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Darwinists are Delegitimizing Science in the Name of Science

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What Darwinists don’t recognize is that, in the name of promoting science, they are actually promoting skepticism about what can be trusted in the name of science.

Bears evolved into whales? No, that’s been rejected. “Scientists” suggest that whales might have evolved from a cat-like animal, or a hyena-like animal, or (fill in the blank).

“It is thought by some that…”

This is “science”?

Evolution is a fact, if evolution is defined as the observation that some living systems are not now as they once were. According to this definition I count myself as an evolutionist.

But Darwinists are unwilling to acknowledge their ignorance concerning how this all came about, and persist in presenting unsupported speculation in the name of science.

This is ultimately destructive of the scientific enterprise. When people read such things as “science has discovered…” or “scientific consensus assures us that…” or some such, people are likely to assume that they are being conned, even if this is not the case, because they have been burned by so many claims in the past that turned out to be transparently false or eventually invalidated by evidence.

Based upon what I’ve learned over my 60 years of existence — mathematics, chemistry, physics, music and language study, computer programming, AI research, and involvement in multiple engineering disciplines — I find this Darwinism stuff to be a desperate attempt to deny the obvious: design and purpose in the universe and human existence.

The irony is that Darwinists are doing much harm to that which they presume to promote — confidence in claims made in the name of science.

Comments
Correction: Given a 10,000 word vocabulary, a 1000 word essay would exist in a sequence space of (10^5)^(10^3) or 10^5000. Making the assumption, for the sake of the example, that there is a geometric 50% of meaningful sequences, out of 10^5000 possibilities we would have 10^2500 meaningful configurations. Now with that number, we’ve long since exhausted the storage capacity of the universe, by so many orders of magnitude as to be completely unfathomable, many times over. Yet somehow we can determine the meaningful sequences. My math in the above paragraph wrong, so I offer this revision: Given a 10,000 word vocabulary, a 1000 word essay would exist in a sequence space of (10^4)^(10^3) or 10^4000. Making the assumption, for the sake of the example, that there is a geometric 50% of meaningful sequences, out of 10^4000 possibilities we would have 10^2000 meaningful configurations. Now with that number, we’ve long since exhausted the storage capacity of the universe, by so many orders of magnitude as to be completely unfathomable, many times over. Yet somehow we can determine the meaningful sequences. Hopefully that fixes it. Gone for the weekend, m.i.material.infantacy
October 28, 2011
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Scott: Me too.gpuccio
October 28, 2011
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Collin, We already know the answer to that. The same mainstream media that bashes ID and promotes darwinism produces films like Contact, in which a signal from outer space is quickly recognized as a message. Once a trace of specificity is determined, there is never any discussion of natural origins. Before someone says that's just the media, don't forget who wrote Contact. The contradiction couldn't be plainer, but abandon all hope of getting it to register. It just won't. It is ideological. It is religious. The explanation that is assumed in once case is outright rejected without consideration in the other, and vice versa. Objectivity is a pretense. This evidence of bias, closed-mindedness, and willingness to put the conclusion before the evidence sits plainly in front of everyone's noses. Be grateful if you're too stupid to be that smart. I am.ScottAndrews2
October 28, 2011
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Can I offer an analogy? I don't do so to PROVE anything, only to illustrate and explain what I am trying to say. Let's say we find a machine on Mars. It is made of metal and rubber and glass and has a hard drive. We also discover a code on the hard drive that governs the actions of the machine. We also discovery that the machine is self replicating. Years later some aliens show up and claim that they designed and built the machine. What scientific principles do we use to determine if this is a true claim or not, assuming we can't get the aliens to offer proof? I assert that ID-ers are the ones who are trying to figure out what those scientific principles might be and they should be applauded. Instead, they are usually dismissed due to the possible religious motivations they may have for their work. ("Creationism in a cheap tux").Collin
October 28, 2011
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I am firmly convinced that no theory of human evolution can be regarded as satisfactory unless the revelations of Piltdown are taken into account. ~ Arthur Keithbevets
October 28, 2011
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A good Darwinist pays no attention to such trifles as common sense or evidence. It is their unbeatable tactic.
Stunning, just stunning. You think 150 years of diligent research, whose results are displayed on groaning shelves in thousands of institutions, constitutes a failure to pay due regard to evidence? Quite simply, the existence of a phenomenon is not evidence of its proposed cause, nor is its resemblance to something else evidence of a relationship beyond that resemblance. You need more.Chas D
October 28, 2011
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A good Darwinist pays no attention to such trifles as common sense or evidence. It is their unbeatable tactic.Eugene S
October 28, 2011
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Cases in point of such unsupported statements.kairosfocus
October 27, 2011
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Liz, Sorry to see you go. If you like, send me an e-mail at GilDodgen@gmail.com with your mailing address and I'll send you a set of my classical piano CDs with program notes, and the story of my wonderful piano teacher who inspired me from the age of seven. I know you'll enjoy the music.GilDodgen
October 27, 2011
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Elizabeth: Cheers :) I hope I can come and visit...gpuccio
October 27, 2011
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OK, sorry I lost my cool there, gpuccio. And I understand your fatigue. I am in the grip of something similar, I think, and so I'm going to take a break from UD. I've learned a lot here, but things have got to the going-round-in-circles stage, and I think a break would benefit everyone :) And I've been neglecting my own site. If anyone from here wants to drop by they'd be genuinely very welcome. I'd love to see more theists drop by, and maybe stay for tea. Or fish. Cheers LizzieElizabeth Liddle
October 27, 2011
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Elizabeth: Well, I was sure that my post would evoke some reaction. It was intended to. But not necessarily from you. Because, as a fact, you are certainly among the "intelligent and sincere". Others are not. But just the same, I take your blame. Because I do think that your cognition is deformed by serious cognitive biases. I am not saying that because I don't agree with your views (there are so many people in my life with whose views I don't agree, and certainly I don't believe that all of them have cognitive deformations. And I am not saying that because I don't understand your views. I think I understand them very well, although I certainly don't understand why you entertain some of them. Please note that I have not said "them", but "some of them". That is a point that you seem not to understand, of me. I am not disturbed in any way by others being atheists, or darwinists, or strong AI fans (well, maybe that just a little... we are human, after all :) ). I am not disturbed by other's convictions, faiths, moral behaviours, moral ideas, and so on. Not at all. I am, unfortunately, disturbed by cognitive inconsistency and bias. And I take your blame, and the full responsibility for it, because you have sometimes (I am saying "sometimes") disturbed me for that. But others have done that much more. And without being, in any way, such fine persons as you are. To them, probably, my post was specially dedicated. Because, you see, I am really tired of certain things. But, being you the fine person you are, you were the first (maybe you will be the only one) to blame me. I am honored of that. With sincere friendship, and sorry for your sorrow, Giuseppegpuccio
October 27, 2011
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gpuccio
KF: My compliments for your excellent biochemistry! Speaking in private, now that nobody can hear us :) , I am really tired. I have tried to believe that darwinists, even with all the basic deformations of thought deriving form having to believe in a completely false theory, still could be able to reason correctly in many occasions. And sone of our best interlocutors here, in the course of years, had reinforced that hope: I know we cannot convince them in the end, but at least we can discuss, sometimes constructively (by the way, sincere thanks to all those who have truly done that). But the recent accumulation of nonsense from the last wave of interlocutors, especially about fundamentals of the scientific thought that should be very clear to everybody, is really discouraging. And the most frustrating thing is that such a nonsense seems to come from otherwise intelligent (well, maybe not all of them), and sincere (well, probably not all of them) people. I am beginning to think that the cognitive deformations of darwinist reductionism and of strong AI theory on human mind are more serious than I believed.
I have to say that I find the response that a view you either disagree with or don't understand must be the result of "cognitive deformation" quite extraordinarily arrogant, and I have seen nothing comparable to your last paragraph from any agnostic/atheist on this site. In fact, I think I'll take my "biased, prejudiced heart" elsewhere, right now, and leave you to yours. In sorrow, LizzieElizabeth Liddle
October 27, 2011
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gpuccio: "And the most frustrating thing is that such a nonsense seems to come from otherwise intelligent (well, maybe not all of them), and sincere (well, probably not all of them) people." ===== What you are describing is more of a heart condition as opposed to a mind condition. The heart as used figuratively in the bible is the seat of motivation. At 2 Corinthians the third chapter Paul gives a good historical illustration where he described the materialistic problem with the ancient fleshly minded Israelites. This in fact fits the subject perfectly here. Basically he recounts the historical scene of Moses coming off Mount Sinai with the Law. The Israelites see the glow of rays being emitted from Moses face as a result of being in God's presence and they make excuses for not wanting to hear what God had said in the Law for them by insisting Moses go put a veil over his face because they said it bothered and made them feel nervous. It was a lame excuse. All that these faithless people were interested in was getting to the promised land and striving after what's in it for me(in the materialist sense) lifestyle. They only wanted for themselves the lifestyle they observed of the Egyptians for themselves in their very own country. They had zero appreciation for the spiritual things contained in the Law Covenant which was to form the foundational basis for their Constitution for running their Nation. Paul goes on to show in verse 13 of chapter 3 what the real problem was. It wasn't their minds so much as their stubborn faithless arrogant heart condition: 2 Corinthians 3:14 Amplified Bible (AMP) "14) "In fact, their minds were grown hard and calloused [they had become dull and had lost the power of understanding]; for until this present day, when the Old Testament (the old covenant) is being read, that same veil still lies [on their hearts], not being lifted [to reveal] that in Christ it is made void and done away." **** This is comparable to the present Atheistic/Agnostic attitudes revealed here. No one but no one will convince them otherwise. There is no amount of evidence you can provide that will shake their Secularist Faith. Again, it isn't that they don't know or see the same things you do or understand the same definitions you do. It's what's inside their biased prejudiced hearts that prevents them from seeing any type of truth of a matter. And ultimately that is their free-willed self-determinationed right to view things as they see fit. There is no predestination here. The truth of the matter does not hinge on their arrogant condescending approval or acceptance of it. But it still remains the truth despite their "What is truth?" game playing.Eocene
October 27, 2011
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KF: My compliments for your excellent biochemistry! Speaking in private, now that nobody can hear us :), I am really tired. I have tried to believe that darwinists, even with all the basic deformations of thought deriving form having to believe in a completely false theory, still could be able to reason correctly in many occasions. And sone of our best interlocutors here, in the course of years, had reinforced that hope: I know we cannot convince them in the end, but at least we can discuss, sometimes constructively (by the way, sincere thanks to all those who have truly done that). But the recent accumulation of nonsense from the last wave of interlocutors, especially about fundamentals of the scientific thought that should be very clear to everybody, is really discouraging. And the most frustrating thing is that such a nonsense seems to come from otherwise intelligent (well, maybe not all of them), and sincere (well, probably not all of them) people. I am beginning to think that the cognitive deformations of darwinist reductionism and of strong AI theory on human mind are more serious than I believed.gpuccio
October 27, 2011
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Acipenser: Youe point here is totally irrelevant. Hemoglobin has nothing to do with this discussion. You are only stating the obvious, that proteins interact and accomplish their functions though various biochemical mechanisms, thye binding of ligands and conformational changes being the most common. OK, we all know that, and so? You seem to state that to erase the concept of the symbolic correspondence of the codons to aminoacids in the genetic code. But that is complete folly, mixed up reasoning at its worst. The point with the genetic code, that all biologists understand, is that it is a code. The codons in themselves have no special relationship with the aminoacids they represent. The tRNA in itself is not capable to couple its anticodon to the right aminoacid. So, for the full mechainsm of translation to go on, two differnet things must have happende: a) The sequence in the DNA protein coding genes must correspond to the functional sequence of amionoacids for a specific protein, according to a well definit abstract symbolic code (the genetic code). b) 20 very complex proteins, the aminoacyl tRNA Sybthetases, must have a specific configuration with very efficient active sites and foldings, all different, and ascribable to two different classes of proteins, so that each enzyne independantly is able to recognize a specific aminoacid and the specific anticodon on the tRNA, exactly according to the same abstract symbolic code that is used in the storage of information in the DNA gene. IOWs, the coding must be respected both in thw writing of the information (which is the mystery we all here are trying to interpret), and in the reading of the information, by the complex translation machinery, and especially by the 20 enzymes, the true depositaries of the decoding key. The laws of biochemistry have nothing to do with all this level of organization, although the implementation of the scheme is obviously realized by the laws of biochemistry. You go on saying: but it is biochemical configurations that the enzymes recognize! That si so obvious and trivial that I realloy don't understand how you dare to offer it as a deep intuition about reality. Your reasoning is superficial and wrong. The enzyme recognizes the anticodon and the aminoacid by their configuration, but only because it is built to do that. A lot of information is needed for that machinery to work that way (hundreds of aminoacids for each of 20 of the most ancient and efficient proteins in the world). When we read, or when an OCR program analyzes a scanned text, the letter "A" is recognized by its form. Then the OCR program transforms it into a digital value. In the same way, the enzyme recognizes the anticodon in the tRNA by its form, and transforms it into the correct aminaocid, that is a digital value in the string of aminoacids that is the final protein. And you also should know that, in protein science, the connection between primary sequence and the final configuratio is extremely complex, as Petrushka loves to remind us for not so clear purposes. It can be understood and computed, but huge coomputational resources are needed just to do that for one single protein. So, the levels of abstraction in the whole mechanism are really stunning: a) DNA is the depository of a treasure trove of information about protein function that even for us would be impossible to accumualte. b) That information, for reasons that nobody can explain, is coded thorugh an abstract symbolic code of 64 values written in base four characters. c) 20 very complex proteins are structured in a very specific way just to read the code. d) A very complex machinery, including the ribosome and a lot of proteins, builds the protein primary structure according to the information received from mRNA. e) That primary structure then folds into the final functional structure, sometimes by itself, more often by the help of other very complex proteins. And this is only the essence. I have overlooked all the regulation nodes, post transcriptional, post translational, and so on. So, if you want, go on thinking that all that is only a matter of biochemical configurations and similar. I am no more surprised by anything, in the darwinist field.gpuccio
October 27, 2011
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Acipenser: I certainly am. And still I don't understand your point about the genetic code and DNA protein genes.gpuccio
October 27, 2011
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Aci, the interactions between AAs in sequences are consequential on specifying and chaining. They are a result of the right chain, allowing folding and function. The chain proper is a rxn between COOH and NH2 ends. Any AA can follow any other, but the functional sequences that fold right and function, are determined independent of chaining. In life, they are informationally specified. That should tell us something. The codon-anticodon match is simply used to say which loaded tRNA with the loading enzyme-set AA on the standard CCA coupler end opposite the anticodon will be allowed to elongate the chain next, till STOP. Again, the chaining is informationally controlled.GEM of TKIkairosfocus
October 27, 2011
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Onlookers: The AA is joined to the CCA end of the tRNA by a loading enzyme. This is the OPPOSITE end to the anticodon that interacts with the mRNA in the Ribosome, i.e. there is no direct chemical relationship between codon, anticodon and AA. In addition, the AA coupler is standard: CCA -- COOH, so in principle we could synthesise an enzyme to load a different AA. Indeed, I think some experiments have been done that reprogram stop codons to carry additional AAs. In turn, AAs chain NH2-COOH ends, and the string of AAs allows any AA to follow any other. The process is a translation not a matter of chemistry or any other force of necessity. This has of course been pointed out before, repeatedly, just brushed aside. The sequences of nucleotides in D/RNA is not chemically constrained, and the AA sequence in proteins is not chemically constrained. The sequences found in life are functionally specified, and are informationally programmed based on stored info, using a translation system and regulatory systems that call up as needed. Information and information processing of highly sophisticated forms lie in the heart of cell based life. All of this points strongly to design. An it seems the real root of many objections on points that could otherwise have been simply resolved, seems to be that that outcome cuts sharply across the institutionally dominant view, creating all sorts of conflicted thoughts. GEM of TKIkairosfocus
October 27, 2011
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"Explaining the operation of a system is a crucial first step in explaining the origin of that system."
Granted. A crucial first step in explaining the origin of a system may very well be determining the intricacies of its operation, especially considering the presupposition that necessity leads step-wise from the simple to the complex. However that still leaves an enigma of progression from simple necessity to integrated functional complexity, yet to be unraveled. It seems premature to assume that simple breeds sophisticated, absent the intermediaries. Thanks for the conversation. m.i.material.infantacy
October 27, 2011
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ACI: As I stated ignoring the obvious flaws in the computer-biology analogy is common with ID proponents. BIPED: I am not retreating to a computer analogy. I am pointing to the observable physical evidence entailed by the transfer of information. ACI: Upr, certainly you are as you’re opening comment on this thread demonstrates.
So, if an ID proponent doesn't speak to the “computer analogy” then they are avoiding its presumed flaws, and if they do say something about it, then they are retreating into a flawed analogy. That’s a nice way to isolate your assumptions from any critique. But your core assumption in the exact topic of my opening comment. You are suggesting that I must address your comment before I can probe your assumptions. That is literally insane. I can immediately ask you a question (which perhaps can’t be answered) yet within that question I can make an assumption that - by your standard here – cannot be then questioned. This is something no rational person would tolerate even for an instant. So I am not sure why you think it flies here and now. In any case, I won’t quibble over this point, but will instead take you at your word.
I would be glad to address the issue you raised once you’ve addressed my questions
Okay, this is the exact question you posed to me in 5.1.4.3.13 “Could you give some examples of ligand binding in computers”. My answer to your question is “No I can’t”. Of course, I would expect to either, and I know enough about information transfer to know that it doesn’t matter anyway. There are no transistors in my fountain pen, there are no magnetic lines of iron oxide when I speak. The comparison being made is not concerned with the system used to transfer information; it's being made to the dynamics of the transfer itself. Hence, your assumption is flawed. Now I’ve answered your question, you are bound by your word to answer mine. I will repeat it for you here:
Will you take a minute to consider the evidence, and please answer this question: If on one hand we have a thing that “is a genuine” representation, and on the other hand we have something that “just acts like” a representation, can you look at the physical evidence and tell me the distinction?
Upright BiPed
October 27, 2011
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Do these know how hard it is to get a protein folding sequence, before we get to actual biofunction? Isn't it about 1 in 10^ 70 or so of AA sequence space, per Axe's studies?kairosfocus
October 27, 2011
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GB: Pardon, but you do come across as one who has not taken time to examine the observed facts, and what has long since been on the table, and is instead tossing around talking points as one looking for a fight. If you are genuinely serious, I suggest you work your way through the post here as an introduction (and also this on the underlying epistemology of empirically anchored inference to best explanation), then look at this on the relevant metric [where also this survey may be helpful -- at least, watch the vid at Fig I(i)b.] -- if you find the just above linked exchange with Dr Liddle by GP not complete enough -- and come back to us. When you do so, summarise what you have learned and then give your responses, with grounds. Please pay particular attention to the discussion of the per aspect explanatory filter and the derivation and use of the closely linked log reduced Chi_500 metric in your response. Silly playground rhetoric stuff like "round and round you go . . . " etc frankly comes across as really disrespectful to a man who has done his homework, and has spent a considerable amount of time in serious and sober-minded, thorough discussion on a matter. To be frank, you come across as someone who has not got the underlying epistemology of warrant for empirical, inductive knowledge claims straight, which is the grounds for science. So, kindly also satisfy us that you understand how inductive warrant works. As a footnote, what is going on in the background is inductive inference on tested, empirically reliable sign. This, I discussed in a background, here, as follows:
Signs: I observe one or more signs [in a pattern], and infer the signified object, on a warrant: I: [si] –> O, on W a –> Here, as I will use “sign” [as opposed to "symbol"], the connexion is a more or less causal or natural one; e.g. a pattern of deer tracks on the ground is an index, pointing to a deer. (NB, 02:28: Sign can be used more broadly in technical semiotics to embrace “symbol” and other complexities, but this is not needed for our purposes. I am using “sign” much as it is used in medicine, at least since Hippocrates of Cos in C5 BC, i.e. to point to a disease on an objective, warranted indicator.) b –> If the sign is not a sufficient condition of the signified, the inference is not certain and is defeatable; though it may be inductively strong. (E.g. someone may imitate deer tracks.) c –> The warrant for an inference may in key cases require considerable background knowledge or cues from the context. d –> The act of inference may also be implicit or even intuitive, and I may not be able to articulate but may still be quite well-warranted to trust the inference. Especially, if it traces to senses I have good reason to accept are working well, and are acting in situations that I have no reason to believe will materially distort the inference. e –> The process of observation may be passive, where I simply respond to effects of the sign-emitting object; or it may involve active emission of signals or interaction with the object. For instance, we may contrast passive and active sonar sensing here, noting that both modes are used by sea-animals as well as technical systems. (NB: “Object” is here used in a very broad sense [u/d 02:17: it includes objects and credibly objective states of affairs].) f –> A sign can also be iconic, i.e sufficiently resembling [u/d, 02:17: or representing] the object to be recognisable as a representation, as a general class [a rock shaped like a face] or in specific [a sculptural portrait]. [u/d 02:28: In the case of a mace in its rest in Parliament, unless an elaborate form of a former weapon sits there, Parliament is not legitimately in session.]
Digitally coded, functionally specific, complex info [dFSCI] is easy to see. All posts in this thread with messages in English or another language of at least 72 ASCII characters are cases in point. None of us probably has met any of the other of us in the flesh, but we routinely know that something as complex and functionally specific as these posts is maximally unlikely to have happened by a burst of lucky noise on the Internet. That is, routinely, we rely on dFSCI as a reliable sign of intelligent action. And, that confidence is amply confirmed. That none of us actually includes you, at least when you are not playing at being selectively hyperskeptical. From the sign of the posts in thread you accept that GP is a real person, not a strange burst of noise on the net. We can extend this to the net as a whole, and see that he net is full of cases in point where dFSCI is a reliable sign pointing to intelligent design. Go over by a university library, and look at the books in it, the picture is the same. To test this idea, there have been infinite monkey theorem experiments. What they tell us is that chance based random walks can generate up to maybe 20 - 25 meaningful words of text, i.e a configuration space of about 10^50 is searchable. Wikipedia has an interesting note on this:
The theorem concerns a thought experiment which cannot be fully carried out in practice, since it is predicted to require prohibitive amounts of time and resources. Nonetheless, it has inspired efforts in finite random text generation. One computer program run by Dan Oliver of Scottsdale, Arizona, according to an article in The New Yorker, came up with a result on August 4, 2004: After the group had worked for 42,162,500,000 billion billion monkey-years, one of the "monkeys" typed, “VALENTINE. Cease toIdor:eFLP0FRjWK78aXzVOwm)-‘;8.t" The first 19 letters of this sequence can be found in "The Two Gentlemen of Verona". Other teams have reproduced 18 characters from "Timon of Athens", 17 from "Troilus and Cressida", and 16 from "Richard II".[21] A website entitled The Monkey Shakespeare Simulator, launched on July 1, 2003, contained a Java applet that simulates a large population of monkeys typing randomly, with the stated intention of seeing how long it takes the virtual monkeys to produce a complete Shakespearean play from beginning to end. For example, it produced this partial line from Henry IV, Part 2, reporting that it took "2,737,850 million billion billion billion monkey-years" to reach 24 matching characters: RUMOUR. Open your ears; 9r"5j5&?OWTY Z0d...
But, that is 1 in 10^100 of the config space specified by 500 bits. The 10^57 or so atoms of our solar system -- our practical universe, running at top speed for nature, the Planck time, would in 10^17 s -- more or less the age of the solar system on the usual timeline -- would go through 10^102 Planck time quantum states, 1 in 10^48 of the possibilities for 500 bits. Note, it takes about 10^30 PTQs's to carry out the fastest chemical reactions. Converting into familiar terms, that's about a 1 straw sample form a haystack 3 1/2 light days across, at 186,000 miles/s for light. Even if a whole solar system were hiding in the hayst6ack, a one straw blind sample would be maximally likely to only pick up what is typical: a straw. Sometimes, there is too much haystack to expect to be able to find a needle on a blind search. And that is the point of dFSCI. if you were to depend on infinite monkey type chance processes and a trial and error filter, using he resources of our solar system, you would be maximally unlikely ever to hit on a case of dFSCI by blind luck. yet, we intelligent designers complete posts here in a few minutes. That's because we are using skill, knowledge and intelligence, not chance and necessity. That is why dFSCI is a pretty good sign of intelligent cause. And no, that is not tail chasing question begging, no matter what some silly objector talking point at one of the usual sites that try to denigrate design theoretic reasoning may have told you. (In case you do not recognise it, this reasoning is actually very close to the statistical reasoning that underlies the second law of thermodynamics, as the Wiki article will hint at, if you read the whole article.) So, now, let us hear your response at a very different level from the above. GEM of TKIkairosfocus
October 27, 2011
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I'm not playing twister, I'm attempting to clarify my terms. You appear to be making a claim that the properties of the nucleotides determine their sequence along the backbone. If not, then you're in basic agreement with my point. It's either one or the other. Either the protein sequence necessitates which nucleotides are required and in what order, or the nucleotides determine the sequence in which they are composed. Which is it?material.infantacy
October 27, 2011
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No, you're ecplanation is not clear at all and appears to me to be an excercise of the game of Twister. The sequence is determined by which bases are present and in what order. In that regard a specific protein does require a specific sequence and not any sequence will result in the same protein although there is great plasticity in this regard as well. For example vertebrate hemoglobin's demonstrate a wide variety of affintity for oxygen ranging from highy sigmoidicity to hyperbolic binding curves. But they are still all classified as hemoglobin even if the sequences of the bases coding for that protein differ. If you wish to discuss 'necessitates' then you will have to discuss the origin which both of us, and all of humanity, are currently ignorant of such origins. Explaining the operation of a system is a crucial first step in explaining the origin of that system. In the case of biochemistry there is a great deal of information available on how various molecules interact with the oft noted plasticity of the biological system(s). Discrete binding is seldom observed in biology and the norm is that many other chemicals may also bind which can in turn generate/suppress a biological response.Acipenser
October 27, 2011
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Acipenser, first my apologies for misspelling your name. I just realized it, and I'll endeavor to avoid that in the future. As a nitpick, in some of your posts you quote me and in some you address me with the same designation, "MI:" so it appears at least in one case that I'm saying something that I'm not. Now to the point. The sequence determines which molecules are necessitated. There is no necessity that is imposed by ATCG that determines the sequence, that necessitates a specific sequence, otherwise every DNA molecule would contain the same sequence. Is the distinction I've made apparent now? By "determines" I mean "necessitates." That's why I used the language analogy, which is apt. The alphabet does not determine the paragraph, that is, the alphabet does not necessitate the sequence of characters in the paragraph. Rather, the sequence imposed on the paragraph determines, or necessitates, the letters that are used. Is the distinction clearer now? I hope so. Do you have any other disagreements with my original point, that explaining the operation of a system does not explain its origin?material.infantacy
October 27, 2011
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MI: Do the molecules determine the sequence? If not, then the above statement is accurate. Of course the molecules determine the sequence. if you substitute one molecule for another you have a different sequence. The sequence of the molecule determines the specificity through the creation of unique sterochemical environments. I think if I were you I would try to drop the agency language, e.g., bases having a say. The bases don't say where they should be anymore than a oxygen molecule says where it should be, hemoglobin, atmosphere, or rust. However, the sequence of bases determines which amino acids are incorporated into a growing protein chain. How the sequences arose is certainly the subject of much research and speculation but there is nothing mystical in the sterochemical interactions of ligands with biological polymers. Yes, I disagree with your original point as it applies to biology.Acipenser
October 27, 2011
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gpuccio, as a MD I would expect that you would be familiar with ligand binding concepts, e.g., allosteric effectors, and how they may influence binding.Acipenser
October 27, 2011
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Expression of the genetic code is dependent on ligand binding at all steps of the process. Allosteric binding of ligands influences protein/RNA 3-D configuration which, in turn, influences specificity of an active site for a different ligand, e.g., tRNA and amino acid specificity. The example of hemoglobin demonstrates a simple allosteric change in a protein due to ligand binding. In the case of hemoglobin (well most vertebrate but not all vertebrate Hb's) binding one oxygen promotes the binding of a second oxygen molecule, then a third, then a fourth due to changes in the structure of the hemoglobin molecule as a result of ligand binding. The binding of protons and carbon dioxide also change the shape of the hemoglobin molecule resulting in decreased affinity for oxygen.....this is a well known system and I'm surprised that someone with a MD would not recognize the importance of ligand binding and the subsequent changes in 3-D configuration in biological polymers. The question on the table was "why does one sequence of codons result in serine versus threonine being bound and incorporated into a growing protein chain." The answer is in the sterochemical nature of each codon and it's interaction with the tRNA molecule. Its been stated many times on this site that the binding of the amino acid and the codon are not connected but this ignores the very real phenomena of allosteric 2-D changes which result in binding of something at one end of the chain and the affinity/binding of another ligand at a distant part of the chain. I'm surprised that you don't recognize this.Acipenser
October 27, 2011
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"The problem for a designer is one of knowledge. How does a designer accumulate the knowledge know what sequences are functional, when the possible combinations of a single gene exceed the number of particles in the universe? Where is the knowledge stored? How is it accessed?"
To borrow an example from John Lennox, we take a ten word sentence: “This ten word sentence is an example of specified complexity.” Now there are 10! ways to arrange the words in that sentence, or 3,628,800 permutations. Of those potential sequences, I think it’s pretty clear that a diminutive number are grammatically meaningful. I’ll expand on that example. Given a 10,000 word vocabulary, a 1000 word essay would exist in a sequence space of (10^5)^(10^3) or 10^5000. Making the assumption, for the sake of the example, that there is a geometric 50% of meaningful sequences, out of 10^5000 possibilities we would have 10^2500 meaningful configurations. Now with that number, we’ve long since exhausted the storage capacity of the universe, by so many orders of magnitude as to be completely unfathomable, many times over. Yet somehow we can determine the meaningful sequences. However this is mathematically intractable. Where are all those sequences stored? The answer, of course, is that they are not stored. They’re determined. We determine them using logic, reason, and the rules of grammar. Such could very well be the case with functional protein sequences -- that there’s a logic, a grammar, to be understood in the laws of chemistry, that determine functional sequences such that no storage is required beyond the expression of them.
The problem from a design standpoint is that nature has far greater resources for generating and testing novel sequences. Now either functional space is such that it can be traversed incrementally, or it isn’t. If it isn’t, then it is inaccessible to designers as well as to evolution.
This is not obviously the case. Now if functional sequence space is not such that it can be traversed incrementally, then it is inaccessible to evolution -- and tremendous genius is implicated.material.infantacy
October 27, 2011
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