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DLL Hell, Software Interdependencies, and Darwinian Evolution

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In our home we have six computers (distributed among me, my wife, and two daughters): two Macs, two Windows machines, and two Linux (Unix) machines. I’m the IT (Information Technology) or IS (Information Systems) guy in the household — whatever is is.

A chronic problem rears its ugly head on a regular basis when I attempt to update any of our computer systems: Software programs are often interdependent. DLLs are dynamic link libraries of executable code which are accessed by multiple programs, in order to save memory and disk space. But this interdependence can cause big problems. If the DLL is updated but the accessing program is not, all hell will break loose and the program will either severely malfunction or suffer an ignominious, catastrophic, instantaneous death. On the other hand, if the program is updated and the DLL is not, the same thing can happen.

I’m still trying to figure out how the circulatory avian lung evolved in a step-by-tiny-step fashion from the reptilian bellows lung, without encountering DLL hell, and how the hypothesized intermediates did not die of asphyxia at the moment of birth (or hatching), without the chance to reproduce.

Of course, we all know that this kind of challenge — no matter how obvious or compelling — presents no problem for the D-Fundies (Darwinian Fundamentalists), who are true believers in the clearly impossible, based on materialistic assumptions in which design could not possibly have played a role.

Comments
Dave Wisker, ------"No question about it: if reproductive isolation is maintained long enough, speciation is inevitable" You can keep repeating the mantra, it doesn't make it true. Rote does not make right. Clive Hayden
June 19, 2009
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Its not the "very" question, Clive. Populations that exchange genes are more alike genetically than those that do not. An empirically verified fact. Reproductive isolation results in genetic divergence of populations, and the divergence grows the longer the isolation is in place. This is another empirically verified fact. Populations that differ enough genetically will not produce fertile offspring. This is still another empirically verified fact (the level of genetic divergence necessary for this to happen can vary, however). No question about it: if reproductive isolation is maintained long enough, speciation is inevitableDave Wisker
June 19, 2009
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Dave Wisker, -------"If reproductive isolation is maintained long enough, speciation is inevitable." That's the very question at hand isn't it? Since it is the question it also cannot be your conclusion or else you're arguing in a circle.Clive Hayden
June 19, 2009
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Hi Clive If reproductive isolation is maintained long enough, speciation is inevitable.Dave Wisker
June 19, 2009
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Nakashima, ------"Since they live on separate islands, I think there are other factors that will push them to speciation." And since I live on a different continent than Asia, eventually we will be different species.Clive Hayden
June 19, 2009
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Nakashima-San: The problem with assuming that minor changes on a hill slope that lead up to the top of the hill through a hill-climbing algorithm adequately model leaps across seas of non-function to create novel body plans, should be plain. 1 --> Consider on a hardware store that like both your archipelago and mine, is subject to hurricanes. Do we expect to ever see a hurricane passing over such a store and spontaneously assembling a livable three-bedroom house with all the trimmings? 2 --> Such is of course logically possible, but is so maximally improbable that it is empirically unobservable on the gamut of our observed universe. 3 --> Underlying is the key problem with GA's as I highlighted earlier: they assume that functionality comes in a smoothly varying "continental" landscape, with local hills and valleys. On such a functionality/ fitness landscape, hill climbing through modest variation of already somewhat functional entities and promotion of the more successful will work to get you to peaks. 4 --> in the real world, the landscape is more like a vast sea of non-function [which would be a flat zero on a functionality metric] with isolated islands of function. So, teh challenge is to first get to shorelines of function, before hill climbing can occur. 5 --> this manifestly holds for origin of life (which you wish to concede then wall off), which BTW directly implies that the Darwinian tree of life is lacking its taproot. [It therefore has no basis for ever getting evolution of biodiversity started. That is already a failure to get our the starting gate in the race . . . ] 6 --> But, the same challenge also holds for body plan level macro-evolution (which is the relevant issue, not micro-evolution within the islands of function.) 7 --> The Cambrian fossil life revolution is a good illustrative case: perhaps 38 phyla and subphyla, with no evident precursors, in a context where unicellular life forms maybe are independently viable at 300 - 500 k base pairs, but to get to novel body plans you have to account for novel cell types, tissues, organs and organisation, requiring a due set of proteins and enzymes and other regulatory mechanisms. All of which calls for increments in DNA. On the evidence of modern arthropods, 10 - 100 mega bits is a reasonable estimate of the novelty that has to happen dozens of times over. 8 --> Moreover, once we are dealing with body plans, we have to create new arrangements of the embryo or basic developing organism,not at late developmental stages, but in early stages, where odds against getting a viable change at random exponentiate. [A mutation that changes how many digits appear is one thing, one that fiddles with the spine or central nervous system, or that creates such etc are a wholly different other.] 9 --> In short, given the abundant evidence for isolated islands of function is a wide sea of non function for complex digitally encoded information, one cannot simply assume or assert that macro-evo is just cumulative micro-evo. (And, onlookers, notice the latest exchange over bird feather colouration!) 10 --> Worse, the fossil record, however one interprets it, is the only direct access to the world of life in the remote past. And its "almost unmanageably rich" evidence [250k+ fossil species, billions of actual fossils] gives a clear testimony: sudden appearance, stasis and disappearance or continuation into the present world are the overwhelmingly dominant features of that record (especially when one duly reckons with the implications of observed mosaic lifeforms like the platypus). ______________ In short, the immeasurably better explanation of the leaps in FSCI we see in body plan level biodiversity is the only directly known source of FSCI: intelligence. GEM of TKIkairosfocus
June 19, 2009
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A couple of things for the queue: 1. I don't know about 500 bits, but, for random biological processes, 200 bits of FCSI (according to KF's calculations, that, as the following shows, is out of touch with reality) is like falling out of bed. I don't think 500 bits is any less accessible. 2. According to Dembski, Behe, Durston, Axe, and every other real ID theorist, the quantity of functional information is computed by deriving the fraction of all possible proteins (or nucleic acids, or sequences) that can satisfy a given biological or biochemical function. This is a value that can be experimentally measured (as opposed to estimated by calculation). Simply prepare a large population of random polymers (polypeptides or polynucleotides, typically) and ask how many of the population can satisfy a given biological or biochemical function. This sort of measurement is inadvertently done on a routine basis. Anyone who does phage display with random libraries, anyone who uses mRNA display to discover new functional sequences, they all do this measurement. And they all routinely reach the same answer - functional sequences are relatively frequent occurrences (if 1 in 10^10 or so is frequent). ID theory, including KF's numbers, insists that random combinatorial approaches can never, ever work. Every time that such an experiment works (and it does all the time), it's yet another stake in the heart of ID.Arthur Hunt
June 18, 2009
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Hi Scott, The process of speciation doesn't always end up with two species-- in some cases the reproductive isolation fails to be maintained and the two once-diverging populations begin to merge again. In addition, the building up of isolation and genetic divergence can be observed and tracked before the actual species are formed. Incipient species are really just populations in the process of diverging, before the barriers are irreversible. They can be identified as such without an actual speciation 'event' occurring. But I’ll concede that the comment was hair-splitting, non-productive, and probably inaccurate. I wouldn't say that. It sparked my interest (of course, how populations begin to differentiate genetically is my are of interest). So it got geek points from me at least ;)Dave Wisker
June 18, 2009
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Mr Hayden, Since they live on separate islands, I think there are other factors that will push them to speciation. Unfortunately the news item does not say how strong the mate preference is today, but does say it will be a long difficult process to set up such experiments.Nakashima
June 18, 2009
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Dave Wisker @201: I had read that it was the early stage of speciation, which would be difficult to know unless speciation occurred. But I'll concede that the comment was hair-splitting, non-productive, and probably inaccurate.ScottAndrews
June 18, 2009
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Hi Scott, The term is used to describe a situation in which reproductiove isolation is beginning to develop. Reproductive isolation is an essential element of the speciation process. So no, it is not a term that can only be used retrospectively.Dave Wisker
June 18, 2009
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Dave Wisker @199: Given that no one knows whether the birds will speciate, it seems the term "incipient speciation" could only be used retrospectively.ScottAndrews
June 18, 2009
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Well then it’s too early to call it speciation. Most evolutionary biologists would agree with you, and call it "incipient" speciation.Dave Wisker
June 18, 2009
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Nakashima, ------"Yes, that is the “in action” part of the story. There seems to be some mate selection preference for similarly colored birds, so depending on your species concept they could be called separate species when they stop interbreeding significantly. Preference for self similarity is quite functional, and is a basic driver of speciation from single celled creatures onward." Well then it's too early to call it speciation. And we could call mate selection a "preference", like I prefer brunettes, but that wouldn't mean that blondes are a different species.Clive Hayden
June 18, 2009
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Mr hayden, Yes, that is the "in action" part of the story. There seems to be some mate selection preference for similarly colored birds, so depending on your species concept they could be called separate species when they stop interbreeding significantly. Preference for self similarity is quite functional, and is a basic driver of speciation from single celled creatures onward.Nakashima
June 18, 2009
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Nakashima, -------"Macro-evolution in action! Speciation based on a one base pair mutation event" Ummmm, different colored feathers doesn't constitute a new species anymore than my brother and I having different hair color constitutes us as being two different species.Clive Hayden
June 18, 2009
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Macro-evolution in action! Speciation based on a one base pair mutation event The comment to that story is also worth reading.Nakashima
June 18, 2009
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Mr Kairosfocus, This is indeed why so many people make a strong distinction between OOL and ToE. Evolution is the can opener of diversity. Since you consistently refer to the complexity of body plan FCSI in the 10-100 Mbit range, that is the relevant comparison to a 33 Mbit GA operating using evolution.Nakashima
June 18, 2009
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Mr Kairosfocus, As easy as this problem is, the fitness function does not present the population with a single target. A burst of cosmic rays passing through the machine would cause it to reboot or perhaps fail permanently. Pace to Mr Dodgen, the active information in the cosmic rays have not added anything to the simulation. Your point?Nakashima
June 18, 2009
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PS: You should be able to see some of what is going on from this summary at Wiki: ________________ Genetic algorithms are implemented in a computer simulation in which a population of abstract representations (called chromosomes or the genotype of the genome) of candidate solutions (called individuals, creatures, or phenotypes) to an optimization problem evolves toward better solutions. Traditionally, solutions are represented in binary as strings of 0s and 1s, but other encodings are also possible. The evolution usually starts from a population of randomly generated individuals and happens in generations. In each generation, the fitness of every individual in the population is evaluated, multiple individuals are stochastically selected from the current population (based on their fitness), and modified (recombined and possibly randomly mutated) to form a new population. The new population is then used in the next iteration of the algorithm. Commonly, the algorithm terminates when either a maximum number of generations has been produced, or a satisfactory fitness level has been reached for the population. If the algorithm has terminated due to a maximum number of generations, a satisfactory solution may or may not have been reached. ___________________ Recall, the key challenge for origin of life and of body plan lecvel biodiversity is to get TO shores of function that have even initial functionality. That term "fitness function" is all too revealing that this is like the physicist the Engineer and the economist on a desert island with cans of food, but no opener. Cutting the joke short -- and, my dad is an Economist -- the economist says: "first, postulate a can opener . . . "kairosfocus
June 18, 2009
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Nakashima-San Please play a little game, called "spot the active information." of course one can pick out a winneer in a much bigger config space than 1,000 bits. We do it allt he time when we compose messages based on intelligent activity. GA's are inherently intelligently designed, and in the cases in view are set up to optimise [or quasi-optimise, heuristics and all that] to a target. they are foresighted search. This is just the opposite of blind necessity and undirected contingency. Just think: if the entire program and PC in question running the algor you link were subjected to significant random variation, what would happen real fast, why? GEM of TKIkairosfocus
June 18, 2009
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Mr Kairosfocus, Since you have many times referred to the size of the problem to be solved in terms of millions of bits, I thought you would be interested in this slide presentation on gigabit optimization using genetic algorithms. Apparently it was possible to search such spaces to optimality for 33-Mbit problems in 2005, using less resources than the known universe. ID advocates may be especially interested in slide 31. Dr Goldberg argues there that to pass proof of concept gigabit optimization and apply the technique to engineering problems (including computational protein cemistry), it will be necessary to use evolutionary methods to build very large cognitive models, something he analogizes to human cognitive capacity.Nakashima
June 18, 2009
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Hi Paul,
Whoa. I’ll wait for the discussion. But in the meantime, are you saying that if someone comes up to me and asks whether life arose spontaneously, I am supposed to say, “I have no idea”? I can’t say, “I don’t know for sure, but at present it looks to me like it didn’t”? No conclusions, however tentative and open to revision, are allowed?
Of course not. Where did you get the idea I think that? If that is the impression my posts are giving, then maybe I need to polish my communication skills.
Does that also apply to the Privileged Planet hypothesis also? If so, have you written to the Iowa State faculty about the gross injustice of closing down the debate prematurely? Or is it only ID adherents who are not allowed to draw any conclusions?
How exactly did the Iowa State faculty close down the debate prematurely? I haven't followed that story very closely, apparently, although I did read som things about Gonzalez's tenure, but as far as I know that is a separate issue. And I have looked at the book in question briefly, but didn't see much in it of substance that added to or improved on the basic Anthropic Principle, which has been floating around in astrophysics circles for some time. Did the Iowa State faculty shut down all debate on the Anthropic Principle as well?
You move from the phrase “how nature does it” to “how living things (i.e ‘nature’) are today”. In the one case it seems to imply that nature is an active agent, and could easily imply that nature does it as opposed to an intelligent designer. The second way of saying it does not carry those implications. But if you didn’t mean them, that’s cool.
Right. The original example I had in mind when I wrote it was the basic design of the aircraft wing, which originally used the shape of bird wings as a starting point. The main point I was trying to make was, even if man eventually manages to create life, that doesn't conclusively show that life has to have intelligence to create it. It will be the first actual empirical example of intelligence creating life. But if it used nature as inspiration for much of its design ideas, all we can really say is, intelligence can create life if it bases much of the design on nature (which may or may not require intelligence for its designs). It would still require substantially more work to establish that life itself needs intelligence for its creation. That was the reason I brought up thge steochemical hyoptehsis in the first place: somebody here (I forget who at the moment) stated as a premise that information requires intelligence for its generation, the genetic code being one. My whole point was that this premise is false, since conceptually the stereochemical hypothesis which shows that many of the associations between entities that make up the code could be explained by chemical affinity, without intelligence as a necessary prerequisite. Just how plausible the hypothesis is remains to be determined, for some of the reasons you and I have been discussing. But the flat, absolute statement that information requires intelligence is false.
It looks like we’ll have to disagree for now regarding your comments on the quickest, surest way to dispatch the hypothesis of Yarus et al. But that’s okay. We don’t have to agree at present.
We don't have to agree at all, actually ;)
I’m glad we have reached agreement on whether, in an evolutionary pathway, if a given step does not have a function, that step cannot be influenced by natural selection.
To put it in flowery evo-language, the evolutionary path to a fitness peak can include neutral steps, and can,in some cases, include steps in which fitness is reduced.Dave Wisker
June 18, 2009
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Hi Dave, In #182 you say,
Is it not reasonable to make a fallible tentative conclusion that when the dust is settled, such “highly evolved anabolic pathways” without DNA control will turn out to be not realistically feasible?
I don’t think so, given the state of the research now being done. We haven’t really explored that yet– there is another interesting review by Yarus discussing what he suggests are the precursors to organisms using the genetic code. I was hoping to discuss that in a later comment.
Whoa. I'll wait for the discussion. But in the meantime, are you saying that if someone comes up to me and asks whether life arose spontaneously, I am supposed to say, "I have no idea"? I can't say, "I don't know for sure, but at present it looks to me like it didn't"? No conclusions, however tentative and open to revision, are allowed? Does that also apply to the Privileged Planet hypothesis also? If so, have you written to the Iowa State faculty about the gross injustice of closing down the debate prematurely? Or is it only ID adherents who are not allowed to draw any conclusions? You move from the phrase "how nature does it" to "how living things (i.e ‘nature’) are today". In the one case it seems to imply that nature is an active agent, and could easily imply that nature does it as opposed to an intelligent designer. The second way of saying it does not carry those implications. But if you didn't mean them, that's cool. It looks like we'll have to disagree for now regarding your comments on the quickest, surest way to dispatch the hypothesis of Yarus et al. But that's okay. We don't have to agree at present. I'm glad we have reached agreement on whether, in an evolutionary pathway, if a given step does not have a function, that step cannot be influenced by natural selection.Paul Giem
June 18, 2009
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Arthur Hunt:
Actually, no one anywhere has actually ever established, by direct experimental measurement, that FCSI (or CSI, or whatever) actually exists, in nature or in biology. Rather, those experimental measurements that have been done pretty clearly establish that FCSI (or CSI, or whatever) is a fictional concept.
1- If you don't like CSI nor FCSI then all YOU have to do is when an IDist says this is CSI/ FCSI is to demonstrate that nature, operating freely, can account for it. IOW all YOU have to do is to actually support YOUR position! However you have proven that the theory of evolution is a fictional concept. No measurements or calculations on how many mutations it takes to get a novel protein machinery. No measurements or calculations on anything. Heck no one even knows if the transformations required for universal common descent can even be produced by an amount of mutatioal accumulation. IOW you should stop complaining about ID and focus on your position. THAT is how you refute ID by demonstrating nature, operating freely can account for it. But you cannot so you have to complain about ID. Too bad your position doesn't have anything as well defined as CSI or IC. Then perhaps we could test it.Joseph
June 18, 2009
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5 --> Or, using an illustration, we may imagine the digitally coded configuration space as being a vast digital pacific ocean, dotted with islands and archipelagos of function. If a search-raft were to begin at an arbitrary location, and with resources limited to 10^150 possible steps, were to now move about on the ocean at random, if the space of the ocean were to be specified by 1,000 or more bits, the search could not cover as much as one part in 10^150 of the map. (In short, such a "lottery" is empirically -- as opposed to logically -- unwinnable.) 6 --> But now, for Koonin's [2000] minimally complex micro-organism, we are at least 600 to 1,000 times the bit depth of the limit of feasible random walk based search on the gamut of the credible search resources of our cosmos. (And, it bears noting that the genetic code table shows that all sixty-four mathematically possible three-letter combinations are used in protein codes as codons for amino acids or as start/stop codes. So, there is no chemical constraint that forbids any of the possible sequences of the letters {A, G, C, T/U}.) 7 --> Then, when we observe the Gerhart et al count of the number of base pairs for a modern arthropod, 180 * 10^6, we see the further search space vs search resources challenge to get to body plan innovation level macro-evolution. For, if we take 10 - 100 million base pairs as a reasonable estimate, we see that this range corresponds to ~ 8.19 *10^ 6,020,599 to ~ 1,36 *10^ 60,205,999 possible configurations. (And, worse, the search space is now constrained to our home planet [[~ 6*10^21 tonnes, and perhaps up to 3.8 - 4.6 BY (ignoring the Cambrian limit of ~ 600 MY!)], not the cosmos as a whole.) 8 --> Consequently, simple chance on the gamut of our observed cosmos is not a credible source of the fundamental functional innovations that have given rise to first life and to the perhaps 30 - 40 major phylum or sub-phylum level body plans in the current world and in fossil forms. 9 --> Now, the issue here is the arrival of the initially functional: such initial functionality is the premise of any onward variation and selection process that may help improve functionality through Darwinian-type evolutionary mechanisms. Indeed, a second look at Darwin's closing summary in Ch 15 of origin will again highlight that Darwin begins his theory with pre-existing life: >>It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the conditions of life and from use and disuse: a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.>> 10 --> In the days when "protoplasm" was imagined to be a fairly simple mixture of organic and inorganic compounds, this may have sufficed. But now, we know that life crucially depends on complex, functionally specific step by step algorithmically implemented digital information, stored in DNA strings that start out at ~ 600,000 bits for independently existing unicellular life forms. We therefore need a reasonable account for the origin of such functionally specific, complex information, including not only for first life but also, for body-plan innovations. 11 --> On best, empirically anchored explanation, the best alternative is simple: in every case where we directly know the origin, complex functional digital strings that have information capacity of at least 1,000 bits, are invariably the product of intelligence. So, FSCI is a reliable sign of intelligence, and we may confidently infer from FSCI as observed, to intelligence as its causal origin. 12 --> The reason for the sort of dismissals above is then quite simple: FSCI cuts clean across the attempt to account for the origins of our cosmos, and of life and its diversity including ourselves, on chance + mechanical necessity only in a postulated materialistic cosmos. So, it will be stoutly resisted by those who are committed to such agendas, and their fellow travellers. _____________ Clearly, despite Mr Hunt's confident declarations to the contrary, the FSCI concept is based on the relevant physics and biology, and is a well observed phenomenon. Indeed, using the 1,000 bit threshold, this or any other ASCII string of length at least 143 characters, is a case of FSCI. Neither Mr Hunt nor any other evo mat advocate here at UD can identify a case of known origin that credibly is the result of chance + necessity, as opposed to intelligence. thee is a whole Inernet full of cases in point on how FSCi is routinely teh product of intelligence. Libraries, Offices bookshops and many other cases provide further instantiation, amounting to literally billions of known cases,with no counter instances. In short,the inference from FSCI to intelligence as its best explanation is one of the best- supported, empirically warranted inferences we make. GEM of TKIkairosfocus
June 18, 2009
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Onlookers: A footnote, re AH at 177:
no one anywhere has actually ever established, by direct experimental measurement, that FCSI (or CSI, or whatever) actually exists, in nature or in biology. Rather, those experimental measurements that have been done pretty clearly establish that FCSI (or CSI, or whatever) is a fictional concept. As I have indicated in this thread, what ID proponents have done is roll out calculations that have no basis in biological or physical reality. This is a big stumbling block for ID - math that is disconnected from reality is no way to explore the nature of something.
In fact, this is a capital example of dismissive rhetoric, driven by selectively hyperskeptical thinking that seeks to brush aside -- rather than face squarely -- a key DESCRIPTIVE and empirically well warranted concept. One that by the way traces to leading scientists at he turn of the 1970's, and which is by no means a strictly design theoretic concept. (Had AH et al simply read the weak argument correctives in the RH column above, they would not be stuck in such an elementary error.) Let us begin with remarks by Prigogine et al, 1972:
The point is that in a non-isolated system there exists a possibility for formation of ordered, low-entropy structures at sufficiently low temperatures. This ordering principle is responsible for the appearance of ordered structures such as crystals as well as for the phenomena of phase transitions. Unfortunately this principle cannot explain the formation of biological structures. The probability that at ordinary temperatures a macroscopic number of molecules is assembled to give rise to the highly-ordered structures and to the coordinated functions characterizing living organisms is vanishingly small. The idea of spontaneous genesis of life in its present form is therefore highly improbable, even on the scale of the billions of years during which prebiotic evolution occurred. [[Ilya Prigogine, Gregoire Nicolis & Agnes Babloyants, "Thermodynamics of Evolution," Physics Today, (Vol. 25, November 1972) p. 23. (Emphasis added.)]
Then, the next year, Orgel went on record:
"[L]iving organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple, well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures which are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity." [[Leslie E. Orgel, The Origins of Life: Molecules and Natural Selection, pg. 189 (Chapman & Hall, 1973). (Emphases added.)]
Clearly we see here a description of functionally specific, complex information as a distinguishing characteristic of life, and the implication of such being in life forms at molecular level: FSCI is maximally improbable to originate by undirected contingency-based processes, without active information that cuts down the search spaces. Going further, in steps: 1 --> DNA/RNA are based on a four state digital component, taking values A/ G/ C/ T (or U). One digit therefore specifies four possible configurations. When two are present, for each state of the first, four different possibilities exist for the second. So, for N four-state digits, there are 4^N possible configurations, or equivalently 2^2N. (N four-state elements are equivalent to 2N binary digits, in terms of basic information storage capacity.) 2 --> Following the Koonin estimate, a minimally complex unicellular organism would therefore use a DNA of capacity equivalent to roughly 600,000 - 1,000,000 bits. That is, a configuration space of ~ 9.94 *10^180,617 to ~ 9.90 *10^301,029. 3 --> To create a comparative yardstick, 500 bits specifies ~ 3.27 *10^150 configurations, and 1,000 bits, ~ 1.07 *10^301 configurations. But, the ~ 10^80 atoms of our observed cosmos, changing state every Planck time [[~10^-43s], and for 10^25 s [[~ 3*10^17 y] would cycle through less than 10^150 configurations. So, hitting on a unique state specified by 500 bits at random would be comparable to finding just one of the possible states of the atoms on a one-shot try. And, with 1,000 bits, if the atoms of our observable universe were to be converted into a random walk search engine runing for a thermodynamically "reasonable" lifetime, it would not be able to search 1 in 10^150 of the possible configurations. [[For, 2^1,000 is of course the SQUARE of 2^500.] 4 --> So, if a fairly specifically functional, coded digital string uses more than 500 - 1,000 bits, it is reasonable to see that it is not empirically feasible to discover such a string by a random-walk search procedure. [ . . . ]kairosfocus
June 18, 2009
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Hi Paul, Many thanks for your last reply. Among other things, it certainly can be presented as a concise rebuttal to the "all religious faith is irrational" argument. I'm afraid I will have little time for comment today, but to your request for "any evidence, even if only suggestive, for life without DNA", I suggest two sources. The simplest one is to go back through this thread and read the comments by Art Hunt on protocells-- he is on moderation, so his responses to our discussion are often buried back in the thread. The second source is another review by Yarus on the evidence he sees for the existence of cells using RNA before the genetic code (they are called ribocytes): Yarus M (2002). Primordial genetics: phenotype of the ribocyte. Ann. Rev. Gen. 36: 125-151. From the abstract:
The idea that the ancestors of modern cells were RNA cells (ribocytes) can be investigated by asking whether all essential cellular functions might be performed by RNAs. This requires isolating suitable molecules by selection-amplification when the predicted molecules are presently extinct. In fact, RNAs with many properties required during a period in which RNA was the major macromolecular agent in cells (an RNA world) have been selected in modern experiments. There is, accordingly, reason to inquire how such a ribocyte might appear, based on the properties of the RNAs that composed it. Combining the intrinsic qualities of RNA with the fundamental characteristics of selection from randomized sequence pools, one predicts ribocytes with a cell cycle measured (roughly) in weeks. Such cells likely had a rapidly varying genome, composed of many small genetic and catalytic elements made of tens of ribonucleotides. There are substantial arguments that, at the mid-RNA era, a subset of these nucleotides are reproducibly available and resemble the modern four. Such cells are predicted to evolve rapidly. Instead of modifying preexisting genes, ribocytes frequently draw new functions from an internal pool containing zeptomoles (<1 attomole) of predominantly inactive random sequences.
Dave Wisker
June 18, 2009
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Hi Dave (#164) I agree with you that negative evidence is always inherently weaker than positive evidence. If that was all I had to offer, then the case for ID in the origin of life would be weaker than it is. That criticism does not apply in the same way to the creation of functional genetic code. We know that humans can create and insert into organisms functional genetic code, and so it is not unreasonable to postulate entities with human-like intelligence to explain apparently sudden increases in genetic information. It is also important to note that this weakness of minimalist ID theory would not make it significantly worse than the hypothesis of Yarus et al. It would simply mean that they would face the same kind of evidentiary challenge. It should also be noted that you have significantly sharpened the argument in your parallel in two ways. First, I asked for any evidence, even if only suggestive, for life without DNA. In your parallel, you asked for "empirical demonstrations" and "clearly demonstrable instances", a much higher standard. Second, I spoke of there being "Evidence against life without a DNA code", and you spoke of how
Without this [empirical evidence that intelligence has designed and created life], the truth of the rest of the tenets of the ID hypothesis cannot save it. If there are no clearly demonstrable instances of intelligence designing and creating life, then the ID hypothesis is false. Period.
That is, your supposed parallel would strengthen "evidence against HY" to "the ID hypothesis is false. Period". But, being as I believe in a variant of ID, I do not have to play by the minimalist rules. And the fact is, we do have evidence for the production of life from non-living material by an apparently superhuman agency. There are several instances recorded, two of which are quite convincing if one takes the record(s) at face value, and one of which was convincing enough that several witnesses were so strongly persuaded that they were willing to die for what they professedly believed to be the truth of the matter. I am speaking, of course, of the resurrection of Jesus. Now, I know that there have been multiple attempts to discredit the testimony of those who shared their experience. So i will not argue that we have a logically airtight case, and you simply must assent. I don't even believe that. This is particularly true with this short presentation of the evidence. It is meant to be evocative rather than probative. And I know that some would say that this is "religious" rather than "scientific" evidence. But this misunderstands the questions involved. For the believer in naturalism, there is no ultimate distinction between history and biology, just as there is no ultimate distinction between biology and chemistry and none between chemistry and physics. So history is just very very complicated physics. On the other hand those who believed in the resurrection of Jesus were quite firm in the belief that it was a historical event. If you like, it took place at least partly in the physical world, and had physical effects The evidence for the resurrection being at least partly physical is fairly clear from several passages. The passages I am citing are not being cited as sacred scripture to which if you do not assent, you are bound for hell. They are being cited as evidence of what the belief of those who had the experiences in question was. But it does seem fair to mention them as a witness to their belief. Some of the passages in question are 1 Cor 15 (the whole chapter, especially verses 5-8 and 12-19), Luke 24:36-43, John 20:24-29, and referring to a slightly different context, 2 Peter 1:16-18. Again, I am not offering those texts to prove that the Resurrection happened. I am simply offering them as evidence of what those who had been there believed, and claimed to believe upon good evidence. So I think that it is arguable that there is indeed positive evidence suggesting a superhuman entity that is able to give life to non-living matter. This would mean that your attempted parallel between ID and the hypothesis of Yarus et al. (HY) would fail to be convincing, as on the crucial point of positive evidence for a supporting prerequisite for the theory, there is a difference. HY does not at present have any positive evidence for life without DNA, and at least one variant of ID has at least some evidence, however weak, for a superintelligent entity that can create living matter our of non-living matter. I see that you are wary of arguments based on negative evidence. Hopefully positive evidence will be a little more to your taste.Paul Giem
June 17, 2009
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Hi Paul,
Is it not reasonable to make a fallible tentative conclusion that when the dust is settled, such “highly evolved anabolic pathways” without DNA control will turn out to be not realistically feasible?
I don't think so, given the state of the research now being done. We haven't really explored that yet-- there is another interesting review by Yarus discussing what he suggests are the precursors to organisms using the genetic code. I was hoping to discuss that in a later comment.
I tend to be a little more careful the way I phrase things. Maybe the authors were too, and they are quoted out of context in this regard. But I would have preferred to say something like, “If our hypothesis is correct, then life . . . employed amino acids that lie at the end of what must have been highly evolved metabolic pathways. . . .” Otherwise, the “must have” switches from a testable consequence of the theory, and a potential liability, to an assertion about reality. But now that I know, I’ll be more careful about accepting conclusions drawn from the paper. I can adjust.
That's cool. I'm just not used to having to explain what is usually recognized as a given. Suffice it to say that the researchers clearly recognize theer are certain conditions upon which the sterochemical hypothesis depends.
You say, Of course, we haven’t seen life designed in the laboratory either, and even if we did, all that would show is that humans can design life—usually after careful study of how nature does it. Note the implicit assumption that “nature” did it, without any help. You really have a hard time letting go of your assumptions. Or maybe you just misspoke, for you go on to say,
No implicit assumption is being made here. I'm simply saying that if humans ever manage to design or create life, much of their practical design inspiration will come from examining how living things (i.e 'nature') are today. I certainly did not misspeak.
I’m not sure it would. For practically any theory, one can find supportive evidence. As I noted above (#161), the best way to destroy the theory that GWB’s invasion of iraq did not cause 9/11 is not to argue that GWB did not make any Muslims mad. It is to concentrate on the time issue. Just so, for any theory, it is not the evidence that supports the theory that is likely to be most vulnerable; it is the evidence about the “highly speculative aspects” that is most likely to destroy the theory. That’s why I do not concentrate on “the experimental evidence claimed to support the stereochemical hypothesis.”
I'm afraid I disagree. Were there any clear experimental evidence unequivocably contradicting the empirical support for the stereochemical hypothesis, it would be abandoned. That is the quickest, surest way for an hypothesis to bite the dust. At least in science it is.
I take it by your silence that you are agreeing that my statement that in a given evolutionary pathway, Each step need not have function. But in that case natural selection cannot select for function, is accurate, as long as the last clause is understood as meaning “for that step”, and are withdrawing your previous objection that what I said is “a massive non sequitur.
Yep. That is much clearer.Dave Wisker
June 17, 2009
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