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

,,, given all the time in the universebornagain77_{June 1, 2010
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Petruska asks: "There would be three billion years or so between OOL and the rise of metazoans. Is there some doubt about this?" The only doubt Petruska is in neo-Darwinians to account for the origination of even one protein domain.bornagain77_{June 1, 2010
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gpuccio, thanks for the background infobornagain77_{June 1, 2010
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The first important point is that about half of the domain information was already present at OOL (or at least, at the level of LUCA, if you believe in a pre-LUCA life): There would be three billion years or so between OOL and the rise of metazoans. Is there some doubt about this?Petrushka_{June 1, 2010
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kairosfocus and gpuccio; My question for "exactly how did they arrive at the 1,984 number for protein domains present at origin of life?" arises from the estimates for the estimated complexity needed for the "first life". "An earlier study published in 1999 estimated (not proven) the minimal gene set to fall between 265 and 350. A recent study making use of a more rigorous methodology estimated the essential number of genes at 382." John I. Glass et al., "Essential Genes of a Minimal Bacterium," PNAS, USA103 (2006): 425-30. Signature in the Cell - Book Review - Ken Peterson Excerpt: the “simplest extant cell, Mycoplasma genitalium — a tiny bacterium that inhabits the human urinary tract — requires ‘only’ 482 proteins to perform its necessary functions…(562,000 bases of DNA…to assemble those proteins).” ,,, amino acids have to congregate in a definite specified sequence in order to make something that “works.” First of all they have to form a “peptide” bond and this seems to only happen about half the time in experiments. Thus, the probability of building a chain of 150 amino acids containing only peptide links is about one chance in 10 to the 45th power. In addition, another requirement for living things is that the amino acids must be the “left-handed” version. But in “abiotic amino-acid production” the right- and left-handed versions are equally created. Thus, to have only left-handed, only peptide bonds between amino acids in a chain of 150 would be about one chance in 10 to the 90th. Moreover, in order to create a functioning protein the “amino acids, like letters in a meaningful sentence, must link up in functionally specified sequential arrangements.” It turns out that the probability for this is about one in 10 to the 74th. Thus, the probability of one functional protein of 150 amino acids forming by random chance is (1 in) 10 to the 164th. If we assume some minimally complex cell requires 250 different proteins then the probability of this arrangement happening purely by chance is one in 10 to the 164th multiplied by itself 250 times or one in 10 to the 41,000th power. http://www.spectrummagazine.org/reviews/book_reviews/2009/10/06/signature_cell as you can see 382 and 482 is a far cry from 1984,, thus why the discrepancy?bornagain77_{June 1, 2010
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bornagain77: This is the method used in the pape I quoted: Mapping of domains and domain combinations to species trees is too time-consuming to do manually. Our approach (see methods), similar to the approach introduced by Snel et al. [30], aims to predict the presence or absence of protein domains in ancestor organisms based on their distribution in present day organisms. Four evolutionary processes govern the presence or absence of a domain at each node in the tree: vertical inheritance, domain loss, horizontal gene transfer (HGT) and domain genesis. (Domain duplication and recombination do not affect domain presence.) Each process is assigned an empirical score according to their estimated relative probability of occurring during evolution, and the minimum overall score depicts the most parsimonious evolutionary processes of each domain or combination (see methods). As you can see, it is based on empirical evidence, and not on functional reasoning. Obviously, it is only an estimate, and different approaches could give different numbers. The authors are well aware of that: Table 1 lists the predicted number of domains and domain combinations originated in the major lineages of the tree of life. 1984 domains (at the family level) are predicted to be in the root of the tree (with the ratio Rhgt = 12), accounting for more than half of the total domains (3464 families in SCOP 1.73). This prediction is significantly higher than what is generally believed [5,31,32]. There are several reasons to account for the discrepancy. First, previous attempts focused on universal and ubiquitous proteins (or domains) in LUCA [5], so one protein has to exist in the majority of species in each of the three superkingdoms (usually 70%–90%) to be considered as LUCA protein [32]. Second, the root of the tree is still not solved. Thus any domains that are shared by two superkingdoms are counted as originating in the LUCA. Endosymbiosis of mitochondria and chloroplasts and horizontal gene transfer across superkingdoms can result in the same effect, which is moving the origin of protein domains towards the root. Third is our limited knowledge of protein domains. On average nearly 40% of predicted ORFs in the genomes under study cannot be assigned to any known domain. When assigned in the future they may turn out to be species or lineage specific domains that emerged relatively late on the tree of life. There are also a significant number of domains which emerge at the root of bacteria and eukaryotes. Likewise, this can be explained by the unresolved early evolution at the origin of bacteria and eukaryotes. So, we are not taking these numbers as absolute, but it is perfectly reasonable that the general scenario will be something like that, even if the numbers can change. The conclusions of the authors appear reasonable: Notwithstanding, these data suggest that a large proportion of protein domains were invented in the root or after the separation of the three major superkingdoms but before the further differentiation of each lineage. When tracing outward along the tree from the root, the number of novel domains invented at each node decreases (Figure 4A). Many branches, and hence species, apparently do not invent any domains. As previously discussed, this might be a result of the incomplete knowledge of lineage specific domains. A functional approach is certainly possible too. That impllies having a model of the simplest living cell, and trying to estimate the number of necessary proteins and of necessary domains. The approach, anyway, is more conceptual, and not necessarily connected to evidence. Moreover, the definition of simplest living cell can vary, and a strictly reductionist approach, a la Venter, is certainly cutting down many of the naturally occurring functions. Therefore, I think that the empiric approach based on the vurrent distribution of damains and sequences is preferable, more scientific, and, I would say, perfectly "darwinian" (so that, for once, we could agree with our adversaries at least about one methodology :) ). Two facts cannot be questioned: 1) A lot of the protein domains were "discovered" at the root of the evolutionary tree. So darwinists must not only find a vaguely credible theory for OOL, but also one which is extremely efficient in respect to time, much more efficient than all later darwinian evolution, in order to explain how approximately half of the basic protein information was avalable after, say, 200 - 300 My from the start (whatever the "start" was). 2) Basic protein domain information is only the start, and definitely not the biggest part of the functional information to be explained. Then you have: a) The space of different protein functions in the context of a same domain (let's remember that the same fold can have many different functions, and different active sites). b) The space of multidomain complex proteins, which implies a search in the combinatorial space of all domains. c) The fundamental space of protein regulation, maybe the biggest of all, which certainly implies at leat gene sequence, non coding DNA and epigenetic mechanisms. d) The space of multicellular integration. e) The space of body plans, system plans, organ plans, tissue plans, and so on. f) The space of complex integration to environment and higher cognitive functions (immune system, nervous system). That's only a brief and gross summary. Each of these levels poses insurmountable impossibilities to the model of darwinian evolution. Unfortunately, most of these levels cannot yet be treated quantitatively for two reasons: 1) They are too complex 2) We know too little about them So, for the moment, let's wait for answers about the first level, protein domain information, which is much easier to analyze. But I am not holding my breath.gpuccio_{June 1, 2010
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BA (& GP): I would note that the requisites of a metabolic automaton that is self replicating a la von Neumann are not at all simple. Gkairosfocus_{June 1, 2010
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Very interesting post gpuccio. Do you know the exact reason why the evolutionists pushed so many protein domains back to the origin of life? i.e. The first important point is that about half of the domain information was already present at OOL (or at least, at the level of LUCA, if you believe in a pre-LUCA life): Protein domains 1984; Combinations 4631. i.e. Was it loosely based on empirical evidence, or was the reason they grouped it as such based on necessity?bornagain77_{June 1, 2010
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Petrushka: Considering that you like to make statements and never support them with data or reasoning, I will try to do the opposite. I am not terribly surprised that most genes, most metabolic mechanisms and all body plans, seem to have been invented or discovered by microbes or very simple organisms, presumably having large numbers and short spans between generations. It is not surprising that few fundamental inventions have been made by larger and slower reproducing creatures. Now, I will just give some data, to show that your affirmations are vague and inaccurate. I will refer to the paper "The Evolutionary History of Protein Domains Viewed by Species Phylogeny" , by Song Yang, Philip E. Bourne, freely available on the internet. This paper analises the distribution of single protein domains as derived from SCOP (the database of protein families) in the evolutionary tree, and even the distribution of their unique combinations. The total number of independent domains in the whole proteome is 3464 and the total number of combinations is 116,400. The first important point is that about half of the domain information was already present at OOL (or at least, at the level of LUCA, if you believe in a pre-LUCA life): Protein domains 1984; Combinations 4631. The mean domain content per protein, at this level, is 2.33 So, the first point you have to explain is how 1984 protein domains were already working at the time of our common ancestor (supposedly 3.5 - 3.8 billion years ago), while not one of them can be found by a random search. The remaining half of the domains was discovered in the course of evolution, with the following pattern of new domains and domain combinations: Archea: Protein domains 31; Combinations 323; Bacteria: Protein domains 467; Combinations 4537. Eukaryota: Protein domains 520; Combinations 7192. Fungi: Protein domains 56; Combinations 3089. Metazoa: Protein domains 209; Combinations 12304. So, the next point is: about 1313 new domains arose after LUCA, and of them only 31 and 467 arose in archea and bacteria respectively, while the rest was "discovered" by more complex organisms. So, again, how do you explain the 209 new domains in metazoa? Another point: in the final parts of evolution, the search for new domains seems to be almost completed: for example, only about ten new domains appear in mammalia. On the contrary, the number of new combinations and the average complexity and length of the single protein definitely increase. So, to sum up: 1) More than half of the information for the proteome is already present at the stage of LUCA (or, if you want, at OOL, unless you can explain how such a complex LUCA originated in a relatively short time from inorganic matter) 2) The remaining new information was "discovered" during evolution, but certainly not only at the time of bacteria: at least half of the new domains appear in organisms more complex than bacteria, and about one quarter appear in metazoa. So, if it is true that the search for new domains "slows down" after OOL, and almost stops in the last stages, the successful search for new domains in the ocean of the search space definitely goes on for the whole evolutionary span. 3) While the search for new domains slows down, the search for new combinations in more complex protein increases along the evolutionary tree. In other words, as the repertoire of elementary folds is almost completed (demonstrating that targets not only exist, but can be fully achieved), the search for function is moved to a higher logical level. 4) Finally, we must remember that this analysis is only acoomplished at the level of protein genes (1.5% of the genome in humans). The non coding part of the genome constantly increases during evolution, and most of us (and, today, I would say most of the biologists) are convinced that non coding DNA is one of the keys to understanding genome regulation, and therefore body plans and many oyther things. Another, more complex level of abstraction and regulatory function which darwinists will have to explain after they have at least tried to explain the previous, simpler levels.gpuccio_{June 1, 2010
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Petrushka: By your pattern of exchanges over some days, we have to take it that ducking out of addressing the issue of the OOL conundrum of getting to the very first body plan from a plausible pre-biotic soup by spontaneous changes on chance and mechanical, chemical necessity, means that you have no good answer. In particular, you have no good explanation -- and remember onlookers, if there was one, it would be all over the Internet on pro evolutionary materialism advocacy sites -- for the claimed spontaneous origin of the very first body plan for a metabolising automaton with integrated self-replication facility that is based on coded information and organised complex molecular machinery. That is, the first cell-based life form. Indeed, neither do the major researchers, as we may see from the exchange between Shapiro and Orgel several years ago. But, based on the rise of information and communication technologies in the past half century and more, we have some very good, empirically anchored explanations for the origin of: codes, machinery for processing coded information, complex, organised machinery for carrying out resulting decoded instructions, and for manufacturing plants that convert components into intermediate or final products based on algorithmic control. Namely, design. In addition, we have excellent reason to see that chance contingencies and trial and error will not credibly account for such, as the set of possible configs is rapidly well beyond the random walk trial and error search capacity of the cosmos, and the tight co-ordination of integrated functional components and associated coded algorithmic instructions means that we have deeply isolated islands of function in vast config spaces of non-function. (Just check how many cars in junk yards are close to working but not working to see what this means.) (Notice onlookers, I went back to the OOL question to answer to the attempt to dismiss the concept of islands of function. Silence on the point tells us this was successful.) So, we have excellent reason to infer to intelligent design on empirically well supported signs of such design for the origin of life, once we reject the attempt to impose evolutionary materialistic ideological blinkers. But, once we see that, we have no good reason to reject the onward inference to similar design to explain the rise of major body plans, at the level of the difference between crabs, sea slugs, sea urchins, worms [of several quite distinct types], and fish, not to mention algae vs ferns or flowering plants and in this last group, a coconut tree vs a guava tree vs. a banana tree. (That is the sort of level of body plan differentiation we see in the Cambrian layer animal fossil diversity. Dogs vs cats is a much more minor level of differentiation. At a lower level, origin of birds, whales and bats with wings or underwater breathing and locomotion organs and associated body transformations is a similar cluster of cases in point.) The point is that the origin of Phyla and sub phyla or the equivalent across other kingdoms is again a matter of a huge jump in coordinated body development information, some genetic, some epigenetic [as BA 77 -- as usual -- reminds us with some apt quotes]. Jumps on the order of 10's to 100's of millions of bases, thus bits of information. Well beyond the FSCI threshold, again swamping the generous 500 - 1,000 bit estimate for the upper limit for what random walk trial and error can plausibly do. So, again, we see good reason to infer to design as the best explanation for origin of complex body plans. And in that context, we see that the origin of life and of biodiversity is thus best explained on intelligence, not random walk based trial and error; which is what darwinian style evolutionary materialism boils down to. So, on evidence we can see directly in the bodies before us and in the fossils we also can inspect, we have many, many reliable markers of design as the best explanation of origin of life and of body plans. And, once the evidence is acknowledged as having a designer's foot in the door, then there is no good reason to dismiss design as a pervasive feature of life as we see it; including of the difference between dogs and cats, or the tabby sitting by the fire place and the puma roaming the hills behind. Briefly going beyond that, it is also quite evident that the physics of the cosmos is finely tuned for the existence of carbon chemistry cell based life, on dozens of co-ordinated parameters. That is, we have further evidence pointing to an intelligent designer and builder of the cosmos who is thus highly knowledgeable and intelligent, powerful and beyond the material cosmos we observe. It therefore seems quite reasonable to infer that the designer of life and its diversity up to and including ourselves, is the same designer who fashioned the heavens and the earth as a suitable habitat for such life. And in our civilisation, such an extra-cosmic designer echoes very tellingly of the God of Judaeo-Christian theism. Which brings science full circle to the pattern of thought of say Newton in Opticks, Query 31, nearly 300 years ago:
In the two first Books of these Opticks, I proceeded by this Analysis to discover and prove the original Differences of the Rays of Light in respect of Refrangibility, Reflexibility, and Colour, and their alternate Fits of easy Reflexion and easy Transmission, and the Properties of Bodies , both opake and pellucid, on which their Reflexions and Colours depend. And these Discoveries being proved, may be assumed in the Method of Composition for explaining the Phaenomena arising from them: An Instance of which Method I gave in the End of the first Book. In this third Book I have only begun the Analysis of what remains to be discover'd about Light and its Effects upon the Frame of Nature, hinting several things about it, and leaving the Hints to be examin'd and improv'd by the farther Experiments and Observations of such as are inquisitive. And if natural Philosophy in all its Parts, by pursuing this Method, shall at length be perfected, the Bounds of Moral Philosophy will be also enlarged. For so far as we can know by natural Philosophy what is the first Cause, what Power he has over us, and what Benefits we receive from him, so far our Duty towards him, as well as that towards one another, will appear to us by the Light of Nature. And no doubt, if the Worship of false Gods had not blinded the Heathen, their moral Philosophy would have gone farther than to the four Cardinal Virtues; and instead of teaching the Transmigration of Souls, and to worship the Sun and Moon, and dead Heroes, they would have taught us to worship our true Author and Benefactor, as their Ancestors did under the Government of Noah and his Sons before they corrupted themselves.
Such a full circle return to science in a genral design frame of thought that lives happily with theistic thinking generally, is of course utterly unwelcome in the more militantly ideologised evolutionary materialistic circles, some of which wield considerable power in the academy and institutional science. So the sort of bitter end resistance commonly seen in the teeth of where the evidence over the past 60 or so years has plainly been pointing is unsurprising. But, like any other bitter ender ideological campaigns, it will gradually falter and fail as the sheer accumulating weight of the evidence breaks it down. G'day GEM of TKIkairosfocus_{June 1, 2010
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Petruska, neither you nor anyone else has a firm clue where the information for body plan morphogenesis resides. For you to pretend it resides in genes and leave it at that as if you have established your point and ignore the evidence I presented shows that you do not really want to know what the truth is. frankly it is ludicrous for you to think that your unsupported conjecture that essential conserved genes/proteins has any weight to explaining body plan morphogenesis. It is a non-explanation period! “Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find the information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing that there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype (Body Plan).” Michael John Denton page 172 of Uncommon Dissent Riddick your youtube foray reminded me of this: Top 10 Excuses for Not Going to Church http://thedawghowse.blogspot.com/2005/11/top-10-excuses-for-not-going-to-church.html and the video also reminded me that it never was about the science with you anyway was it?bornagain77_{May 31, 2010
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What genes code for body plans?Phaedros_{May 31, 2010
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I will stipulate that although cellular machinery is more conserved than genes, it is not entirely identical across species. It isn't identical within species. But for the moment I think it would be interesting to discuss a point that you brought up, that evolution at the level of molecular machinery seems more likely in organisms that have high numbers and short generation times.Petrushka_{May 31, 2010
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do you care to enlighten us to where the information for a body plan resides?
The genes for body plan seem to be rather ancient. They certainly go back to the era I discussed, which is characterized by large numbers and short generation spans. Are you suggesting there is some demonstrable discontinuity involved in the first body plans?Petrushka_{May 31, 2010
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A bit off-topic, but it's what we've come to. http://www.youtube.com/watch?v=isGrCmCFFmYriddick_{May 31, 2010
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Petruska you state, I am not terribly surprised that most genes, most metabolic mechanisms and all body plans, seem to have been invented or discovered by microbes or very simple organisms, do you care to enlighten us to where the information for a body plan resides? This inability for the DNA code to account for body plans is also clearly shown by extensive mutation studies to the DNA of different organisms which show "exceedingly rare" major morphological effects from mutations to the DNA code. Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681 The Origin of Biological Information and the Higher Taxonomic Categories - Stephen Meyer"Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion." http://eyedesignbook.com/ch6/eyech6-append-d.html Hopeful monsters,' transposons, and the Metazoan radiation: Excerpt: Viable mutations with major morphological or physiological effects are exceedingly rare and usually infertile; the chance of two identical rare mutant individuals arising in sufficient propinquity to produce offspring seems too small to consider as a significant evolutionary event. These problems of viable "hopeful monsters" render these explanations untenable. Paleobiologists Douglas Erwin and James Valentine “Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find the information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing that there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype (Body Plan)." Michael John Denton page 172 of Uncommon Dissent Fearfully and Wonderfully Made - Glimpses At Human Development In The Womb - video http://www.metacafe.com/watch/4249713 This includes the highly touted four-winged fruit fly mutations: ...Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection." - Jonathan Wells http://www.evolutionnews.org/2008/08/inherit_the_spin_the_ncse_answ.html#footnote19 Darwin's Theory - Fruit Flies and Morphology - video http://www.youtube.com/watch?v=hZJTIwRY0bs As well as "cloning" studies: "There is now considerable evidence that genes alone do not control development. For example when an egg's genes (DNA) are removed and replaced with genes (DNA) from another type of animal, development follows the pattern of the original egg until the embryo dies from lack of the right proteins. (The rare exceptions to this rule involve animals that could normally mate to produce hybrids.) The Jurassic Park approach of putting dinosaur DNA into ostrich eggs to produce a Tyrannosaurus rex makes exciting fiction but ignores scientific fact." The Design of Life - William Dembski, Jonathan Wells Pg. 50bornagain77_{May 31, 2010
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Petruska, you haven't answered anything from any topic. You just dream fuzzy dreams and state them as if they are plausible and never go anywhere near any empirical evidence to prove any point, all the while you pretend you are being reasonable in all this. It would be funny save for the fact all of evolutionary biology is dreaming with you. Bring me to life by Evanescence http://www.youtube.com/watch?v=UKer9hry-Ggbornagain77_{May 31, 2010
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I am not terribly surprised that most genes, most metabolic mechanisms and all body plans, seem to have been invented or discovered by microbes or very simple organisms, presumably having large numbers and short spans between generations. It is not surprising that few fundamental inventions have been made by larger and slower reproducing creatures.Petrushka_{May 31, 2010
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OOL is certainly an interesting question, but I'll have to stipulate that we don't know much about it, and probably will never know the details. But from where I stand on this particular thread, the argument has been moved back from the question of whether dogs and cats are descended from a common ancestor, to questions from deep history that may never be resolved.Petrushka_{May 31, 2010
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Petrushka I find it extremely disappointing that you are now playing art debating terms to describe realities, e/g/ clouds vs islands. (and thinly veiled assertions that just any and every config will have minimal functionality so its a smooth climb up a fitness landscape from just about anywhere. To correct this gross error, let us go back to the very first island of bio-function. That is, a metabolic automaton with self-replication, which must meet this functionality target, on the logical requisites identified in the late 1940's by von Neumann:
(i) an underlying storable code to record the required information to create not only (a) the primary functional machine [here, a metabolising automaton] 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 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.
Parts (ii), (iii) and (iv) are each necessary for and together are jointly sufficient to implement a self-replicating machine with an integral von Neumann universal constructor. That is, we see here an irreducibly complex set of core components that must all be present in a properly organised fashion for a successful self-replicating machine to exist. [Take just one core part out, and self-replicating functionality ceases: the self-replicating machine is irreducibly complex (IC).] This irreducible complexity is compounded by the requirement (i) for codes, requiring organised symbols and rules to specify both steps to take and formats for storing information, and (v) for appropriate material resources and energy sources. Immediately, we are looking at 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. So, your first challenge is to get from a reasonable prebiotic soup or vent or comet and credibly spontaneously get to a self-replicating cell or some reasonable analogue thereto. By blind chance and mechanical necessity starting from happenstance initial conditions. Suffice to say that as of the recent Shapiro-Orgel exchange, this has ended in mutual self destruction of the RNA world and metabolism first scenarios, and as to the actual requisite that BOTH metabolism and replication on stored info be put together to form life as we know it, that is a definite non-starter on chance plus necessity. But already serious pre-design studies on building self replicators have been done, in the context of galactic exploration. When we get to novel body plans, the problems do not vanish. As Meyer summarised in his well known paper in 2004 that left the NCSE activists foaming at he mouth with lynch-mob fervour that unfortunately targetted the Journal editor who had the integrity to publish a paper that critiques the magisterium's favoured view, and passed peer review:
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) . . . [PBSW, Aug 2004]
Again, we find a functional target comprising a cluster of integrated complex entities that implement a novel body plan. And the credibility of getting to such on chance plus necessity plummets to a practical zero so soon as we -- very rapidly -- run past the 1,000 bit threshold. Summed up, the idea of islands of coordinated integrated, organised function is very well warranted. The problem, plainly is that you have no good empirical evidence of body-plan level macroevolution on CV + NS, so we find rhetorical challenges to an empirical issue: spontaneous generation of highly complex coordinated multipart information rich entities is extremely implausible as an explanation. But intelligence does this sort of thing all the time. Indeed, over the next few decades our own technology will be good enough to make a 3-D kinematic self-replicator. Already we can conceive what is needed. So, have you any good reason to infer that an intelligence to produce life or body plans for multicellular life forms is IMPOSSIBLE? Failing that, we have excellent reason to infer form known, reliable empirical traces of intelligence to intelligence as the best explanation of life. GEM of TKIkairosfocus_{May 31, 2010
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Better yet, "Junk" DNA?Phaedros_{May 31, 2010
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Petrushka- Just as anything would be a better mascot for for Darwinians than "Ida"?Phaedros_{May 31, 2010
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"Islands" is a bad metaphor. There are not dead or impassable seas between variants. Gradients would be a better term. HIV managed the jump from one species to another in our lifetime. But there is no biological imperative for any species to change into something else, any more than there is an imperative for someone to win the lottery every week. Biological change simply doesn't seek targets or goals. It follows, like a river, the path of least resistance. But even that is a limited metaphor, because species don't always find a path. More often than not, they go extinct. As for mammals and their supposed innovations, I'm not aware of many inventions of metabolic machinery that distinguish one mammal from another. If there were, I suspect they would make a better mascot for ID than the flagellum.Petrushka_{May 31, 2010
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Petrushka: Fine. all that selection needs to do is rank differences in genomes according to fecundity. What accumulates is bits of genome that contribute to fecundity. Or at least don’t prevent reproduction. Yes, and for genomes to exist, and fecundity to exist, and enzymes and metabolism to exist, and so on, all that selection needs to do is to find the thousands of different individual functional protein domains that we observe in the proteome. Again I ask you explicitly: if evolution can only select existing function, how could it find thousands of independent configurations, each of them functional, in an ocean of non functional, non folding primary sequences? I invite you to read the recent review by Douglas Axe on Bio-Complexity, "The Case Against a Darwinian Origin of Protein Folds". If one has a specific target, such as the works of Shakespeare, odds are that random variation and selection will not produce it Nor will they produce the proteome. Again, the argument of "evolution can take any direction" is a false argument. Once you have a basic structure for life (DNA, proteins, cells, etc.), directions are extremely narrow. You need proteins which fold and have active sites, and those active sites must do something useful in the context where they are supposed to arise, and must interact with what already exists, and the new proteins must be regulated in the correct way, and so on. Targets, targets everywhere! But viability is a cloud having gradations of density rather than a single island or point Viability is one thing, the information which can ensure viability is another. A long protein sequence has nothing to do with viability unless and until it acquires a specific, well integrated function which can be added to the existing function. Otherwise, no selection can take place. The fundamental flaw in the ID analysis of evolution lies in the concept of target. It seems to imply that what is was destined Wrong. It just implies that what is had to work. Funtion is a target. And in a specific context, specific functions (and not any possible function) are very specific targets. There may certainly be several possible functional targets in a specific context, but anyway always in a limited number. And practically all of them, in a complex context, require functional complexity. New functional complexity. And random search cannot find them. And, for the same reasonm NS cannot select what has not been found. Things like the flagellum or the works of Shakespeare keep cropping up in the argument. But specific structures are not necessary to biology, just as Shakespeare is not an inevitable outcome of literature. Wrong. Specific functional structures are necessary to biology, exactly as good, meaningful and beautiful works by gifted authors are necessary to literature. In your statement you meaningfully shift from "necessary" to "inevitable". Individual events may not be "inevitable", but authors are absolutely necessary to literature exactly as complex functional structures are necessary to biology. Would you affirm that a random search in the search space of letters can give us valid literary works, new valid literary works I mean, not the copy of the weasel? Please give me the reference of the evolutionary algorithm which has given us a new drama, meaningful and beautiful. It needs not be Shakespeare. Any good drama will do. Indeed, even a mediocre one. If that is possible, then certainly darwinian evolution could produce the proteome. So, I am here waiting for the reference to the drama creating algorithm. As far as life goes, most of it is content being single celled, minus flagellum. And, I suppose, minus DNA transcription and translation, cell membranes, metabolism, ATP synthase, rybosomes, etc? And the hundreds of very complex proteins and structures that even the simplest of archea or bacteria possess? Where did darwinists get this strange idea that the flagellum is the repository of all unexplainable complexity? Wake up. That is only one example, the example Behe used in his book a few years ago. One of thousands. One of millions. And, anyway, if I remember well, flagella do exist. Like multi celled beings. Like body plans. Like long distance cellular communication. Like nervous systems. Do these things exist, or are they ID myths? That prokaryotes are, still today, probably the best adapted form of life on earth is only evidence of what I have always affirmed: that there was no real reason for them to evolve, if the only driving principle is better survival or reproduction. But, if the driving principle is design and purpose, things change...gpuccio_{May 31, 2010
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Petrushka: Plainly, you are diverting. We have described islands of FunctIon in a sea of configurations, constrained by the requisites of codes, algorithms and data structures. We have pointed out that the resources of the universe are grossly inadequate to traverse even a tiny fraction of the implied config spaces. We have pointed out that there is abundant evidence that chance and necessity cannot credibly spontaneously reach islands of function for chance variation to begin to compete on differential performance of sub populations. We note that FSCI is routinely produced and observed as coming from intelligence. You appear unable to address that, instead trying to assert that "target" suggests purpose -- well language and algorithms and data structures as we see in the cell more than merely suggest purpose. You speak about fuzzy clouds in a sky (most inapt as clouds are easily seen form way off; the problem is to ger=t the DNA, body plan and metabolic machinery to get TO an island of function, by drifting). Have you ever been on an island in the sea? If you have done so, you will know that the shoreline varies by the second, hour, day, month and year, and is considerably variable across the years. But that is immaterial to the relevant point: islands and even archipelagos isolated in a large ocean are notoriously hard to find unless you have intelligent guidance. And the relevant search resources of our observed cosmos are vastly inadequate to undertake the relevant search, or random walk if you will. Until you are ashore on an island of function, chance variation and natural selection on superiority of function are irrelevant. But we know that FSCI routinely comes from intelligence, as posts in the tread demonstrate. Think about that. GEM of TKIkairosfocus_{May 31, 2010
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Petruska, here are the results for evolution from the real world with no preordained "complex structures" in mind: A review of The Edge of Evolution: The Search for the Limits of Darwinism The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have "invented" little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155). http://creation.com/review-michael-behe-edge-of-evolution Dr. Behe states in The Edge of Evolution on page 135: "Generating a single new cellular protein-protein binding site (in other words, generating a truly beneficial mutational event that would actually explain the generation of the complex molecular machinery we see in life) is of the same order of difficulty or worse than the development of chloroquine resistance in the malarial parasite." That order of difficulty is put at 10^20 replications of the malarial parasite by Dr. Behe. This number comes from direct empirical observation. Richard Dawkins’ The Greatest Show on Earth Shies Away from Intelligent Design but Unwittingly Vindicates Michael Behe - Oct. 2009 Excerpt: The rarity of chloroquine resistance is not in question. In fact, Behe’s statistic that it occurs only once in every 10^20 cases was derived from public health statistical data, published by an authority in the Journal of Clinical Investigation. The extreme rareness of chloroquine resistance is not a negotiable data point; it is an observed fact. http://www.evolutionnews.org/2009/10/richard_dawkins_the_greatest_s.html Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution "Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell--both ones we've discovered so far and ones we haven't--at best extremely limited benefit, since no such process was able to do much of anything. It's critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing--neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered--was of much use." http://www.evolutionnews.org/2009/05/swine_flu_viruses_and_the_edge.html This following recent study solidly confirms the severe limit for evolution found by Dr Behe: Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness - Ann K. Gauger, Stephanie Ebnet, Pamela F. Fahey, and Ralph Seelke – 2010 Excerpt: In experimental evolution, the best way to permit various evolutionary alternatives, and assess their relative likelihood, is to avoid conditions that rule them out. Our experiments, like others (e.g. [40]), used populations of cells growing slowly under limiting nutrient conditions, thereby allowing a number of paths to be taken to higher fitness. We engineered the cells to have a two-step adaptive path to high fitness, but they were not limited to that option. Cells could reduce expression of the non-functional trpAE49V,D60N allele in a variety of ways, or they could acquire a weakly functional tryptophan synthase subunit by a single site reversion to trpAD60N, bringing them within one step of full reversion (Figure 6). When all of these possibilities are left open by the experimental design, the populations consistently take paths that reduce expression of trpAE49V,D60N, making the path to new (restored) function virtually inaccessible. This demonstrates that the cost of expressing genes that provide weak new functions is a significant constraint on the emergence of new functions. In particular, populations with multiple adaptive paths open to them may be much less likely to take an adaptive path to high fitness if that path requires over-expression. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.2/BIO-C.2010.2 Shoot petruska I would be happy if you just provided even one example of the fitness test being passed by evolution by 3 point mutations or 4 functional information bits: Is Antibiotic Resistance evidence for evolution? - "The Fitness Test" - video http://www.metacafe.com/watch/3995248 Testing the Biological Fitness of Antibiotic Resistant Bacteria - 2008 http://www.answersingenesis.org/articles/aid/v2/n1/darwin-at-drugstorebornagain77_{May 31, 2010
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The fundamental flaw in the ID analysis of evolution lies in the concept of target. It seems to imply that what is was destined. Evolution searched for complex structures. Things like the flagellum or the works of Shakespeare keep cropping up in the argument. But specific structures are not necessary to biology, just as Shakespeare is not an inevitable outcome of literature. As far as life goes, most of it is content being single celled, minus flagellum.Petrushka_{May 31, 2010
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gpuccio @ 163, What Petrushka is stating,
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.
and Dawkins was trying to demonstrate, is biological feedback. The output is text because that's easy to show on a computer display. The "Weasel" text is fixed so that we can monitor the progress of the algorithm, not because the algorithm requires a fixed output to function. The ID side is fixating on how the demonstration was set up, instead of the algorithm that was being demonstrated, which is, "biological feedback influencing selection".Toronto_{May 31, 2010
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Any algorithm using random variation can easily accumulate from any arbitrary oracle all the information which already is in the oracle.
Fine. all that selection needs to do is rank differences in genomes according to fecundity. What accumulates is bits of genome that contribute to fecundity. Or at least don't prevent reproduction. If one has a specific target, such as the works of Shakespeare, odds are that random variation and selection will not produce it. But viability is a cloud having gradations of density rather than a single island or point.Petrushka_{May 31, 2010
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Petruska: Frankly, I don't know if it is worthwhile repeating again issues which should be well established, but let's try: What Weasel does do is demonstrate that an algorithm using a completely random variation generator can accumulate information from any arbitrary oracle. Any algorithm using random variation can easily accumulate from any arbitrary oracle all the information which already is in the oracle. That is so obvious that there should be no need even to debate it. Take the weasel phrase. I already know it, you already know it, the oracle already knows it. All you have to do is to cycle randomly through the existing letters to find the first position, and check with the oracle until you find the right one, then fix it and pass to the second, and so on, until you have "found" the whole phrase. Piece of cake. But what do you think we have demonstrated? Only that we can "copy" information by a random writing, instead of copying it directly. If we wanted to be smarterm we could look at the oracle first, position after position, and just "write" the correct letter. Ah, but I forgot, we do love games! All so called "evolutionary" algorithms accomplish some variation, more or less brilliant, more or less explicit, of that same process. Even if the oracle does not know the solution explicitly, the system as a whole is designed to make the solution easy and possible. But it is not up to me to show that. Just read the papers of the evo informatics lab, and look at the very good work that is being done there. What is really strange is your convinction that, in that type of context, random search if finding the information. Well, a random search in a small search space, with the right oracle available to do intelligent selecion, can certainly find all that we want, from the whole works of Shakespeare to a detailed description of all known protein sequences. What do we need after all? Only a volume of Shakespeare's works, possibly digitalized for easier use, and some good database of protein sequences downloaded from internet, and a very simple and patient search software, and the result is there. Why are those silly IDists complaining that random variation cannot do these things? But, as I really am one of those silly IDist, just show me one thing: try to find the primary sequence, let's say, of human myoglobin (just 153 AAs), without knowing it in advance, and having only a lab instrument, let's say, which can test available to evaluate if each newly generated molecule can bind the heme group and iron (but beware, only when the binding is really strong and efficient, in other words functional). And as you are so worried about the importance of time, I will be generous: I give you a billion years from now. But, in the end, you will have to admit that I was right :)gpuccio_{May 31, 2010
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