A Simple Gene Origination Calculation

_{PaV
July 27, 2008

Intelligent Design

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Intelligent Design}

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In this month’s Nature Genetics, there is an article by Zhou, et. al., dealing with the generation of new genes in Drosophila melanogaster—the fruit fly. While only having access to the abstract, I nonetheless was struck by one of their findings: the rate of new functional gene generation. As finding number 6 in the abstract, the authors write: “the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup.”

Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 new functional genes per million years= 1.75 billiion years for the formation of the fly genome. This, of course, assumes that somehow the fly is ‘alive, and reproducing’ the entire 1.75 billion years—-this, without the aid of a full-blown genome. If we apply this to the monkey/human difference which, IIRC, is about a 1000 genes, then using this same rate, it would take 200 million years for man to have evolved from the monkey. This published rate for new functional gene generation cannot be good news for Darwinists.

Here’s the link to the abstract.

Comments

GEM:
, we could for a first instance look at the proportion of stop codons — UAG, UGA, UAA, i.e three out of 64 — and notice that this high proportion means that most arbitrary DNA/RNA sequences would be non-functional.
So if we induce a start sequence into DNA, then on average we can expect to encounter a stop sequence about 21 triplets later. So the average de novo gene would be 21 aminos long. Assuming the validity of the neo-Darwinian paradyme, as the average gene is about 100 aminos long, either short genes are very unlikely to be effective, or genes must somehow grow in length. My math skills are not quite good enought to figure out what percentage of random sequences would produce 100 triplets before a stop, but its got to be rather small.bFast_{July 31, 2008
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Yeah KF, But you know the issue here that I am concerned with is not the magnitude of the complexity and specificity. Life has always seemed such to me before learning anything thing about the micro world. The issue is that of matter and motion. That is product and destination. I know that the biological matter that makes up identical twins is almost identical but it is obviously not the matter that constructs and validates a person’s existence. The encoding process of the matter- that is the characteristics that make up what we call DNA are the real mystery and the true defining factor of what a living object with becomes. This digital code cannot be accounted for via materialistic mechanisms nor chance and necessity. What then do we appeal to? When we talk about design we are usually talking about issues of functionality- and DNA exhibits this in full. It is the form, function and improbability of the arrangement of matter that is needed be accounted for here. Intelligence is the only known cause of FSCI. Intelligence implies design—and, though weaker, a design(er). "Intelligent Design is best described as the study of patterns in nature which as best explained as the result of intelligence." -Bill DembskiFrost122585_{July 31, 2008
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PS: Royal Truman, excerpting Gary Parker, gives us an illustrative example in summary here: _________ A cell needs over 75 "helper molecules", all working together in harmony, to make one protein (R-group series) as instructed by one DNA base series. A few of these molecules are RNA (messenger, transfer, and ribosomal RNA); most are highly specific proteins. ‘When it comes to "translating" DNA’s instructions for making proteins, the real "heroes" are the activating enzymes. Enzymes are proteins with special slots for selecting and holding other molecules for speedy reaction. Each activating enzyme has five slots: two for chemical coupling, one for energy (ATP), and most importantly, two to establish a non-chemical three-base "code name" for each different amino acid R-group. You may find that awe-inspiring, and so do my cell-biology students! [Even more awe-inspiring, since the more recent discovery that some of the activating enzymes have editing machinery to remove errant products, including an ingenious "double sieve" system.[2],[3]] ‘And that’s not the end of the story. The living cell requires at least 20 of these activating enzymes I call "translases," one for each of the specific R-group/code name (amino acid/tRNA) pairs. Even so, the whole set of translases (100 specific active sites) would be (1) worthless without ribosomes (50 proteins plus rRNA) to break the base-coded message of heredity into three-letter code names; (2) destructive without a continuously renewed supply of ATP energy [as recently shown, this is produced by ATP synthase, an enzyme containing a miniature motor, F1-ATPase.[4],[5],[6],[7]] to keep the translases from tearing up the pairs they are supposed to form; and (3) vanishing if it weren’t for having translases and other specific proteins to re-make the translase proteins that are continuously and rapidly wearing out because of the destructive effects of time and chance on protein structure! [8] ___________ That is the kind of complexity to be accounted for per chance + necessity only, to sustain evolutionary materialist OOL models.kairosfocus_{July 31, 2008
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Gentlemen: First, thanks for some kind remarks. A few follow-up points: 1] CEC09, 64: Bayesianism-subjectivism? I have a little familiarity with the use of Bayes' work to do probability estimates and revisions, and with how it intersects with the issues at stake relative to the explanatory filter. That frame of reference is precisely what is not at work here. indeed, you will see that I am precisely not using Bayesian methods, as was discussed at length online and offline with former commenter here, PO. We are, instead, looking at something else: a statistical thermodynamics-tinged look at state spaces, of discrete form, and the issue of "searching out" functional states in the resulting configuration space. In that regard, we also start from the usual scenarios proposed since Darwin [cf my always linked], and ask, what happens in the context of polymerisation chemistry which is not intelligently directed. The answer is plain: functional states are vastly isolated in the config space, and even if we envision a very generous provision of islands and archipelagos of functionality, the sea of non-functional states swamps them -- recall what we need for OBSERVED life function through the DNA-RNA-enzyme ribosome system and associated issues of protein folding and functionality. Indeed, the need for codes and algorithms to make the elements of the cell's systems work together compounds the problem. have you ever seen a complex code [language] or a similarly complex algorithm originate by chance-driven contingent processes? [And, the isolation issue is what drives any probability estimates. There are only so many search resources in the observed cosmos, and not all things which are logically or physically possible are sufficiently thermodynamically accessible that we can see them arising by chance + mechanical necessity. Indeed, that is the foundation of the statistical form of the 2nd law of thermodynamics.] Do you routinely see codes and algors produced by intelligent agents? So, which is the better, empirically anchored explanation, then? --> The answers are obvious, once you see the issue of search-space, isolation and probabilistic resources to undertake the search. --> intelligent agents, of course, use their imagination and insight to cut down the search space dramatically, so we routinely produce entities that are vastly beyond the credible reach of random search; e.g. posts in this thread. [Think about just the space on an ASCII state space search for your last post: 128^1418 ~ 1.06 *10^2988. Which is the better explanation: chance and necessity or agent? Why? (And, if you wish to inject the notion that agents are known to exist now, the point at OOL is that agents are possible absent your ruling them out on solid grounds.] --> And, on tone: I do not at all like to see loaded terms such as "duped"; this seems grossly disrespectful and dismissive! (As well as inaccurate.) 2] Sparc, 63: antibodies stuff Kindly reread the wider context of the remark at 38 above:
Regarding the immune system, the scenario is completely different. Primary antibody diversification is a process which uses random variation very intelligently targeted to generate a repertoire of basic antibody specificities to cover, at a low specificity level, a search space which is very big, but not immense, referring to possible epitopes in nature (an epitope is a very small aminoacid sequence, usually a few aminoacids, or up to ten -fifteen). . . . there is nothing in what we know about antibody generation which is inconsistent with my “assumptions”. Antibody generation is a perfect example of intelligent engineering using the realistic resources of probability. It is therefore perfectly natural and reasonable that the immune system of birds or mammals can “produce antibodies against antigens that they or their ancestors never encountered before”.
In short omission of material context is misleading you. 3] DK,57: You assume that questions about how life arose and diversified on planet earth are answerable sufficiently and definitively by speculation. Kindly, first, tell me what is speculative about calculating a configuration space based on a digital element? [This is how memory spaces are routinely calculated, in case you have not done basic digital electronics, for one instance.] Last I checked it was uncontroversial that DNA/RNA used a 4-state element, and that there were 20 protein monomers that appear in the vast majority of proteins (a few oddballs notwithstanding). So, to calculate the relevant config spaces is not speculative. That DNA/RNA and proteins are sensitive to perturbations from known functional states is a commonplace. Similarly, we could for a first instance look at the proportion of stop codons -- UAG, UGA, UAA, i.e three out of 64 -- and notice that this high proportion means that most arbitrary DNA/RNA sequences would be non-functional. (Some have observed that the likelihood of getting to a stop codon if one starts to code from an arbitrary initial point on a DNA chain is as sign of the degree of optimisation in the code.) So, we first have laid out the config space challenge, onwe that is plainly unmet on the merits. on the broader issue of methodology, science works by empirically anchored inference to best explanation. There is a lot of evidence on the above, and so the explanation that a phenomenon such as is observed most credibly traces to agency from the set agency, chance and necessity, is not speculation unlinked to empirical data. Further to this, we have yet to see the proposal of a fourth effective, empirically observed source of cause. Finally, that intelligent agents exist and cause events in our world is a matter of direct experience and observation. So, such agents are plainly possible in our cosmos. (Or, are we here dealing with the evolutionary materialists' self-referential absurdity of denying the reality of intelligent choice, decision and action, i.e. denial of the reality and credibility of mind?) If you desire to deny the reality of cause and of mind as a relevant causal force, you have wandered from the realms of both science and reason. 4] Events that have occured in the past are historical events. Hypotheses about historical events can only be tested empirically And, how is the config space issue non-empirical? How is the incidence of stop codons non-empirical, how is the nature of DNA/RNA as a 4-state code chain non empirical? How is the nature of proteins as based on 20 monomers none empirical? We know a lot about such digital systems and the likelihood of accessing desired states by chance, DK. Just, the empirically anchored answers plainly don't go where you want. And, besides, you will note that above and generally, we have pointed out that if you can provide evidence that FSCI can be replicably generated by chance plus necessity, then the EF would collapse as a reliable test of intelligent/non intelligent cause. That is, the EF is subject to empirical test [and if necessary to falsification or corrective refinement in that light. Cf Hyp testing and type 1 and 2 errors thence degree of confidence.] We have many observed cases of intelligent action giving us FSCI, but so far over the course of a long time no one has provided a single counter instance of chance plus necessity doing the same. Onlookers, what is that telling you about the actual balance of the case on the merits? 5] As new data are ascertained, some hypotheses will be rejected Over the past 50 years, a lot of new data has been coming in. It reveals the intricacy and FSCI-richness of cell based life34. Indeed, it puts such life in the context of information and communication systems and technologies. The degree of complexity involved -- which is getting higher not lower -- is pointing very strongly to the known source of such systems: intelligence and design. However, as that does not sit well with the beliefs, worldview commitments and agenda of institutionally powerful forces in our civilisation, that is being stoutly resisted. (BTW, that is why this is not just a scientific issue, bFast.) But, plainly, the tide is turning. GEM of TKIkairosfocus_{July 31, 2008
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What can be done empirically is to formulate hypotheses based on current understanding of the properties of matter (living and non-living) and its earthly history, and test them for fruitfulness in terms of increasing our understanding. As new data are ascertained, some hypotheses will be rejected, whereas others will lead to further understanding. And on and on.
Daniel, you have been duped by the Bayesian priesthood! All it takes to transform Bayes into Fisher is a time machine. OK, maybe you logically have to go all the way back to the singularity. That's an absurdity. But let's not pick nits. Let's not be pedantic. Paul, if you don't see the humor, then you might want to look into interpretations of probability. Frequentism does not permit assignment of a probability to the proposition "life on earth originated by abiogenesis." Bayesianism does. But Bayesian probabilities are subjective, not objective, and don't give you a basis for making proclamations about Reality. Bummer. Dr. Dembski offered a frequentist workaround, hinging on something like objectification of a subject describing events, but it seems that other frequentists didn't go for it. gpuccio, thanks for differing respectfully. It's nice when someone recognizes that I'm not just pulling contentious rabbits out of the hat. I apologize to you and others that I've got a lot going on, and have to drop out after provoking many responses.CEC09_{July 30, 2008
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Antibody generation is a perfect example of intelligent engineering
Wouldn't that require an engineer? If I understand you correctly you are implying that random variation and selection both are intelligent processes.
an epitope is a very small aminoacid sequence, usually a few aminoacids, or up to ten -fifteen
Isn't that true for sequences involved in other protein-protein interactions.sparc_{July 30, 2008
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F2XL, "a Darwinist evolutionist" Hey! I'm no Darwinist, but I accept common descent, so I am an evolutionist! F2XL, another huge problem for the RNA world is that experiments (controlled environments seeded by replicating RNA) have allowed RNA to replicate itself. However, the darn replications simplify rather than becoming complex! See http://en.wikipedia.org/wiki/Spiegelman_MonsterbFast_{July 30, 2008
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Regarding the RNA world: A chief problem with it is that for RNA strands to form IN THE FIRST PLACE, you need sufficient amounts of concentrated carbon-5 sugars, phosphates, and also nucleotides bases (adenine, thymine, guanine, and cytosine). The catch is that these three constituents can only be artificially synthesized in completely different circumstances for each of those things listed. A phosphate group cannot develop in the same mix as a carbon sugar, and so on. That wouldn't even begin to explain how the information in the RNA got there in the first place.F2XL_{July 30, 2008
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Kairosfocus, I can't put in words how often I will likely end up linking to that comment you made on Ian Musgrave's article. Seems like design critics love to mindlessly cite claims in that article time and time again. I remember one debate I was in on youtube in which a ~~Darwinist~~ evolutionist started to mindlessly vomit point after point on that article. First, they insisted earlier life was much simpler prior to a living cell (while never elaborating on what it could've been or explaining how that proto-life changed from there), then went on to say that multiple sequences of amino acids could be functional, etc. And this was after I stated that specificational resources were in play. I guess if you can rebut most of the stuff on TO then you can pretty much take on 90% of all design critics.F2XL_{July 30, 2008
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Daniel King, (57) So speculation cannot "sufficiently and definitively answer "questions about how life arose and diversified" (that would be "a fundamental logical error"), and we need to "formulate hypotheses based on currrent understandings of the properties of matter (living and non-living) and its earthly history, and test them fro fruitfulness in terms of increasing our understanding." Well, let's see. Is the RNA world "speculation", or a hypothesis with a lot of evidence behind it, and no major flaws created by the evidence? Or is it one of those "hypotheses" that should be "rejected"? How about the protein world? How about the clay hypothesis? Come to think of it, I seem to recall that DNA code is remarkably similar to computer code, and that computer code is usually produced by living matter with the ability to reason and plan ahead. Well, perhaps not entirely matter, but at least where matter interacts with intelligence, and certainly something we know exists. Do you suppose that the code-like quality of DNA could be evidence that it was produced by some intelligence? Maybe we could start a blog about that idea. Sorry. That was insulting. But no more so than your comment that kairosfocus and I were assuming "that questions about how life arose and diversified on planet earth are answerable sufficiently and definitively by speculation." There is a lot of experimental evidence to back us up. If you have questions about it, feel free to ask. And the more respectful you are when you ask, the more respectfully you will be answered. P.S. Some of us even think that there vas someone who vas dare, but then you don't believe in old nomadic fairy tales, do you?Paul Giem_{July 30, 2008
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Sorry, I should have said, "...when I tried to convince him of the reality of an afterlife," because I knew he wasn't going to heaven.Daniel King_{July 30, 2008
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kairosfocus and Paul Giem, Regarding underlying assumptions: You assume that questions about how life arose and diversified on planet earth are answerable sufficiently and definitively by speculation. This is not only a questionable assumption, it is a fundamental logical error. On the contrary, it is a given that the processes that brought about life and its diversification on earth occurred at some time in the past (scientists have evidence that this was somewhere between 3.8 and 3.5 billion years before the present). Events that have occured in the past are historical events. Hypotheses about historical events can only be tested empirically. (Unless you was there, Charlie.)* Therefore, a scenario explaining life's origins is not discoverable solely by speculation. What can be done empirically is to formulate hypotheses based on current understanding of the properties of matter (living and non-living) and its earthly history, and test them for fruitfulness in terms of increasing our understanding. As new data are ascertained, some hypotheses will be rejected, whereas others will lead to further understanding. And on and on. Will we ever know exactly what happened? I doubt it, but science frequently surprises us. (Well, it has surprised me. Repeatedly!) -------------- *Should be said with a vaudeville Germanic accent, as by my dear departed grandfather, when I tried to convince him of the reality of heaven: "Vas you dare, Chollie?"Daniel King_{July 30, 2008
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Kairosfocus (43) gives a good rundown on the talkorigins site on OOL. However, he omitted the money quote:
I will try and walk people through these various errors, and show why it is not possible to do a "probability of abiogenesis" calculation in any meaningful way.
Note that the claim is not that the "creationists" are doing the calculations wrong and that here are the correct ones, or even that we don't know what the calculations are, but that the calculations can't be meaningfully done ("it is not possible"). The chutzpah is staggering. This sounds like more lawyerlike (sorry, bFast) argumentation that has no place in science. BTW, thanks DaveScot and bFast.Paul Giem_{July 30, 2008
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Sometimes UD bores me. We spend so much time on the politics of the debate. Periodically we get into a topic about the real data. This has been one of those times. This thread is the reason I spend energy here at UD. Paul Giem:
Now, if you want to challenge the numbers, go ahead. But if the numbers are reasonably accurate, it seems to me that we have a major difficulty here.
Yes! And if you Darwinists can convince me that the numbers work out, here and in about 15 other places (OOL), you will have converted one to your side. ID is in the data. If it were not so, ID would be religion.bFast_{July 30, 2008
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Good response, Paul. Double standards abound.DaveScot_{July 30, 2008
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CEC09, (31) PaV, in the original post, made an estimate for 200 Ma for the calculated human-monkey split, based on new genes and the presumed rate of new gene production in Drosophila. I don't know if it is safe to assume that he meant the human-chimpanzee split, but if so it would be relevant to your comment. The split from a common ancestor would be 6 million years ago by generally accepted fossil evidence, and thus effectively 12 million years ago. That is still too small by over an order of magnitude. Comments by various people on this thread have pointed out that Drosophila multiply some 1200 times faster than humans, and that their numbers vastly outnumber humans, even now when humans are populous, let alone during prehistoric times. This would seem to make the problem worse rather than better. A comment by bFast (34) indicates that 689 new genes are found in humans that are not found in chimpanzees. Those are the data. They indicate a real problem. Those who wish to explain away the problem by nibbling around the edges, like pointing out that humans and chimps, according to theory, evolved from a common ancestor rather than humans evolving from chimps, should realize that the problem will not be resolved by one or two such arguments, any more than you will make a million dollars if I give you 5 bucks. Quantity is important. I would have more sympathy with the claim (CEC09, 30) that it is dangerous to extrapolate if the person making that claim would also say that it is dangerous to extrapolate from microevolution (variation within species) to megaevolution (differences between classes, orders, and higher taxonomic groups). (BTW, I did not make the term up. See Simpson, G. G. 1944. Tempo and mode in evolution. Columbia Univ. Press, New York.) As it is, without the recognition that the caution goes both ways, this seems like an advocate's way to shut down the opposition regardless of whether it is fair or not, rather than someone cautiously trying to approximate the truth. Does this person really believe that humans evolving new enzymes some 10,000+ times as fast as fruit flies is not a problem, especially in view of the difference in population size? Now, if you want to challenge the numbers, go ahead. But if the numbers are reasonably accurate, it seems to me that we have a major difficulty here.Paul Giem_{July 30, 2008
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KF, at 49- Yes and the body plans are what is really needed. Without an understanding of how we got to "B", the question of "origins" is not be adressed. While everything seems to at some point dissapear into the mysterious voide of first non cause cause- however we can look at formations and determine alot about where they came from- that is where the information, the SC came from. Take a computer- it is dependent on a human for its formation- the computers SC is secondary to the human beings. The question is how do we get from simple to complex when the steps are degenerative- that is each step is secondary to the specified complity of the first? What kind of an evolution thinks "ahead"?Frost122585_{July 30, 2008
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DK: Appreciated. GEM of TKIkairosfocus_{July 30, 2008
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kairosfocus #43: I beg your pardon and that of the administrators for addressing you improperly. I see now that my unwanted expression of familiarity was thoughtless and rude, and I appreciate your forbearance.Daniel King_{July 30, 2008
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PS: I have looked up a relevant timeline, and find one here:
The Diptera are commonly known as (true) flies and include many familiar insects such as mosquitoes, black flies, midges, fruit flies, blow flies and house flies. Flies are generally common and can be found all over the world except Antarctica. Many species are particularly important as vectors of disease in man, other animals, and plants. In addition, much of our knowledge of animal genetics and development has been acquired using the vinegar fly Drosophila melanogaster (family Drosophilidae) as an experimental subject (Lawrence, 1992). The earliest fossil flies are known from the Upper Triassic of the Mesozoic geological period, some 225 million years ago (Evenhuis, 1995). Since that time they have diversified to become one of the largest groups of organisms. There have been about 120,000 species of flies formally described by scientists; thus about 1 in every 10 animals described is a fly. An equal number of species may await description and most of these will be found in environments that remain to be studied intensively, such as tropical forests.
225 MY or 600 MY, we are looking at significant constraints. And, we have not got to the level of addressing origin of the body plans and the original genomes, underlying codes and algorithms -- not to mention the issue of epigenetic information as DS raised in another recent thread -- that can diversify by whatever mechanism du jour.kairosfocus_{July 30, 2008
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A thought: Here is Wiki on Drosophila, as a little 101-level context will I think be helpful:
Drosophila is a genus of small flies, belonging to the family Drosophilidae, whose members are often called "fruit flies" or more appropriately vinegar flies, wine flies, pomace flies, grape flies, and picked fruit-flies, a reference to the characteristic of many species to linger around overripe or rotting fruit . . . D. melanogaster, has been heavily used in research in genetics and is a common model organism in developmental biology . . . The entire genus, however, contains about 1,500 species and is very diverse in appearance, behavior, and breeding habitat . . . . Drosophila are found all around the world, with more species in the tropical regions. They can be found in deserts, tropical rainforest, cities, swamps, and alpine zones. Some northern species hibernate. Most species breed in various kinds of decaying plant and fungal material, including fruit, bark, slime fluxes, flowers, and mushrooms. A few species have switched to being parasites or predators. Many species can be attracted to baits of fermented bananas or mushrooms, but others are not attracted to any kind of baits. Males may congregate at patches of suitable breeding substrate to compete for the females, or form leks, conducting courtship in an area separate from breeding sites . . . . The genus Drosophila as currently defined is paraphyletic (see below) and contains 1450 described species,[3][4] while the estimated total number of species is estimated at thousands.[5] The majority of the species are members of two subgenera: Drosophila (~1,100 species) and Sophophora (including D. (S.) melanogaster; ~330 species). The Hawaiian species of Drosophila (estimated to be more than 500, with ~380 species described) are sometimes recognized as a separate genus or subgenus, Idiomyia,[3] but this is not widely accepted. About 250 species are part of the genus Scaptomyza, which arose from the Hawaiian Drosophila and later re-colonized continental areas . . . . Drosophila are extensively used as a model organism in genetics (including population genetics), cell-biology, biochemistry, and especially developmental biology. Therefore, extensive efforts are made to sequence drosphilid genomes . . . . The data will be used for many purposes, including evolutionary genome comparisons. D. simulans and D. sechellia are sister species, and provide viable offspring when crossed, while D. melanogaster and D. simulans produce infertile hybrid offspring. The Drosophila genome is often compared with the genomes of more distantly related species such as the honeybee Apis mellifera or the mosquito Anopheles gambiae.
In short, the study reported by Zhou et al as linked in the OP, is based on a major focus on this genus, a genus that shows fairly wide diversity and apparently fairly high mutation rates. Doubtless, the projected timelines on the various members and evolutionary divergence are due to the various conventional dating schemes. (BTW, a Q: if "sister species" are interfertile, why are they regarded as separate species?) The key inference in Zhou et al, as observed by PaV is: 6) the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup. That has led to the following calc in the OP:
Noting that Drosophila melanogaster has 14,000 genes (a very low gene number), the simply calculation is this: 14,000 genes/8 [i.e. mid point of the range 5 - 11] new functional genes per million years= 1.75 billion years for the formation of the fly genome. This, of course, assumes that somehow the fly is ‘alive, and reproducing’ the entire 1.75 billion years—-this, without the aid of a full-blown genome. If we apply this to the monkey/human difference which, IIRC, is about a 1000 genes, then using this same rate, it would take 200 million years for man to have evolved from the monkey. This published rate for new functional gene generation cannot be good news for Darwinists.
Obviously, the calc is in large part meant to highlight the basic problem: accounting for body-plan level genetic information within the time claimed to be available on the usual reported timeline for life on earth. That problem is of course most notoriously seen in the Cambrian life revolution, where dozens of novel body plans appear in a window reported as being about 10 MY, some 500 - 600 MYA. 600 or so MY is a lot less than 1.75 BY, i.e. something is wrong with rates and/or dates. Independently of dates issues, we know that the genomes and associated proteins are long-chain discrete state systems, i.e. information-rich, functionally specified polymers. This is already so problematic for the macroevolution and OOL models that we can focus on just this part, taking the usual dates as givens for this discussion. The basic information storage capacity of a digital entity such as D/RNA or proteins, is reasonably estimated at 4^N for the former, and 20^M for the latter; and whatever variations in frequencies of component monomers we may bring up, this will not shift the basic order of the calculation. There just is not enough time, mass and material on earth -- or in the observed cosmos -- to get to the observed patterns and complexity, with reasonable probability relative to chance + necessity without intelligence. But, intelligence easily and routinely produces functionally specified information-rich systems that are of this order of complexity. So, Q: why is there such a strong resistance to the idea that intelligence is a reasonable -- indeed the best -- explanation for the FSCI in life forms? Answer: worldview level commitments, often backed up by attempted redefinitions of the nature of science that seek to constrain scientific inference to themes friendly to materialism. So, there is a serious issue that needs to be seriously addressed. GEM of TKIkairosfocus_{July 30, 2008
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GP Well said again. GEM of TKIkairosfocus_{July 30, 2008
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CEC09 (#40): You say a lot of correct things which do not change a comma of what I have said. The 100 aminoacid protein is obviously a standard example, just to try a computation. I have to recall that most proteins are much longer, and much more complex. It is obvious that the length is not fixed: that makes things even more difficult, and the search space even bigger. It is possible that sometimes we can pass from one functional gene to a similar functional gene, with some slight change in function: that's exactly the rare situation which could in theory occur by random mutation, and the few artificial examples of darwinists (see corticosteroid receptor experiments) are of that kind. But are you sayin that all functional genes are similar? Or that all types of proteins (and genes) cluster in the search space? That's simply absurd. Proteins are extremely different, they fold in completely different ways, they have very different domains and functions. Some proteins have completely no homologues. Even the best known protein families (see myoglobin) exhibit striking variations, often of a compensative nature, so that very different sequences may fold in a similar way. So, it is not true, imo, that "we know very little about the topology of the set of functional genes". We certainly know little, but we definitely know something, and nothing of what we know encourages the strange and fantastic topologies which darwinists like to imagine, like the smooth transitions from one cluster to another in the immense ocean of possibilities. It is certainly true that it is difficult to calculate the probabilities exactly, but that does not mean, in any way, that we cannot have a definite idea of their order of magnitude. Frankly, objections like the one you make about the asymmetric nature of the genetic code seem really irrelevant. I made my calculation from aminoacid sequences, and that was just a generous simplification. If you look at DNA sequences, you must add, to all the possibilities of protein sequences, also all the sequences which would never be transcripted and/or translated, and I can't see how that would help your argument. Finally, I see in your reasoning a common misunderstanding: when I use the term "random variation" I refer to any possible variation, and not only to single nucleotide substitutions. You can put in any mechanism which is non directed, be it deletion, duplication, inversion, insertion, and so on. The result does not change. Any of this act is random, and the result is a random sample of the whole search space. So, it's not true, as you say, that "“random search” is highly misleading in suggesting “uniform sampling with replacement.” It does not suggest anything like that. It only suggests that the cause of variation is not directed, and has no informational relationship with the function which is the final result of the variation (is that non teleological enough as a substitute for "search"?). It is not even necessary that all results are equally probable. Unless you can demonstrate that there is some law of necessity which determines special probability distributions which favor function, any real probability distribution, having no informational relationship with function, is blind to the result's functionality. So, the search is still random. In other words, if variation is caused by laws which have no relationship of any kind with a special informational pattern which allows function, the emergence of that pattern is possible only either by chance or by design. If chance is too unlikely, as it definitely is in the case of biological information, then only design is a reasonable answer.gpuccio_{July 30, 2008
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PS: I would love to see a case of an observed life-form using small sets of short-length genes, RNA and proteins that in aggregate does not get us into trouble relative to the UPB as I just discussed [and pardon the typos -- ouch!]. DK, Sparc and CEC09, might you be able to provide us a link? Failing such, could you provide us with cogent -- non question begging -- reason to infer that chance + necessity with no intelligence is a superior explanation to agency for the origin of the functionally specified, complex information in observed life forms? Or, just, can you give us an example of FSCI beyond the Dembski type bound i.e. ~ 500 - 1,000 bits of information storage capacity, that -- per direct knowledge of the causal process -- originated by chance and necessity only? [In short, can you show us that the explanatory filter is an empirical failure, instead of the reliable test for intelligence that we have claimed, per massive observation on the origin of cases of FSCI? (Just as, an observed perpetual motion machine would at once disestablish the laws of thermodynamics.)]kairosfocus_{July 30, 2008
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PaV: Thanks GEM of TKIkairosfocus_{July 30, 2008
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Now, on matters of substance: 1] "Assumptions" Mr King, we are dealing with a known context, not an abstract discussion of logico-mathematical method. In that context, you have invited by pretty direct inference, the conclusion that the sort of calculation above by PaV and/or the design thinkers more broadly, is unwarranted. Above, I therefore challenged you to substantiate -- which is plainly not an act of pride but of asking for the reasons for YOUR hope. In response, sadly,you have resorted to disrespectful behaviour as I just had to note, and have thereafter tried to improperly reverse the burden of substantiation. Worse, in 22 above, I actually provided a link to my always linked substantiation in outline of the sort of configuration space-based calculation that is often presented in an ID related context. (So much for the remark: "As an exercise in humility, you might answer your own questions above…" For, the "exercise" has been long since done, and you as a long time participant here know or should know that.) That calculation, anchored in the inherent nature of digital systems, raises serious challenges regarding the reasonableness of the idea that chance + necessity within the gamut of the observed cosmos, could give rise to the sort of discrete state information entities that lie at the heart of cell based life. You have provided neither a serious response on the merits nor a link to such. [Onlookers: PG's link to TO is illustrative of just how unserious the response from the evolutionary materialist side too often is. That's why he linked it without further comment.] The logical conclusion is that you are diverting from the substantial matter, and are taking up personalities instead. That speaks volumes on your real estimation of the substantial weight of your side's case on the merits. 2] The TO assertions: TO of course, first, does not wish to acknowledge that anyone other than "creationists" raises serious questions; never mind teh presence of men like Fred Hoyle -- a distinguished scientist and a life-long agnostic -- in the immediate context:
Problems with the creationists' "it's so improbable" calculations 1) They calculate the probability of the formation of a "modern" protein, or even a complete bacterium with all "modern" proteins, by random events. This is not the abiogenesis theory at all. 2) They assume that there is a fixed number of proteins, with fixed sequences for each protein, that are required for life. 3) They calculate the probability of sequential trials, rather than simultaneous trials. 4) They misunderstand what is meant by a probability calculation. 5) They seriously underestimate the number of functional enzymes/ribozymes present in a group of random sequences.
Let's look a bit closer: a --> Events are caused, per massive observation immemorial from the day of Plato, by chance and/or mechanical necessity and/or intelligent action. If we, ex hypothesi, rule out intelligence, that leaves chance [for high contingency situations or aspects -- which side of the die is upppermost] and necessity [for low contingency situations or aspects -- if dropped the die will fall]. b --> Cell based life, notoriously, rests on macromolecules assembeled from monomers, and cells are thus discrete-state systems, with very high contigency states. For the component DNA and RNA, 4^N, where N for OBSERVED -- note TO's artful, dismissive use of "modern" to dodge this key point -- life systems starts at 300 - 500,000. For proteins, 20^N, with 100 - 500 being typical chain lengths. The relevant config spaces therefore START at ~ 10^130, and go up from there, WAAY up from there. c --> Biofunctional states of DNA and proteins are highly constrained, the former by a code process and the onward link to proteins, which as GP outlines abiove, are massively functionally constrained. Sensitivity of funcitonality to perturbation of chain structure simply underscores this point. d --> Thus, we easily see why the observed functional systems are highly vulnerable to perturbation. (AKA: Why is there no market for deliberate exposure to mutation inducing irradiation? Why is it that most cases of observed microevoltuion are by loss of function?) That immediately means that the probability of gatting to such entities in biofunctional clusters per one variety or another of Darwin's soup in a prebiotic pond or geothermal vent or a comet, etc, is vanishingly small on ther scale of the observed cosmos. There are many upper bound estimates that show that, very strongly; these are the probability calcs that TO wishes to dismiss. e --> So, contrary to assertion no 2, as GP shows above, and taking in the calculations as a class, there is not any imposition of a dubiously arbitrary bound on proteins etc. Instead, there are reasonable estimates of models, with a consistent pattern of results, one that cuts across what TO wishes to sustain. [Much, much more reasonable than say the basis for the GCMs that have so much of the world in a tizzy over climate change.] f --> 3 is either a bald lie or reveals grossest incompetence. For, the Dembski type bound is based on the number of quantum states attainable by the observed cosmos as a whole, some 10^80 partticles, sifting through combined states at the rate of one combination of states for 10^80 or so particles, every 10^-43 seconds or so. That is as "simultaneous" AND as "sequential" as it gets. Worse, the very FIRST ID technical level book, TMLO, used an equilibrium state thermodynamic discussion, which is plainly and explicitly based on an overly generous concentration of monomers in a planet-scale prebiotic soup. And the issue is the monomer to biofunctional polymer transition, not hte assembly of a bacterium de novo out of the monomers. g --> Furtehr to this, probability calculations, of course are usually based on observed frequencies, or on the Laplacian equal chance of alternatives hypothesis, perhaps biased by some non-uniformity in probability distributions. The equiprobability of microstates is foundaitonal to statistical thermodynamics, a highly successful sceintific discipline. As my point 6 app 1 the always linked therefore shows, this sort of approach is a more or less standard way to look at the relevant probabilities. (In TMLO, which specifically addresses polymerisation [so the simple chemicals to bacteria assertion in TO is a strawman misrepresentation!], polymer expert Bradley actually addresses the Kenyon Biochemical Predestination chemical-bias argument through a statistical study and so convincingly was it overturned that Kenyon took advantage of writing the foreword to publicly recant.) In short, TO's 4th assertion is little more than a slander. h --> Finally, one may assert away all s/he wants that there is a large number of combinations of monomers that are "functional." The vastly yet larger number that are not, immediately reduces the suggestion to absurdity -- the smallest known functional genomes are of order 300 - 500 k. i --> That sets up a config space of minimal order 4^300,000 ~ 9.94 *10^180,617. With a generously assumed 10^1,000 islands of biofunctionality, each with 10^1,500 functional configs to choose from, we would be looking at 1 in 10^178,000. Negligibly different from zero probability on the gamut of our observed cosmos, or even for an array of 10^500 such sub-cosmi in some sort of brane sheet or the like. j --> "Generous"? Indeed: 10^1,000 or 1,500 is vastly larger than the number of not only bacteria -- to a first approximation, every lifeform is a bactrerium! -- that could have ever lived in our cosmos, but of the proteins or DNA or RNA strands that could have ever formed. For, the observed cosmos could enfold up to only 10^150 quantum states across its lifespan. k --> So, it is safe to conclude that a random walk through such a config space starting at an arbitrary initial point -- what a prebiotic soup would do -- is maximally unlikely to ever find the shores of any single island of funcitonality, much less get to apply any hill-climbing algorithms such as some vcariety of prebiotic natural selection. [Which itself is a questionable notion.] l --> And, if there is an assumed natural law that programs the emergence of life, we should note that the term "natural law" relates to natural regularities, i.e. situations that are of low contingency: if you have heat, fuel and air, you have a fire. But, life systems are just the opposite of low contingency. That would leave only chance or agency as the credible explanations. [Cf the config space taken up by this post's character sequences -- chance or agent or law?] m --> Worse yet, the future discovery of such a "life-program law" in the face of such a vast config space and resulting set of oterwise accessible contingencies, would imply pretty directly that the cosmos was programmed at its origin to create life. Programs of course require programmers. In short, there is a serious case on the merits to address. And, neither DK nor TO have taken it seriously. GEM of TKIkairosfocus_{July 30, 2008
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kairosfocus, I deleted Mr King's post containing your first name. Let's hope this practice is not repeated.PaV_{July 30, 2008
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CEC09:(25) [PaV]: "Should we thus conclude that whereas species of fruit flies are separated by whole genes either being present or not, this isn’t the case when it comes to apes and men. Does this sound reasonable at all?" [CEC09]: "Yes. There are many more Drosophila than humans at present, and the human population has exploded only recently. It seems safe to say that the number of Drosophila has been huge throughout the past 6 million years......" You seemed to have missed the point. Are we to assume that de novo gene origination takes place when it comes to two types of flies that are hardly distinguishable from one another, and yet it hasn't taken place at all when we're now dealing with the huge differences that separate humans and chimpanzees? Again, does that sound reasonable to you? CEC09: (30) "When within-species extrapolation of the rate of genetic innovation is so strongly contraindicated for humans, and has been shown to be strongly related to population size, how can you possibly defend extrapolating results for a species group with populations that have long been much larger than the present human population to the human species? My objection to extrapolation of the numbers in the Zhou et al. abstract is not merely a matter of principle. Rigorous scientific study of the human genome clearly tells us not to extrapolate. This is not just one of my unexpert guesses.' It appears that you are "bloviating" here: "Rigourous scientific study of the human genome clearly tells us not to extrapolate." Really? You seem to want to argue that what applies to flies, doesn't apply to humans. To do so, you suggest, is to engage in wrongful extrapolation. We shouldn't be applying the rates found in flies to that found in humans. Well, OK, let's try to fix this problem. You tell us along the way that flies generate 1200 times faster than humans. Well, does that then mean that the rate of "newly functioning gene formation" in humans should be 1200 times less than that of flies? Oh, but you say that humans are "evolving" twice as fast as other organisms. So, then, the rate in humans should only be 600 times less, making it 5-11 "newly functioning genes" per 600 million years. Doesn't this mean that chimps and humans should have exactly the same compliment of genes? This is what Musgrave claims, and this might be why he is claiming it, but there are studies suggesting that we have 689 genes that are not found in chimps. So, then, how do you explain this if "newly functioning genes" arise every 600 million years? You see, "extrapolating" fly data to human/chimp data makes it easier to explain the genetic difference between humans and chimps, not harder. But you seem to prefer the harder way. I don't suggest it.PaV_{July 30, 2008
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gpuccio: From the perspective of most geneticists and evolutionary biologists, "evolutionary search" is an oxymoron. The term search immediately suggests a goal, contradicting their belief that biological evolution is non-teleological. As Norbert Wiener pointed out in Cybernetics, evolutionary adaptation is much like learning in individuals and in cultures. But it's easier if we stick with terms familiar to you, provided no one uses them to beg the question of teleology.
10^30 molecules would seem a very big target, and it really is. But, in a search space of 10^130 sequences, there would still be a probability of only 10^30/10^130, that is of 1:10^100, of finding that kind of target by chance in a random search.
The 100-amino-acid protein is a very old example, predating Dembski. No one claims that there has been a search of 100-amino-acid proteins. No one even claims that there has been a search of length-306 strings of nucleotides (I'm including START and STOP codons). Evolutionary search is on the space of genomes (and even that is a modeling fiction, ignoring epigenetic information). Furthermore, "random search" is highly misleading in suggesting "uniform sampling with replacement." In fact, the nucleotide mutation rate is quite low. Genomes tend to grow, not shrink, in size due to such phenomena as gene duplication and retrotransposition. And these introduce new genetic regions that are anything but initialized uniformly at random. They start out with much or all of the information of functioning genes. Other interesting biases in the search arise from the fact that some amino acids are coded for by as many as six codons, and some are coded for by just one. AUG codes for both START and methionine, with interpretation according to context. These are just a few aspects of genetic change tossed off by a computer geek too tired to see straight. But they're enough to make analysis incredibly difficult for a Rip Van Einstein on his second cup of coffee. A key problem, in my mind, is that we know very little about the topology of the set of functional genes. Do functional genes tend to cluster, in some sense, in the space of nucleotide sequences? What is the probability that a short, functional gene homologous to none other will grow into a slightly longer functional gene? This could happen if an AUG codon arrived, by mutation or some other cause, just ahead of the existing start-AUG, changing the original start-AUG into methionine-AUG. What I'm driving at is that you cannot fix the length of codon sequences in your analysis. If I recall correctly, there are 10-amino-acid artificial proteins. Another important consideration is that the search over genomes may produce new genes in many overlapping regions. To get the flavor of what I'm talking about, compare these two questions: What is the probability that four tosses of a fair coin will yield the outcome HTHH? Now what is the probability that sixteen tosses will yield an outcome with HTHH as a subsequence? The regions of the genome that might give rise to genes are much longer than genes, so the analysis should look more like an answer to the latter question than the former (though, again, the sequence length should not be fixed, and sampling is not uniform). In other words, if you restrict your focus to a certain subsequence of nucleotides, you greatly underestimate the probability that a functional gene of a certain length will arise.CEC09_{July 30, 2008
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CEC09: "How can you establish a very low upper bound on the probability of an event when nobody knows its cause(s)?" It's very simple. The probability of an event is calculated for the hypothesis that a random process of variation is the cause. That is the assumption in darwinian evolution, or whatever you want to call it. If the cause is not random variation, but some other causative process (like laws of necessity or design), no calculation of probabilities makes sense. Probabilities are calculated for random events. For events which have a specific cause (necessity) the probability is always 1 (the event has to happen). The point is, as we have often discussed here at UD, the kind of information we observe in biological systems (CSI, or FSCI) simply "cannot" be the result of laws of necessity. So, if you can exclude random processes as a cause (and that's why we calculate their probabilities), then design is the only known causal process which gan give that kind of result. So, to sum up: we don't know how a new gene originates: we are not sure about the causal mechanism and we certainly don't know the details of the process. But, about the mechanism, we can make some sound inferences: a) It cannot be the result of necessity (as often discussed, necessity cannot give that kind of complex information). b)It cannot be the result of random variation (probabilities are absolutely against that). c) It can, definitely, be the result of intelligent design (we see that happening every day in human artifacts). That's why, as we always say, design is at present and by far the best explanatory theory for CSI in biological beings.gpuccio_{July 30, 2008
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