower jaws contain several bones not found in mammals. Over the course of the evolution of mammals, one lower and one upper jaw bone (the articular and quadrate) lost their purpose in the jaw joint and were put to new use in the middle ear, connecting to the stapes and forming a chain of three bones (collectively called the ossicles) which amplify sounds and allow more acute hearing. In mammals, these three bones are known as the malleus, incus, and stapes (hammer, anvil, and stirrup respectively). The evidence that the malleus and incus are homologous to the reptilian articular and quadrate was originally embryological, and since this discovery an abundance of transitional fossils has both supported the conclusion and given a detailed history of the transition.[2] The evolution of the stapes was an earlier and distinct event.
The after the fact ad hocness of the account leaps out. Anatomically and embryologically, certain bones are related. A claimed ancestral sequence of fossils is laid out, and loss of function joined to emergence of new function is woven as the standard just so story. But at no point do we hear of a detailed genetic, developmental and biochemical pathway that credibly competently creates the new function based on the claimed dynamic principles. A library of adaptable anatomical parts that can be shaped to do different jobs in different animals is just as compatible with the evidence as is he standard narrative, but of course, such an alternative is not to be permitted to interrupt the neat little story. Not to mention, we do not see an explanation for how at each stage of minor variations, advantages drove change, leading to a continuum from reptilian to mammalian ears. Same for wings for birds and bats, same for all the diverse co-ordinated features needed to make a whale out of a bear or a wolf or a hippo or whatever ancestor de jour is in favour just now. Anyone who has had to design an audio amplifier and sensor system associated therewith can tell you that even with a generic block diagram or even a circuit level framework easily in hand, the trouble lies in the specific details, and in the careful matching and coodination of the several components to form an integrated functional whole. Just so, after the fact generality based tales of incremental changes resting on the question-begging assumed validity of the Darwinian framework -- as opposed to level playing field inference to best explanation across relevant competing explanations -- do not make the grade. What evidence do you have that the variation (assuming reptilian ancestry of mammals) was not built-in, or loaded in from a library of parts modified for the particular purpose in mind for the new group of animals? Etc? Or, that there is a credible continuous tree-of-life genetic and embryological path that generates the masses of coordinated functional information incrementally, generation by generation? Where in each hypothesised increment of advantageous change is there enough time and advantage to fix the small steps? In short, what demonstrated and calibrated mechanism can -- per empirical data -- credibly generate the required increments in DNA and epigenetic information [remember the 1,000 bit or 500 base pair threshold], for the culling out process to work to transform a reptile into a mammal complete with different reproductive system and ears, by chance variation and natural selection, in the supposed ~ 70 mn yrs "available" here on earth? 7] OOL And of course all of the above come back with full force when we ask about the origin of the first life forms, bearing in mind that we have to account for spontaneous origin of codes, algorithms, coordinated molecular scale implementing machinery, and the sheer mass of relevant information stored in the DNA. Including in particular, origin of the irreducibly complex elements of the sort of von Neumann self-replication involved in a metabolic automaton that reproduces itself:
(i) an underlying storable code to record the required information to create not only (a) the primary functional machine, but also (b) the self-replicating facility; and, that (c) can express step by step finite procedures for using the facility; (ii) a coded blueprint/tape record of such specifications and (explicit or implicit) instructions, together with (iii) a tape reader [called “the constructor” by von Neumann] that reads and interprets the coded specifications and associated instructions; thus controlling: (iv) position-arm implementing machines with “tool tips” controlled by the tape reader and used to carry out the action-steps for the specified replication (including replication of the constructor itself); backed up by (v) either: (1) a pre-existing reservoir of required parts and energy sources, or (2) associated “metabolic” machines carrying out activities that as a part of their function, can provide required specific materials/parts and forms of energy for the replication facility, by using the generic resources in the surrounding environment.
Immediately, we are looking at irreducible complexity leading to islands of organised function for both the machinery and the information in the wider sea of possible (but mostly non-functional) configurations. In short, outside such functionally specific -- thus, isolated -- information-rich target zones, want of correct components and/or of proper organisation and/or co-ordination will block function from emerging or being sustained across time from generation to generation. So, once the set of possible configurations is large enough and the islands of function are credibly sufficiently specific/isolated, it is unreasonable to expect such function to arise from chance, or from chance circumstances driving blind natural forces under the known laws of nature. And as one moves form that root organism up the claimed tree of life, we keep on running into needs to jump vast informational increments to get to novel body plans, which come first before the variations into diverse types that the fossil record interpreted on the typical timelines shows -- the Cambrian fossil life revolution being capital among these. Where did those dozens of major body plans come from in a short window of time relative to the multiplied megabits of information generation challenge? [And 3.5 BY is just as hopelessly inadequate to scan the sea o configs for just 1,000 bits [500 base pairs] as 5 - 10 my: our whole observed universe across a lifespan 50 mn times the usual timeline to date (13.7BY], would not sample as much as 1 in 10^150 of the configs of a space of just 1,000 bits. That is the search rounds down to zero.] ================ Until we have solid, observationally anchored answers to questions like that, the dominant neo-darwinian school of thought will remain a hypothesis whose plausibility rests on a priori metaphysical impositions implicitly accepted by those who happen to dominate current science [based on the recent intellectual history of our civilisation], rather than a solid scientific theory backed up by bodies of relevant observational evidence. Evidence there may well be of common derivation and family resemblance across life forms, but is that by design or by undirected chance plus necessity? Onlookers, these questions have been on the table but not heard out, or even begged or ducked for decades. (And when someone as eminent as Hoyle -- holder of a Nobel-equivalent prize -- raised some of them in the context of origin of life on the cosmic scale, the issue was rapidly lost in the choking, blinding, polarising smoke of burning strawmen.) Let us see if P can provide cogent answers on the merits. GEM of TKIkairosfocus_{May 30, 2010
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Mr Timaeus, Thank you for your clarifications of your opinions. I feel we have been having a good dialogue. As much as I would like to continue, I am constrained by my impending marriage on Friday to stop at this point, however unsatisfactory that might be.Nakashima_{May 30, 2010
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Petrushka, "Why not look at a well preserved sequence, such as the evolution of the mammalian inner ear?" This is perfect example of how your faith drives your conclusions. It is not scientifically legitimate to simply take the a series of structural similarities and declare that they constitute an actual evolutionary lineage. One is free to believe that two jaw bones migrated in the middle ear of the mammals over the course of time, although we have no fossil record of this miraculous process. To make it a scientific proposal, Darwinists would need to describe a stepwise, viable, theoretical pathways of such a process.inunison_{May 30, 2010
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Petrushka @ 136: "Why not look at a well preserved sequence, such as the evolution of the mammalian inner ear?" I answered this in detail in 132. You must have missed it. Petrushka @ 135: "Biologists since the 1930s have been quantifying the frequency of mutations and the mutational distance between species. This activity has been near the top of the priority list since we have been able to study biology at the molecular level. "It’s a good question. It occupies the center." Glad to hear it. Now let me know when they've learned enough to get me from a hippo ancestor to a whale, and let me know the venue the results are published in. Until then, as I've said, neo-Darwinian theory, at least as the primary explanation for major macroevolutionary change, remains for me a grand speculation - interesting, but utterly non-binding upon my intellect. I doubt we'll get much further here, so if you don't come up with a new angle, I'll exit now. T.Timaeus_{May 30, 2010
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Petrushka, "Given time, this algorithm can produce any genome." You might be satisfied with just-so stories, but that only demonstrates the strength of your faith. As Timaeus and others keep on pointing out to you, what is needed is empirical facts or theoretical pathway(s) describing evolutionary transitions.inunison_{May 29, 2010
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Show me where it’s been done for the whale, or any crucial macroevolutionary transition.
Why not look at a well preserved sequence, such as the evolution of the mammalian inner ear?Petrushka_{May 29, 2010
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Science is about quantity. You have to say “How much time would it take to perform evolutionary transition X, and is there enough time for that, given the fossil record?” You have to be specific.
Biologists since the 1930s have been quantifying the frequency of mutations and the mutational distance between species. This activity has been near the top of the priority list since we have been able to study biology at the molecular level. It's a good question. It occupies the center.Petrushka_{May 29, 2010
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Timaeus, Regarding Nilsson's and Pelger's eye simulation, see http://www.discovery.org/a/1416 where you can find all relevant linksinunison_{May 29, 2010
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1 –> First, natural selection is demonstrably about the culling out of relatively “underperforming” sub-populations in the “struggle for life.” 2 –> So, it is only capable of being responsible for REMOVAL , not origin of relevant bio-information. If underperforming individuals are culled, one might ask where their underperforming genes came from. The answer would be, from the same source that all variation comes from. A changed allele can result in the individual failing to reproduce, or it can affect the probability of the individual reproducing. The effect can be statistical rather than absolute, as you have indicated. Given time, this algorithm can produce any genome. For evolution to be true, all existing genomes must be placeable in a nested hierarchy, and historically, every individual must have exact or nearly exact copies of its parents genes.Petrushka_{May 29, 2010
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