Information and Genetics

Hi Chase,Now that you are back, maybe you will follow up in this thread: http://www.evcforum.net/cgi-bin/dm.cgi?action=page&f=5&t=3&p=4

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Originally posted by ChaseNelson:
SLPx,

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I am not necessarily back--if so, only for a short while.

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I'm sorry but I will not follow up in that thread. Upone my entrance to evcforum, I believe I stated somewhere that I would not be responding if others 'threw the elephant' at me. As soon as it looked (to me, anyway) as if Quetzal was losing, he, Peter, Dr_Tazimus_Maximus, and you all gave rather lengthy responses to me. I'm not about to compete against four.

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If you have a specific point you want to make, please bring it up here. However, I will not spend hours typing against numerous arguments.

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True, thanks for the welcome. I hope if I'm attacked here that you will come to my aide... .

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Chase

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If you will not spend hours typing against numerous arguments, then I have to wonder why you make claims that attract numerous arguments...Anyway, if you are to be 'attacked', it would probably be for relying a bit too much on creationist literature as per your bibliography.One question - did you actually read the Lewontin article that you quote from on your home page?That same quote appears on AiG, and about a hundred other creationist sites, including Fred Williams'. Problem is, if you read the article, you would know that he was not referring to evolution ....

And by the way, sorry, but Questzal wasn't 'losing'...Quoting Meyer and Bergman, however, that is a sign of something else. Did you know that Bergman wrote in a book that the coccyx is bifid?

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Originally posted by Mister Pamboli:
This thread is getting extremely tiresome...

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I notice you brushed off the tree ring problem with "they are abviously not a code" which was a pathetic answer, which begged more questions than I think you have either time or arguments enough to answer in full.

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Indeed.... Argument via personal definiton is a creationist staple...

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Originally posted by ChaseNelson:

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If you will not spend hours typing against numerous arguments, then I have to wonder why you make claims that attract numerous arguments...
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I was discussing genetic information with Quetzal, and I intended to discuss it with Quetzal. He could have presented anything he'd like--however, I'm not going up against four. It's not a fair debate.

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You do understand that this is a public board, do you not? If you want only to discuss specific issues with specific individuals, then I suggest that the proper place for that is via email. Of course, this is a discussion board, not a debate board.

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SLPx:
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Anyway, if you are to be 'attacked', it would probably be for relying a bit too much on creationist literature as per your bibliography.
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As per my bibliography, I've read many evolutionist books including Climbing Mount Improbable (which I am in the process of reading, as I stated above), Transducing the Genome, Genome, Finding Darwin's God, Black Holes and Baby Universes (which I do not mention) and others. As I also stated, my bibliography does not include articles, of which I've read many by evolutionists. (Inlcuding Rennie's new one, in which half of his objections are raised against things I don't even believe, and in which he suggests sources on the issue to his readers on the last page--85--and failed to mention one creationist source. Perhaps he's relying a bit too much on evolutionist literature to tell him what the creationists actually believe?)

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I don't read too many popular science books myself. I prefer to get the information from the primary literature. Of course, it is nice to have someone condense it all once in a while. I don't know who 'Rennie' is, so I cannot comment on all that. I did just read Intelligent Design Creationism and its Critics, and I have read Icons of Evolution (in which I found a major out of context quote used as the basis for a ridiculous extrapolation), Refuting Evolution, and The Biotic Message. I found them to be entertaining. Not very informative, scientifically, but entertaining nonetheless.

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It seems to me that Lewontin is referring to naturalism in science, SLPx, which is the basic philosophy that forms the basis of evolutionary humanism.

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I have never heard of evolutionary humanism, Chase. Is that the newest thing that I must be a proponant of even if I don't know it? Just like naturalistic materialism? Of course, naturalism in science - methodological naturalism, that is - also forms the basis of physics, geology, medicine, etc. Are all fields of science therefore caput? Or just evolution?

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I did not know that about Bergman, and, embarrassingly, I do not know the definition of 'bifid'. However, I would prefer that you argue against the scientific validity of the specific quote I mentioned, not downsize Bergman and expect to be done with it.

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I did not expect any such thing. I merely pointed out that he is not the expert that he is often heralded as being. Of course, I in fact DID already supply an argument against the specific quote by Bergman:"The use of hemoglobin to prop up his claim is disingenuous, in my opinion.
Indeed, there are examples of "necessary" proteins - cytochrome C for example - that are found in nearly all forms of multicellular life and yet can function while being as much as 50% different in amino acid sequence in different lineages. Does Jerry mention this fact? Or just the one fact that he can use to support his implications?"

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His [Robert Sauer of MIT] results have shown that, even taking the possibility of variance into account, the probability of achieving a functional sequence of amino acids in several functioning proteins at random is still ‘vanishingly small’, roughly 1 chance in 10^65...[21]

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Explain to me, Quetzal, how all of these specific conditions were successfully met, and how the sequence specificity in DNA (and thus the specific sequence of amino acids in protiens, and thus information) came about by chance and evolutionary processes.

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This is a common, but quite fallacious form of argument that is seen from creationists. I call it the argument via cart before the horse. Not a very accurate or encompassing title, but allow me to explain.
First, it is all well and good that the odds of some extant protein forming via 'random chance' is very low. So is being dealt a specific hand of cards froma standard deck. Providing, of course, thjat you specify the order, suit, and value of each card prior to them being dealt.
On the other hand, the odds of being dealt a hand of cards is 1. Now, if you take the hand of cards you were dealt and consider the odds of getting that particular hand - that is, specifying the hand after the fact - we once again get that extremely low probability.
So, the problem with such arguments (thus far) is that the specificity that creationists love is an after the fact specificity, that is, cart before the horse.
You ask how such specificity can arise via chance and evolutionary processes.
Back to the cards. Say the dealer (the environment) has in mind a winning hand (the best suited phenotype). He deals the cards, you (an organism) get a random hand (DNA sequence). Say there are a thousand of you playing - a big deck of cards. Chances are slim that even with 1000 players, the 'winning' hand was dealt. You all show your cards. The dealer looks at the hands, and takes away the cards from each player that are not in his 'winning hand.' Some players lose all their cards, and they are out of the game - they become extinct. The dealer then hands out more cards to each player. Again, the dealer goes round and takes away the cards - selects - that are not in the 'winning hand.' Some of the players decide to work as a team. Together, these groups have hands that are getting close to the 'winning hand.' After a few more rounds of taking cards away and dealing more, several players have hands that are really close to the dealer's 'winning hand.' He decides that is good enough. Game over.Random processes generate variability. Selection and other mechanisms determine which variation succeeds. The successful variations contian the 'information' that some now refer to as specified and wonder how it could have arisen at all...But I will refer you to the same paper I referred Fred to:Natural Selection as the process of accumulation of genetic information in adaptive evolution. 1961. Kimura, M. (working on scanning it for Percy).

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I would prefer that you take up my challenge that "If you have a specific point you want to make, please bring it up here".

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Forgive me for not rising to your challenge. I shall be sure to pass on your challenge at the next evilutionist conspiracy meeting I attend.

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However, if you'd like to bring some scientific evidence to my attention, I'd be willing and happy to discuss it with you.

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Strange - I was thinking the same thing...

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Originally posted by ChaseNelson:
SLPx,

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John Rennie is the editor in chief of Scientific American, and he just authored an article entitled "15 Answers to Creationist Nonsense,"

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Yes, I found this out after replying to you. I don't read SciAm.

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Ooo, you read Intelligent Design Creationism and its Critics! I want to get that book so bad! It's something like $50 though, so I'm not sure how soon I'll be purchasing it.

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Yes, it was pricey. Goota love those extra travellers checks... (bought it on the last day of vacation).

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I would also like to read The Biotic Message someday. I found Miller's book (Finding Darwin's God) to be quite entertaining, as well.

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The Biotic Message is swell, if you like reading a non-expert pat himself on the back on every page. ReMine provides no citations whatsoever for his positive claims/implications, so basically it is a sub-par rehash of a litany of standard creationist arguments, with an emphasis on genetics.

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I'm not claiming that you're a proponent of anything, SLPx. But you do agree that natrualism is the basis of science today (actually, you claim that it is science).

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I do? Well, how are we to examine the supernatural? How does one go about setting up controlled conditions to perform experiments on the same?

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I prefer to stick to my dictionary's definition: "STUDY OF THE PHYSICAL WORLD the study of the physical world and its manifestations, especially by using systematic observation and experiment." Of all, however, I actually prefer Talk.Origin's definition:
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Science: A method of determine [sic, determining?] how the universe works by use of the scientific method.
Scientific method: The process of proposing a hypothesis, and then testing its accuracy by collecting data on events the hypothesis predicts. If the predictions match the new data the hypothesis is supported. Generally the best supported hypothesis is considered correct.
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This can be found at http://www.talkorigins.org/faqs/faq-god.html .

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Is not 'natural' a synonym for 'physical', at least in this context? Is the supernatural physical? If so, how was this determined, and can it be examined by anyone?

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Bergman was giving an example of what he was talking about. I gather that your example is not about his topic of discussion, and thus would not have been accurate for him to use. He used an example that did.

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As so often happens - an error of omission. My example, in fact, is on the very topic he was discussing, just not the same specific example. My example would not have been 'accurate' for him to use because it would not have supported his contention.

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Your analogy is certainly a thought-provoking one, but I would like to point out a critical flaw.

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Do tell...

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I'm going to re-shape the analogy.

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Say there is one of you playing (since we are talking about the origin).

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And thus endeth the flaw-finding mission. What is the justification for this? Why one?

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One because there's only one right way to get a correct protein.

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Wrong. What is a 'correct' protein? Your reformulated analogy is already moot, as it suffers from the same fatal flaws that all such endeavors do.

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Now, Stephen Meyer calculates the probability of all the neccesary conditions, etc., to be met at 1 in 10^130 (I believe that 10 ^65 might be more accurate, perhaps) [Meyer 1998, pp. 127-128]. If you'd like the specific quote, I could provide it, but let's just take that as a rough estimate for the time being.

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Meyer the anti-evolutionist philosopher and DI fellow - what were those 'necessary' conditions? Necessary for what? For an after-the-fact specified event? The problem with these scenarios is that were the conditions different, were we based on, I don't know, silicon or something, the exact same arguments could be made!

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You say that everyone--thousands--is dealt a hand of card, which is specified (and to that I agree). However, a certain specification is needed (a certain protein or something of the like is made of only CERTAIN amino acids at CERTAIN places, which MUST be left-handed, etc.). So a more appropriate analogy

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And here you are wrong - you are SPECIFYING in advance what it is you want to see. That is the whole point - you are assuming that some extant protein X was the goal. What is the evidence for that?

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How did life get started in order for natural selection to begin its work?

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I don't have any idea. Maybe the Titans?

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I read in the recent Nature that they're still having problems with the "RNA-World" hypothesis, as well, as is conveyed by this quote:

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Snip quote. Yes, I understand that any hypothesis about the OOL will be prone to fault-finding. Frankly, I expect this, as it is difficult if not impossible to know the exact conditions of the event(s).

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But enough of analogies. I consider probabilities and analogies to be insightful, but not entirely accurate and most certainly not definite (which is why I try to avoid them).

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I wholeheartedly agree, and I wonder then why creationists so often rely upon them...

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I'm simply wondering if you have a scientific (naturalistic, as you say) explanation of how these conditions could have been met. What mechanisms are involved, etc.?

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I have no idea. I am not an abiogenesist(?), or a biochemist, or someone who does any sort of research or even pleasure reading on the topic. However, I find the notion of Divine Fiat to be unsatisfying.

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Thank you very much, I would love you to email me that if you get the chance (Kimura's article).

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See what I can do...

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SLPx:

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Strange - I was thinking the same thing...
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That's nice, perhaps we will get to discussing something.

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Indeed.... I was wondering about the Meyer book you cite - what, exactly, does Design 'explain'?

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Originally posted by ChaseNelson:
Sorry for the delay--I was gone for the weekend, and I'll be leaving again Tuesday morning for a short camping trip with my dad and cousins.

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Me too. I tend to 'cycle' between different boards. That and, after all, it is summer![quote] SLPx:

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I do [claim that science is naturalism]? Well, how are we to examine the supernatural? How does one go about setting up controlled conditions to perform experiments on the same?

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In post #28 of this thread you stated that "Of course, naturalism in science - methodological naturalism, that is - also forms the basis of physics, geology, medicine, etc." I read the 'in' as 'is', so I made that mistake, but your point seems basically the same--that naturliasm is foundational to science. We can examine the supernatural by inferring something was designed, and by realizing that natural processes have no ability to explain it.

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But that is a non sequitur. Inferring that something was designed (how is that done?) is not examining it. How does one conduct experments to test whether this inferred design really is design? And would not the creationist claim design if/when experiments were performed to show that it can occur naturally? Thios caveat is, in fact, already in place and has been employed by creationists since the early 1970's. Randy Wysong, creationist veterinarian, wrote a book in I think 1972 (The Creation Controversey, or something like that) in which he wrote that life had been created in the lab (news to me) but that rather than it being evidence for natural processes, it was evidence for design. After all, scientists had to add "KNOW HOW" (emphasis his) to the mix to get it to work. This same escape clause has been used on discussion boards recently, in fact. It was claimed by a creationist that indicing speciation in a lab would be a "good place to start" so that we can see how much "intervention" is required. That is, no matter what, the creationist will cry Design!

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Wrong. What is a 'correct' protein? Your reformulated analogy is already moot, as it suffers from the same fatal flaws that all such endeavors do.

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Proteins are made of specific amino acids that fold into specific structures. As we know it, life can only be made of the specific proteins--of which I believe there are 19--which it is. That's why I said 19 could work, too. But other than these proteins, none others could support life. Therefore, the 'correct proteins'.

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"As we know it." Do we know what the original life was? Do replicating molecules qualify? If so, where are their proteins? Do viruses have these 19 proteins? Do you KNOW that "none others" can support life?
Here is an analogy:I am going to hang a picture on a wall. I ask my kid to bring me a screwdriver. He brings me a cross-tip. I ask him to bring me some screws. He brings me a box full of assorted screws of every type. I fish around in the box and pull out a hex head. No good. A flat-blade type. No good. A socket head. No good. Ah! A cross-tip screw, the only one I can use.Does this mean that the only screw types that will hold pictures on walls are cross-tips?

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Meyer the anti-evolutionist philosopher and DI fellow - what were those 'necessary' conditions? Necessary for what? For an after-the-fact specified event? The problem with these scenarios is that were the conditions different, were we based on, I don't know, silicon or something, the exact same arguments could be made!

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But we weren't based on silicon.

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You missed the point...

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We know what life is made of and what makes it work (at least to a good extent). What needs explaining is how these things came about naturalistically (or else fron an intelligent source). There's a difference in detecting design and simply giving up on all naturalistic explanations and falling back on design. Proteins, DNA, irreducibly complex systems, etc., all contain detectable design.

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But THAT is the question, is it not? You are saying that these things DO contian detectible design. Who detected it? How was it done? Where can I read this myself? I do hope, however, that you are not referring to Dembski's "filter"?

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It's not that they aren't explained naturalistically at the time being, it is that they almost can't be--unless a natural process can be shown that can assemble such a system or meet requirements such as left-handedness, which bring us back to my question, and of which neither of us know the answer (you say, "I have no idea. I am not an abiogenesist(?), or a biochemist, or someone who does any sort of research or even pleasure reading on the topic. However, I find the notion of Divine Fiat to be unsatisfying.").

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Why does it surprise you that I cannot answer your question? Do you think everyone should be conversant in biochemistry? I understand that any creationist with a degree in anything is an 'expert' in all areas of science by default. Sadly, I do not measure up. I, for one, would feel uncomfortable presenting myself as being 'expert' or even conversant in an area that I am not. But, see my screw analogy above for handedness...

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That is the whole point - you are assuming that some extant protein X was the goal.

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I am not saying that a certain protein was the goal--in fact, irreducible complexity relies on evolution as a random, undirected process in which mutations are random, and don't have a certain endpoint in mind (that's why Behe asks how natural processes can explain them). I'm just saying that what we know about what life needs today, and what we know about the only proteins that work for life, evolution doesn't add up.

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Allow me to emphasize:"I'm just saying that what we know about what life needs today..."Do we know that what we need today was what the first life needed? Subsequent life? I read recently an analogy to a modern automobile. A modern automobile requires certain things to run. If we just start taking parts out, pretty soon - maybe even immediately - the car stops running. Does this mean that the a Model T NEEDED the same parts?

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Meyer's essay (found in the book Mere Creation) shows how design can explain theses designed (or designoid, as Dawkins would refer to them) structures.

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I've read some of Meyer's online essays and I find them fairly innocuous. At least he didn't analogize 'Darwinists' to Communists, like Wells does in his 'Icons...' video...

Perhaps of interest to Chase and others (re:chirality, other stuff):This is from a post by Tim Thompson on a board that is now defunct:Racemic amino acids from the ultraviolet photolysis of interstellar
ice analogues
Nature 416: 401-403, March 28, 2000
Max P. Bernstein, et al.Abstract: The delivery of extraterrestrial organic molecules to Earth
by meteorites may have been important for the origin and early
evolution of life. Indigenous amino acids have been found in
meteorites - over 70 in the Murchison meteorite alone. Although it has been generally accepted that the meteoritic amino acids formed in
liquid water on a parent body, the water in the Murchison meteorite is depleted in deuterium relative to the indigenous organic acids.
Moreover, the meteoritical evidence for an excess of laevo-rotatory
amino acids is hard to understand in the context of liquid-water
reactions on meteorite parent bodies. Here we report a laboratory
demonstration that glycine, alanine and serine naturally form from
ultraviolet photolysis of the analogues of icy interstellar grains.
Such amino acids would naturally have a deuterium excess similar to
that seen in interstellar molecular clouds, and the formation process
could also result in enantiomeric excesses if the incident radiation
is circularly polarized. These results suggest that at least some
meteoritic amino acids are the result of interstellar photochemistry,
rather than formation in liquid water on an early Solar System body.Amino acids from ultraviolet irradiation of interstellar ice analogues
Nature 416: 403-406, March 28, 2000
G.M. Muoz Caro, et al.Abstract: Amino acids are the essential molecular components of living organisms on Earth, but the proposed mechanisms for their spontaneous generation have been unable to account for their presence in Earth's early history. The delivery of extraterrestrial organic compounds has been proposed as an alternative to generation on Earth, and some amino acids have been found in several meteorites. Here we report the detection of amino acids in the room-temperature residue of an interstellar ice analogue that was ultraviolet-irradiated in a high vacuum at 12 K. We identified 16 amino acids; the chiral ones showed enantiomeric separation. Some of the identified amino acids are also found in meteorites. Our results demonstrate that the spontaneous generation of amino acids in the interstellar medium is possible, supporting the suggestion that prebiotic molecules could have been delivered to the early Earth by cometary dust, meteorites or interplanetary dust particles.Just to make the story complete, earlier studies on the stability of
amino acid molecules in space are encouraging. Once formed, they are
subject to fairly rapid destruction by the same UV that made it
possible, unless they are protected in ice mantles on interstellar
grains, or in a dense cloud protected from UV (The photostability of
Amino Acids in Space, P. Ehrenfreund et al., Astrophysical Journal
Letters 550: L95-L99, March 20, 2001). There is also evidence, as
suggested in both papers, that if the UV impacting the ice is
circularly polarized, the result could be a non-racemic product. There is some experimental evidence to support this view (Mechanism of pH-dependent photolysis of aliphatic amino acids and enantiomeric
enrichment of racemic leucine by circularly polarized light, H.
Nishino et al., Organic Letters 3(6): 921-924, March 22, 2001), and it is also evident that the necessary environment can be found in space (Astronomical sources of circularly polarized light and the origin of homochirality, J. Bailey, Origins of Life and Evolution of the Biosphere 31(1-2): 167-183, Feb-Apr, 2001).

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Originally posted by Peter:
... but is there actually any information content
of DNA, or is it just the way we view it?

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Good question. I think that most would say that yes, DNA contains information. However, I don't think anyone competent in any related field would claim that the information in DNA is anything like the 'meaning' definition that creationists append to it.

Looks like Freddie took his marbles and went home...