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The Odds That End: Stephen Meyer’s Rebuttal Of The Chance Hypothesis

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The Andes mountains opened up on both sides of us as we drove on one July afternoon along a highway that links Quito, the capital of Ecuador, with the smaller town of Ambato almost three hours further south. The setting sun shone head-on upon two volcanic giants- Tungurahua and Cotopaxi with its snow covered peak just visible through the cordillera. I had traveled along this road many times in previous years and had been repeatedly awe-struck by the sheer beauty of the surrounding land. Today fields extend as far as the eye can see, with the lights of small communities and villages illuminating the mountain slopes.

Volcanoes that periodically eject dangerous lava flows are a rich source of soil nutrients for Ecuadorian farmers. Still, in the eyes of organic chemists such as Claudia Huber and Guenter Wachtershauser there exists a more pressing reason for studying the world’s ‘lava spewers’- one that has everything to do with the unguided manufacture of prebiotic compounds (1). Huber and Wachtershauser’s 2006 Science write-up on the synthesis of amino acids using potassium cyanide and carbon monoxide mixtures was heralded as groundbreaking primarily because of the ‘multiplicity of pathways’ through which biotic components could be made using these simple volcanic compounds (1).

Others have similarly weighed in with their own thoughts on volcanic origins (2-6). In the words of one notable Russian research team “the opportunity to define the pressure and temperature limits of [volcanic] microbiological activity as well as constrain its rate of evolution in a primordial environment is an exciting one, with implications for the origin of life on earth and existence of life elsewhere in the solar system” (3).

Whether it be Darwin’s warm little pond or contemporary speculations over life-seeding environments we see in both a search for continuity from the non-living to the living- a search that was exemplified in Walt Disney’s color and sound extravaganza Fantasia almost seventy years ago. Disney popularized origin of life theories by artistically proclaiming that volcanoes exploding and comets colliding were all that were needed to get life under way. According to such a portrayal the evolution of more complex multi-cellular forms would then naturally follow (7). Disney enthusiasts will no doubt find comfort in the decade-old New York Times prescription for a life-yielding brew:

“Drop a handful of fool’s gold (the mineral iron pyrites) and a sprinkle of nickel into water, stir in a strong whiff of rotten eggs (caused by the gas hydrogen sulfide) and carbon monoxide, heat mixture near the crackle and hiss of a volcano and let simmer for an eon.” (8)

Along a similar thread, journalist Tony Fitzpatrick cavalierly asserted that “conditions favorable for hydrocarbon synthesis also could be favorable for other life ingredients and complex organic polymers, leading…eventually to all sorts of cells and diverse organisms” (9). Of course skeptics of such depictions have their own armory of scientifically-valid reasons for denying that naturalistic earth models could have given us anything more than a geothermal sludge.

Perhaps the most persuasive of these comes from philosopher Stephen Meyer who in his most recent book Signature In The Cell supplied a mathematical treatise on the synthesis of bio-molecules (10). Following in the footsteps of fellow ID advocate William Dembski, Meyer has done us all a great service by showing how the chance assembly of a 150 amino-acid protein (1 in 10exp164) pales in front of the available probabilistic resources of our universe (10exp139 is the maximum number of events that could have occurred since the big bang) (10). In other words, we are stopped dead in our tracks by a probabilistic impasse of the highest order before we have even begun assessing the geological plausibility of competing origin of life scenarios.

The scientific method commits us to finding the best explanation for the phenomena we observe. Drawing from the opinions of NIH biologist Peter Mora, Meyer shows us how the chance hypothesis- that purports to explain how life arose without recourse to design or necessity- has been found wanting particularly in light of the ever-growing picture of the complexity of the cell (10). But the debate-clincher in Meyer’s expose comes from his comprehensive summarization of the bellyaches associated with chemist Stanley Miller’s controversial spark discharge apparatus (10).

Former colleagues of Miller concede that the highly reducing conditions he used in his experiments could not have been the mainstay of prebiotic earth (4). Nevertheless they further posit that localized atmospheric conditions around volcanic plums may have been reducing after all and that these could have given rise to life-seeding compounds (4). In their assessment:

“Even if the overall atmosphere was not reducing, localized prebiotic synthesis could have been effective. Reduced gases and lightning associated with volcanic eruptions in hot spots or island arc-type systems could have been prevalent on the early Earth before extensive continents formed. In these volcanic plumes, HCN, aldehydes, and ketones may have been produced, which, after washing out of the atmosphere, could have become involved in the synthesis of organic molecules. Amino acids formed in volcanic island systems could have accumulated in tidal areas, where they could be polymerized by carbonyl sulfide, a simple volcanic gas that has been shown to form peptides under mild conditions.” (4)

Of course with so many ‘could-haves’ and ‘may-haves’ such a picture leaves us sitting on a vacuous flow of speculation rather than on a substantive bedrock of firm evidence. For seasoned biologist David Deamer the realization of implausibility, at least for a direct volcanic origin, comes from his own direct observations:

“Deamer carried with him a version of the “primordial soup”- a mixture of compounds like those a meteorite could have delivered to the early Earth, including a fatty acid, amino acids, phosphate, glycerol, and the building blocks of nucleic acids. Finding a promising-looking boiling pool on the flanks of an active volcano, he poured the mixture in and then took samples from the pool at various intervals for analysis back in the lab at UCSC. The results were strikingly negative: life did not emerge, no membranes assembled themselves, and no amino acids combined into proteins. Instead, the added chemicals quickly vanished, mostly absorbed by clay particles in the pool. Instead of supporting life, the bubbling pool had snuffed it out before it began.” (6)

Not only has Meyer’s probabilistic analysis supplied us with the odds that end the discussion for ‘chance-philes’, but contemporary extravagations over prebiotic earth have done nothing to bolster their credibility. We are left with little choice but to discard chance as a serious contender in the ‘life origins’ debate.

Literature Cited
1. Claudia Huber and Guenter Wachtersheuser (2006) a-Hydroxy and a-Amino Acids Under Possible Hadean, Volcanic Origin-of-Life Conditions, Science, Vol 314, pp. 630-632

2. A.J Teague, T.M Seward, A.P Gize, T. Hall (2005) The Organic Chemistry of Volcanoes: Case Studies at Cerro Negro, Nicaragua and Oldoinyo Lengai, Tanzania, American Geophysical Union, Fall Meeting 2005, abstract #B23D-04

3.John Eichelberger, Alexey Kiryukhin, and Adam Simon (2009) The Magma-Hydrothermal System at Mutnovsky Volcano, Kamchatka Peninsula, Russia, Scientific Drilling, No. 7, March , 2009, pp. 54-59

4. Adam Johnson, H. James Cleaves, Jason Dworkin, Daniel Glavin, Antonio Lazcano, Jeffrey L. Bada (2008) The Miller Volcanic Spark Discharge Experiment. Science 17 October 2008: Vol. 322, p. 404

5. David Grinspoon (2009) This Volcano Loves You, Denver Museum Of Nature & Science, COMMunity Blogs, See http://community.dmns.org/blogs/planetwaves/archive/2009/03/19/this-volcano-loves-you.aspx

6.Chandra Shekhar (2006) Chemist explores the membranous origins of the first living cell, UC Santa Cruz, Currents Online, See http://currents.ucsc.edu/05-06/04-03/deamer.asp

7.Fantasia, Walt Disney Home Video, Copyright by the Walt Disney Company, 1940

8. Nicholas Wade (1999) Evidence Backs Theory Linking Origins of Life to Volcanoes, New York Times, Friday, April 11, 1997

9.Tony Fitzpatrick (2000) Life’s origins: Researchers find intriguing possibility in volcanic gases, http://record.wustl.edu/archive/2000/04-20-00/articles/origins.html

10. Stephen Meyer (2009) Signature In The Cell: DNA And The Evidence For Intelligent Design, Harper Collins Publishers, New York, pp. 215-228

Comments
tgpeeler at 67, Many people try to hide behind the “what is information, really?” curtain. It’s a flimsy one indeed. I strongly disagree. If we don't have an explicit, rigorous definition of the term, we quite literally don't know what we're talking about. I've read your posts on this thread and find them interesting, but in order to discuss them rationally I do need to know: What exactly is your definition of "information"?Mustela Nivalis
December 17, 2009
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Zachriel (and CJYman) at 66, Hey, that was my first delurking at UD! I should have remembered you were talking about Titin. CJYman, I'd very much like to continue the discussion of my questions about your calculation: https://uncommondescent.com/philosophy/what-is-intelligence/#comment-341846 Perhaps we can get to a sufficient level of detail to code this thing.Mustela Nivalis
December 17, 2009
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IrynaB re 64 You say: "If you’ll pardon me, perhaps it didn’t occur to many because it doesn’t seem to make sense. At the very least you need to define your terms first before I can even try to make more sense of it: information and life. As far as I know, life is a slippery concept and all definitions are somewhat arbitrary. Ergo, your claim implies that the same must hold for the concept of information." Regarding your confusion concerning my assertions about information and life that "do not make sense" here are some popular citations that may shed some light on this subject for you. Francis Crick, Of Molecules and Men: "…we have, in effect, to translate the information from a four-letter language into a twenty-letter language, and this is by no means easy." speaking of the genetic code/language. FC, OMM: "…so that the language that is used in the nucleic acid polymers is universal." Francis Crick, Life Itself: “In spite of our differences we all use a single chemical language, or, more precisely, as we shall see, two such languages, intimately related to each other.” FC, LI: “A protein is like a paragraph written in a twenty-letter language, the exact nature of the protein being determined by the exact order of the letters. With one trivial exception, this script never varies. Animals, plants, microorganisms and viruses all use the same set of twenty letters although, as far as we can tell, other similar letters could easily have been employed, just as other symbols could have been used to construct our own alphabet.” Richard Dawkins, River Out of Eden: "You can treat the genetic code as a dictionary in which sixty-four words in one language (the sixty-four possible triplets of a four-letter alphabet) are mapped onto twenty-one words in another language (twenty amino acids plus a punctuation mark)." RD, ROE: "… we know that genes themselves, within their minute internal structure, are long strings of pure digital information. What is more, they are truly digital, in the full and strong sense of computers and compact disks, not in the weak sense of the nervous system. … The machine code of the gene is uncannily computerlike …" RD, ROE: "Life is just bytes and bytes and bytes of digital information." RD, ROE: "Indeed, the whole DNA/protein-based information technology is so sophisticated – high tech, it has been called by the chemist Graham Cairns-Smith – that you can scarcely imagine it arising by luck, without some other self-replicating system as a forerunner." RD, The Blind Watchmaker: "We have seen that DNA molecules are the centre of a spectacular information technology." Bernd-Olaf Kuppers, Information and the Origin of Life: “To start with, a brief introduction to modern evolution theory is given (chapter 1). A central and fundamental concept of this theory is that of “biological information,” since the material order and the purposiveness characteristic of living systems are governed completely by information, which in turn has its foundations at the level of biological macromolecules (chapter 2). The question of the origin of life is thus equivalent to the question of the origin of biological information.” BOK, IOL: “The term “biological information” requires clarification, and this is the purpose of part II. It will be shown that three dimensions of information can be distinguished: its syntactic, semantic, and pragmatic aspects.” BOK, IOL: “The smallest catalytically active protein molecules of the living cell consist of at least a hundred amino acids. … This shows that already on the lowest level of complexity, that of the biological macromolecules, an almost unlimited variety of structures is possible. … It is therefore to be expected that the construction and the coordinated interplay in the cell of these molecular function-carriers is determined by a plan, that is to say, information.” Hubert Yockey, Information Theory, Evolution, and the Origin of Life: “The existence of a genome and the genetic code divides the living organisms from nonliving matter. There is nothing in the physico-chemical world that remotely resembles reactions being determined by a sequence and codes between sequences.” “The belief of mechanist-reductionists that the chemical processes in living matter do not differ in principle from those in dead matter is incorrect. There is no trace of messages determining the results of chemical reactions in inanimate matter. If genetical processes were just complicated biochemistry, the laws of mass action and thermodynamics would govern the placement of amino acids in the protein sequences.” “Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies.” “The genetic information system is the software of life and, like the symbols in a computer, it is purely symbolic and independent of its environment. Of course, the genetic message, when expressed as a sequence of symbols, is nonmaterial but must be recorded in matter or energy.” “Life is guided by information and inorganic processes are not.” Perhaps this will help clarify that information and life are related and how they are related. If you want all of the details, of course, you should read the books. There are many more but I have a tennis match tomorrow and need my rest. :-)tgpeeler
December 16, 2009
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IrynaB You misunderstand me. Many people try to hide behind the "what is information, really?" curtain. It's a flimsy one indeed. You can't read about life/evolution/intelligent design without understanding that all writers agree that life and information are inextricably linked. It's a brute fact. Do you want me to cite a bunch of authors from both sides of the debate? Will that help? There can be no information apart from a mind. I think that's pretty clear. When life first appeared in the universe it came from a pre-existing and eternal life. Even modern cell theory says that life only comes from life. All you have to do is take that to its logical conclusion. Since the first life could not come from non-life, the first life had to be eternal. It's quite rational, really. It's either that or you can create life from non-life and prove me (and Pasteur) wrong. Good luck. As far as your intellectual commitment to further your knowledge of the natural world that's not what I meant either and I suspect that you know that. I am speaking of ontological (what exists), epistemological (how do we know), logical (first principles and part of epistemology, actually), and ethical (moral law, right/wrong - exists or not, if so why? if so based on what?) commitments. What is non-negotiable for you in this sense? I think I've been pretty clear about it from my side.tgpeeler
December 16, 2009
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CJYman: Where were we discussing the CSI of Titin?
Here:
CJYmanCJYman: - So, let’s look at Titin (34,350 amino acids [aa]). I am going to give as much of the benefit of the doubt to the critics when calculating probabilites.
The problem is that you use probability figures that are quite possibly wrong, but clearly believe the argument to be so strong as to overthrow well-established and strongly supported science. Specifically, you are substituting a random variable wherever there is a gap in human scientific knowledge. For instance, a plausible mechanism for chirality changes your calculation by a factor of a mere 2^34350.Zachriel
December 16, 2009
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Zachriel: The information I provided gives us a rough idea of the *minimum* frequency of functional sequences in such a random pool. CJYman: It is possible that I missed the relevant material in another comment of yours but the information you provided that I quoted does no such thing.
My comments have concerned the claim in the original post that chance assembly of long proteins "pales in front of the available probabilistic resources of our universe.” Of course it provides a minimum. We can take a random library and consistently find functional sequences.
CJYman: You left out answering how constrained is the functional pattern.
The original sequences have weak activity, and then are optimized by selection. You may want to reread Szostak's paper. It follows that of the 10^60 possibles sequences, ~10^50 can bind to a given ligand. They also provide a rough estimate that, for a given function, there are probably only a few hundred different sequence families for a given binding site.
CJYman: What is that number of catalytically active molecules and how many of those are relevant to living systems? Furthermore, how many will work at a specific cite, providing function which at least does not decrease survivability?
That wasn't the issue raised.
CJYman: Where is specificity relaxed? Artificial evolution increases what activity?
These experiments start with weakly interacting enzymes that are then optimized through rounds of amplification and selection. The function is defined by the experiment, and is usually of biological or medical significance. The original experiments were directly related to ideas about abiogenesis.
CJYman: *ALL MEASUREMENTS ARE BASED ON OUR IGNORANCE.*
Measurements are meant to reduce our ignorance, not be directly proportional to it. A tree doesn't get larger the more ignorant we are, but CSI does.
Zachriel: Oddly enough, the calculation also depends on the wordiness of the Semiotic Agent as it is the class of shortest descriptions that are used in Dembski’s formula. CJYman: … which is also the basis of K-Complexity. What’s the problem?
K is noncomputable. It explicitly depends on the description language. And it doesn't make pseudo-scientific claims.Zachriel
December 16, 2009
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tgpeeler:
But somewhere along the line it occurred to me (and still very few, if any, others) if the question of the origin of life is the question of the origin of information then what has to be explained in order for information to be explained?
If you'll pardon me, perhaps it didn't occur to many because it doesn't seem to make sense. At the very least you need to define your terms first before I can even try to make more sense of it: information and life. As far as I know, life is a slippery concept and all definitions are somewhat arbitrary. Ergo, your claim implies that the same must hold for the concept of information. Also: Are you saying there was no information before life first appeared? What about your earlier claim that there can be no information without reference to a mind? When life first appeared there were no minds around as far as I know. If true, does that imply that information first appeared when the first mind arrived at the scene? By the way, here is one of my intellectual commitments: to further our knowledge (information - ho ho) of the natural world.IrynaB
December 16, 2009
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Mark Frank @ 61 "No – I am saying the bounds of physics includes events that do not have causes. Inconceivable? More inconceivable than the idea that space might be bent by matter? Or that the interior angles of a triangle might have more or less than 180 degrees?" And I am saying give me some empirical evidence. Anything that is not logically contradictory is conceivable. And where did you come up with "the bounds of physics includes events that do not have causes"? And what does that have to do with anything that is under discussion anyway? I know I asked the question but it was in the context of denying first principles, of which sufficient cause is one. So more stuff out of thin air that doesn't really mean or explain anything. I might as well say that physics embodies the idea of one hand clapping.tgpeeler
December 16, 2009
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paulmc @ 60 "Firstly, I said that you are incorrect to state that the laws of physics should be sufficient to a materialist to explain everything. This is patently incorrect, as I have explained via the concept of emergent properties. This is not trivial – you claim this ‘problem’ is central:" Perhaps you would be so kind as to show how information is an emergent property of the random or lawful arrangement of matter. "Emergent" properties are the refuge of the one who is unable to account for what needs to be accounted for. Information? Oh, it's "emergent." O.K. I'll bite. Show me. Show me how the laws of physics can begin to account for the symbols and rules that are necessary to encode information and thus explain life. The symbols are emergent? The rules are emergent? The arrangement of nucleotides is governed by the laws of physics? I don't think so. I'm not 100% sure but I don't think I'm the one missing the point here. And this: "My point is that there is absolutely a physical basis, as I explained." Here is that explanation: "There is a physical explanation for why the genetic code is the way it is. Codons are not some abstract language but are literally physically related to the amino acids they “code” for – in the case of DNA via mRNA and tRNA. To refer to DNA as abstract or immaterial information in is misleading. It is tempting to look at DNA as a language – after all we use C, G, A and T/U to represent the bases – this is purely a human abstraction of their physical reality." This is actually kind of funny as you are making my point for me. I know that codons are literally related to the amino acids they code for. Why do you suppose that is? Why is one string of codons meaningful and another meaningless? The human abstraction (what other kind is there?) to recognize that the language and information exist does not mean that the language and information isn't real. What you need to do is show how certain arrangements of codons code for certain amino acids and ultimately proteins based upon what physical law(s). This was Yockey's point. I will repeat it. "If genetical processes were just complicated biochemistry, the laws of mass action and thermodynamics would govern the placement of amino acids in the protein sequences." And I will repeat again. They don't. To claim that "emergence" conquers this problem without providing further details doesn't do it for me. Speaking of intellectual commitments, I notice that I'm still the only one who's made them. What are yours??tgpeeler
December 16, 2009
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How can you challenge the principle of causality, for example? Are you saying that things happen, in this universe, outside of the bounds of physics (and I would add living agency)? No - I am saying the bounds of physics includes events that do not have causes. Inconceivable? More inconceivable than the idea that space might be bent by matter? Or that the interior angles of a triangle might have more or less than 180 degrees?Mark Frank
December 16, 2009
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tgpeeler @ 44: In your response you have disregarded both of my arguments. Firstly, I said that you are incorrect to state that the laws of physics should be sufficient to a materialist to explain everything. This is patently incorrect, as I have explained via the concept of emergent properties. This is not trivial - you claim this 'problem' is central:
But here lies the rub. If a materialist is intellectually committed ... to the idea that all that is real is material, that is matter and energy, or the physical world, or the natural world, or the things described by the natural sciences, or whatever the latest version of the nonsense is, THEN, the only explanatory resources they have are the laws of physics.
You quote Yockey in the same post and later claim I ignore him, but Yockey, like yourself, does not consider the concept of emergent properties. To reject this concept is to accept reductionism of the type that Dawkins was frequently guilty of in his scientitic writings. Secondly I took issue with you saying that:
There is no physical explanation for why the genetic code is the way it is. It cannot be explained, it is impossible for it to be explained, by reference to physical laws.
My point is that there is absolutely a physical basis, as I explained. Denying its physical basis is patently incorrect.paulmc
December 16, 2009
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Mark Frank @53 again: " It is part of the intellectual stance of an atheist and a scientist to be prepared to challenge even the deepest assumption. It is really hard to challenge logical laws but metaphysical beliefs such as “every event has a cause” can be challenged and indeed I hold them to be false." I'm fine with challenging assumptions as that's what I've been doing non-stop for about the last 8 or 9 years, but that's not what atheists (granted, in my limited experience, it should go without saying) typically do. It seems to me, from the theistic side of the fence, that atheism starts with an unfounded, unexamined assumption and then draws an inviolable conclusion from that. i.e. If naturalism is true then God does not exist. But is naturalism true? Atheists seem to be reluctant to seriously engage on that front. Challenging first principles doesn't seem intellectually bold or daring to me as much as foolish. How can one argue against the law of identity, that something is not what it is, and have a shred of intellectual credibility? Communication can't take place unless words mean what they say and that they REPRESENT things, even imaginary things, in the universe. How can you challenge the principle of causality, for example? Are you saying that things happen, in this universe, outside of the bounds of physics (and I would add living agency)? That seems very intellectually 'mushy' to me. Mystical, almost. Anyway, I'd be seriously interested in your refutation of causality. p.s. You might find Causal Asymmetries (Cambridge Studies in Probability, Induction and Decision Theory) interesting.tgpeeler
December 16, 2009
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Mark @ 53 "Would it be fair to describe intellectual committments as metaphysical beliefs that you assume to be true rather than seek to demonstrate their truth – as StephenB puts it – what you argue from as opposed to what you argue to?" I think that is a very fair description. The question then immediately arises: What metaphysical beliefs are we justified to "assume to be true?" Or to have without question? i.e. What are our first principles? For myself, I think only those that are undeniable. Only those that by their negation create a logical contradiction. (e.g. existence, or being, previously mentioned.) In my view, God is a conclusion, not an assumption, for example. It creates no logical contradiction to say god does not exist or that He does. And in this case, as it is in all matters of opposing truth claims (as distinct from 'different' truth claims where both may be true or false), it is certain that one or the other is true and the other false. In those cases (without self-contradiction), I think we can only decide what is true by reason applied to the empirical evidence that we have. In other words, who has the biggest pile of evidence? One of the frustrating (all too obviously frustrating, I'm sure) things to me about the design/information conversation is that this particular discussion almost inevitably degenerates into "can to" "cannot." Are odds of 10^-100 possible? How about 10^1500? Well you see my point. But somewhere along the line it occurred to me (and still very few, if any, others) if the question of the origin of life is the question of the origin of information then what has to be explained in order for information to be explained? In other words, I think that to start computing the odds of information being created by accident or by law are premature because we haven't yet explained how information arises in the first place. What are the pre-existing conditions for having information? So that's when I made the (now) obvious (to me) connection between information and language and what language, at it's most fundamental level, is. Now as far as I can tell, it is entirely reasonable to ask this question of the naturalist/materialist: How do you account for the existence of information (life) when your only explanatory tool is the laws of physics or what the laws of physics might look like in the future? One thing seems certain. Since physics deals with the material world of forces and particles no matter how much more advanced the discipline may get, it will still always and only deal with the physical world. And since information is abstract, it is not now nor will it ever be something physics will speak to. So that right there seals the deal for me. It's conceptually impossible for physics to have these answers. It's as if you were searching for the rules of tennis in a golf rule book. It's never going to happen. But as an added bonus, I broke it down to what I think is the most fundamental level of language, the essence of language, all language, and that is symbols and rules. And then I asked the same question. How does physics account for the existence of symbols? How does physics inform the rules of grammar and syntax of any language, including the language of mathematics, in which the laws of physics are written? Again, the short answer is that it does not and it will not and it cannot because that's not what physics is about. And this gets back to the guts of the issue. The materialists deny the existence of things that obviously exist. It's a mystery to me why it has such a hold on so many otherwise bright people. At any rate, that's pretty much how I came to view this question, the question of the origin and propagation of life. If you'll allow me one quibble. I think that saying "assume to be true rather than seek to demonstrate their truth" is a pejorative way to say that. It implies, or rather, I at least, infer from that statement that somehow these beliefs are not actually true (they are) or that they are somehow inferior to empirical (scientific) "truth." Perhaps I am being overly sensitive but I typically find that reason gets short-changed with regard to empirical data and I think that is a huge error. The scientific method uses both reason and empirical data to arrive at (provisional, mostly) truth. I haven't worked out a way to say this exactly but I think that reason is the ultimate authority or sovereign of truth. In other words, nothing can contradict reason and be true. But what about facts? What about empirical data? Here comes the tricky part - facts aren't subject to reason - facts are just facts. But it's the story that the facts tell that involve the use of reason. It's making the best inference from the data. Science by necessity does both but sometimes, it seems to me, reason (or metaphysics) doesn't get its rightful due.tgpeeler
December 16, 2009
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Mr CJYman, Keep reading! Those sentences are the abstract of the problem, not the abstract of the solution. :)Nakashima
December 16, 2009
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Mustella @ 52, I'm trying to find that post in which I measured CSI of Titin. I was following it on another computer and I don't remember which thread it is in. Zachriel, if you see this, perhaps you can help out. Where were we discussing the CSI of Titin?CJYman
December 16, 2009
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Nakashima @42, It doesn't seem that the question I asked would be answered in the paper that you directed me to since right at the opening they state, "The RNA World model for prebiotic evolution posits the selection of catalytic/template RNAs from random populations. The mechanisms by which these random populations could be generated de novo are unclear." The question I asked: "Has anyone shown that under realistic prebiotic conditions, a sufficiently sized pool of amino acids will form and then string together into any type of catalytic RNA?" [edit: "amino acids" should be nucleic acids]CJYman
December 16, 2009
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Zachriel: "The information I provided gives us a rough idea of the *minimum* frequency of functional sequences in such a random pool." It is possible that I missed the relevant material in another comment of yours, but the information you provided that I quoted does no such thing. You left out answering how constrained is the functional pattern. You merely replaced "Scientists regularly find ribozymes (catalytic RNA) in random sequence libraries.” with "... will contain a number of catalytically active molecules." You did not answer the question of "specificity." What is that number of catalytically active molecules and how many of those are relevant to living systems? Furthermore, how many will work at a specific cite, providing function which at least does not decrease survivability? Zachriel: "We know the specificity is relaxed as artificial evolution can increase their activity significantly. Indeed, that’s the very crux." Where is specificity relaxed? Artificial evolution increases what activity? Can you give an example using the English language, since that is what you have used to model evolution is the past. Thanks. Zachriel: "CSI is an ambiguous measure. This is Dembski’s formula for specified complexity: ? = –log2 [ BIGNUM · ?S(T) · P(T|H) ] Notice that the calculation depends on the background knowledge of the Semiotic Agent, hence it depends on the Agent’s ignorance. " ... as is the case with every function. It is dependent on the data collected. Garbage in, garbage out. If that were the reason for "disqualifying" CSI from scientific consideration, then we'd also have to disqualify measurements of the age and size of the universe from scientific consideration, since they are open to being either revised for accuracy (making the numbers or percentage of error slightly larger or smaller) or completely changed (discovering that the numbers are wrong by orders of magnitude) as new data comes in. There is nothing any more ambiguous about measuring for CSI than for any equation. Every variable is based on real-world measurements that actually have a non-ambiguous value. Of course, some of the variables are based on complex measurements themselves and we may only be able to provide estimated values, but this doesn't stop any other scientific endeavor such as measuring for the age and size of the universe, so why should it stop us measuring for CSI? And, just in case you didn't hear me during our last conversation or indeed in this one, *ALL MEASUREMENTS ARE BASED ON OUR IGNORANCE.* IOW, all measurements are amenable to being updated based on our ignorance being removed. We will always be ignorant of something and even in our knowledge we could be incorrect -- which again adds to our ignorance. That is why science is open to change and that is why CSI is rightfully a part of science. Zachriel, how many ways do I have to spell it out for you to understand that very simple point? Zachriel: "Oddly enough, the calculation also depends on the wordiness of the Semiotic Agent as it is the class of shortest descriptions that are used in Dembski’s formula." ... which is also the basis of K-Complexity. What's the problem? Furthermore, in life, there is a completely objective description, f(pattern)=event, flowing from DNA to protein complex, the translation and transcription mechanisms (information processor) being the semiotic agent.CJYman
December 16, 2009
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#50 tgpeeler Thanks. Would it be fair to describe intellectual committments as metaphysical beliefs that you assume to be true rather than seek to demonstrate their truth - as StephenB puts it - what you argue from as opposed to what you argue to? If so, I would agree that atheists and indeed scientists in general have few intellectual commitments. It is part of the intellectual stance of an atheist and a scientist to be prepared to challenge even the deepest assumption. It is really hard to challenge logical laws but metaphysical beliefs such as "every event has a cause" can be challenged and indeed I hold them to be false. I think this is a good thing. After all 200 years ago many people would include in their intellectual committments such things as Euclidian geometry and a Newtonian vision of space time.Mark Frank
December 16, 2009
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CJYman at 40, In fact, I’ve used the calculation in that paper to roughly measure the CSI of the protein Titin. Could you please share that with us? As discussed in another thread here, there are apparently no available worked examples of a CSI calculation, as described in No Free Lunch, for an actual biological component, let alone any that take into account known evolutionary mechanisms. My interest in this is that I would like to understand CSI well enough to write software to quantify it. Thus far I haven't been able to get sufficient detail to do so.Mustela Nivalis
December 16, 2009
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fG @47 "In this essence ‘information’ is not different from ‘beauty’. It is all in the eye of the beholder." I think this is the point. There is a "beholder" that is apart from the matter that is reacting in interesting ways. This is what any naturalistic story of life cannot do and will never do - account for the "beholder." It can't do this because it rejects the existence of the "beholder" in the first place. Mind = brain. There is no mind apart from the neurons. This is what the naturalistic enterprise is all about - explaining things solely in terms of natural, i.e. physical laws. But there is an impenetrable circularity here. Nothing outside of nature exists (the primary intellectual commitment of the naturalist/materialist) therefore whatever MAY be real that we would think is part of nature but is not material MUST BE, THEN, only an illusion, since our primary commitment is that only the natural world exists. That means our conclusions are already determined by our premise, which premise is not based on reason or evidence. Thus the position of Dawkins and his ilk that design and purpose are only "apparent." How could he say otherwise? But why does he say otherwise? Simply because he's declared real design and purpose off limits from the beginning. How rational is that? Not very. "They've" been able to get away with this (my speculation) because to deny design, say, does not involve an internal contradiction. If I say design does not exist then I am not saying something that contradicts itself. Unlike, for example, if I said that: I do not exist. That involves a logical contradiction. I have to exist in order to deny my existence. In cases like this, then, that involve no internal contradictions, one has to, in my view, then weigh the piles of evidence for either side and make a determination on that basis. But the problem of information, which is an abstract entity, is different because they cannot deny the existence of information without using information. And they certainly cannot explain information without resorting to "mind" which they are unwilling to do because it's not part of the decreed ontology. And now we're back to the beginning of saying that "we" (not me) can explain information/design/purpose/agency/moral law/etc... in terms of physical laws. But clearly they cannot, so the only move left is to deny the actual existence of those things and declare them "apparent." Whether that is intellectually responsible is a choice everyone has to make for himself. At the most fundamental level, how can quarks and leptons, in any combination, be self-aware? And how can that possibly be explained by reference to physical laws? It's a fool's errand. To reject the very existence of what you are trying to explain. Dawkins doesn't not believe in God. Who would write a book about "The Klingon Delusion" for instance? Dawkins just doesn't like the God of the Bible and he desperately hopes that He is not real. Well, He either is or he is not. My advice is to treat that question with the respect that it demands if for no other reason than the consequences for getting it wrong are potentially terrifying. Being a true blue coward myself, that is all the motivation I need to investigate this honestly. It's not a justification for believing anything, but I think it's a good reason to take the investigation seriously. IMO.tgpeeler
December 16, 2009
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Mark @ 46 "I am fascinated – can you explain what an intellectual committment is? Perhaps with an example?" Sure. I'd be delighted to. Intellectual COMMITMENTS are essentially one's first principles. For example, my primary epistemological commitment is that reason is the ultimate authority of what is true and what is not true. I take this position because its denial involves a self-contradiction. (This is a clue to identifying first principles. The denial of a first principle alwasy involves a self-contradiction.) If you reject that principle, then, since the original claim does not involve a self-contradiction, you would have to argue (reason) for your denial. Which puts anyone who disagrees with the original claim in the position of using reason to deny the efficacy of reason. (And thus the self-contradiction) Another one would be that the truth about reality can be known. That is also undeniable (that is if one is wedded to reason) since to claim that the truth about reality cannot be known is to make a truth claim about reality. Another one is that opposing truth claims cannot both be true. This is called the law of non-contradiction. For example, it is impossible for it to be true that God exists and does not exist. He either does or does not. (Law of excluded middle) And there is also the law of identity. A thing is what it is (Aristotle was the first, as far as I know, thinker to describe these first principles of logic.) The law of identity is abused by writers like Dawkins all the time. He's very fond of saying things like there is no design in nature because what we think is design is really only "apparent design." hee hee. So my immediate question is how in the hell does he know the difference between apparent design and real design unless there really is design in the first place? This isn't rocket science, which is why it appeals to me, your basic garden variety simpleton. So Dawkins' assertion that there is no such thing as real design in nature is just nonsense, literally. He opens "The Blind Watchmaker" with this hilarious sentence: Biology is the study of complicated things that give the appearance of having been designed for a purpose. Oh really? And how would he know that? And this one, this is one of my all-time faves, it's from "River Out of Eden" where he says: The illusion of purpose is so powerful that biologists themselves use the assumption of good design as a working tool. Is that too funny or what?? Biologists themselves. Those paragons of reason and intellectual integrity. hee hee. Talk about being blind to reality. Oh, and one other thing. An intellectual commitment, as I think of it, is something you don't get to change when you think it's inconvenient or it's leading you down a path you'd rather not walk. Let's say, for example, when the exercise of reason points you directly to Reason. :-) Does this help?tgpeeler
December 16, 2009
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Hmm. Apparently this blog doesn't handle Greek letters. Oddly enough, the calculation also depends on the wordiness of the Semiotic Agent as it is the class of shortest descriptions that are used in Dembski's formula.Zachriel
December 16, 2009
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CJYman: Zachriel makes a statement: “Scientists regularly find ribozymes (catalytic RNA) in random sequence libraries.” Mung asks a very relevant and important question: “How large is the library, how complex is the ribozyme, and how specific is the does the sequence have to be?” … and Zachriel provides (as I have seen him do many times before) a non-answer by, in effect, simply re-phrasing his initial statement: “A typical random sequence library of a few quadrillion (10^15) nucleotide or amino acid sequences of length 80-100 will contain a number of catalytically active molecules.”
The comment quantified the qualitative statement, which is much more than a mere restatement. The exchange has to do with the claim that chance assembly of long proteins "pales in front of the available probabilistic resources of our universe." In fact, given a reasonable pool of random sequences, many will be functional. The information I provided gives us a rough idea of the *minimum* frequency of functional sequences in such a random pool. We know the specificity is relaxed as artificial evolution can increase their activity significantly. Indeed, that's the very crux. CSI is an ambiguous measure. This is Dembski's formula for specified complexity: ? = –log2 [ BIGNUM · ?S(T) · P(T|H) ] Notice that the calculation depends on the background knowledge of the Semiotic Agent, hence it depends on the Agent's ignorance. - We apologize for the long, and heretofore unexplained moderation delay. Perhaps it is due to magnetic storms in the vicinity.Zachriel
December 16, 2009
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I think that information is a label we stick on certain configurations of matter. Some configurations correspond to a lot of information, others to very little, but without a concrete configuration (of 'things') there exists no demonstrable information at all. The reason configurations can 'contain information', as we say, is that in our universe, matter can and does react to other matter in variable ways. Sometimes not in very significant or interesting ways, at other times in more complicated and more consequential ways. What we call 'information' is a label we stick to that subset of configurations that cause reactions, events, that strike us as remarkable and/or interesting. In this essence 'information' is not different from 'beauty'. It is all in the eye of the beholder. fGfaded_Glory
December 16, 2009
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#45 tgpeeler I am fascinated - can you explain what an intellectual committment is? Perhaps with an example? MarkMark Frank
December 16, 2009
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IrynaB @36 (again) I'll take up the gauntlet you have thrown down. Tell me what your intellectual commitments are and I will change my mind.tgpeeler
December 15, 2009
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paulmc @ 38 "Again, not true. There is a physical explanation for why the genetic code is the way it is. Codons are not some abstract language but are literally physically related to the amino acids they “code” for – in the case of DNA via mRNA and tRNA. To refer to DNA as abstract or immaterial information in is misleading. It is tempting to look at DNA as a language – after all we use C, G, A and T/U to represent the bases – this is purely a human abstraction of their physical reality." I only refer you to Kuppers, Yockey, Crick, Dawkins, etal, not to mention Meyer and Dembski, who absolutely understand that DNA does contain biological information and that it is information in every sense of the word. Your assertion that it is "purely a human abstraction" is hardly relevant as all information seems to fall into that category and so what of it? Just because it's abstract means it isn't real? Just because mathematics is abstract means it isn't real? Let me cite Yockey again although I'm sure you will pay him no mind either. "Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies." (page 6) So maybe you tell me how DNA does NOT contain biological information and that there is no real language involved. Oh what the hell, I've got my notes out now so let me give you a couple of other quotes that suggest that information and biology are, um, linked... Yockey p.2 "The existence of a genome and the genetic code divides the living organisms from nonliving matter. There is nothing in the physico-chemical world that remotely resembles reactions being determined by a sequence and codes between sequences." Yockey p.3 "The genetical information system, because it is segregated, linear, and digital, resembles the algorithmic language by which a computer completes its logical operation." Sanford (2005) p.1 "The genome is the instruction manual which specifies life. (An organism's genome is the sum total of all its genetic parts, including all its chromosomes, genes, and nucleotides." Dawkins (1995) p.19 "Life is just bytes and bytes and bytes of digital information." And Francis Crick seems to think something of this idea in Of Molecules and Men, p.43 "…we have, in effect, to translate the information from a four-letter language into a twenty-letter language, and this is by no means easy."tgpeeler
December 15, 2009
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IrynaB @ 36 Sigh, as I predicted. My "insult" was based on my experiences and you will end up proving my point, I'm sure. You say: "Please give us an example of immaterial information. If it is always encoded into a physical substrate, how do you know there is immaterial information?" You are joking, right? The fact that you recognize that it is encoded in a material substrate should be proof enough. How do you not understand that? Do I really need to explain to you that the information, although encoded in a material substrate, is not the same thing as that substrate? All information is immaterial. We know it's immaterial because it doesn't have mass or inertia, it is not affected by gravity, it can't be converted to energy, it can't be used to heat or move matter, and so on. We can't weigh it, smell it, see it, hear it, touch it, or taste it yet we know it exists. And before you go off and say you can "see" information, I remind you that you see the physical letters that encode the information but you do not "see" the information itself. That's how I know that information is immaterial. Plus, committed darwinists also recognize that so I know it MUST be true. ha ha. See Yockey (2005). OK. So here is the quote: "The genetic information system is the software of life and, like the symbols in a computer, it is purely symbolic and independent of its environment. Of course, the genetic message, when expressed as a sequence of symbols, is nonmaterial but must be recorded in matter or energy." Page 7, Information Theory, Evolution, and the Origin of Life. I trust this will help clear things up. By the way, Yockey thinks this proves Darwinian evolution. He's wrong, of course, it proves that Darwinian evolution cannot possibly be true. But just in case I haven't made my case, try this little thought experiment on for size. Consider "IrynaB" as opposed to "BIaynr." Same letters. Same physics account for their representation on a computer screen. But something seems different. Hmmm. I'll leave it to you to figure out the implications.tgpeeler
December 15, 2009
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M CJYman, I think you mean nucleic acids. Here is an article on function and short RNAs of about 20-mer in length.Nakashima
December 15, 2009
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Nakashima, it also seems that at the end of the paper you posted, the authors imply that it should be easy to find "functional" RNA in a small random pool of RNAs 22 amino acids long. But does this make the problem any "easier." Has anyone shown that under realistic prebiotic conditions, a sufficiently sized pool of amino acids will form and then string together into any type of catalytic RNA?CJYman
December 15, 2009
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