Some mutations sound too good to be true

I wonder if we aren't getting bogged down in so much marsh gas. As I understand it, Faith doesn't understand how different letters can code for the same amino acid, given that the system used for chemicals means that H2O is always water and nothing else is.When I talked about the four bases, adenine, guanine, cytosine and thymine and I used A, G, C and T, I neglected to mention that the letters have absolutely nothing to do with the chemical constituents of the bases, but are just the initial letters of their names!!! When you're deaing with a sequence of 2000 bases, you use only the initial letters as writing each one out in full would be a waste of time and effort.

Does Faith perhaps think that, like the chemical formula of water is H2O, that the codon letters are actually the chemical formula of those amino acids? Does Faith think that, for instance, CAA is the actual chemical forumula of glutamine?

How does one get bogged down in marsh gas? I can see getting bogged down in a marsh, maybe, but (er...no, wait, forget about that). It might be considered to be essentially the same question at different levels of abstraction. It certainly seems like anyone having trouble grasping the fact that the letters don't have anything to do with the chemical constituents of the nucleotide bases is likely to have even more trouble with the proposition that the chemical constituents of the nucleotide bases don't have anything to do with the chemical constituents of the amino acids.

1. We live in a vast complex universe some of which appears to be very old. But some of which (if Einstein was right) must be very young. The age of a particle relative to the Big Bang is entirely dependent on the speed it has been traveling.2. According to the very (very) scarce fossil record there has been an evolution of form from simpler creatures to complex creatures. Again the stress here should be on the scarcity of data. There are about 300,000 fossils in the record out of a conservative estimate of 5,000,000,000 species that may have existed. Imagine trying to decide what picture your computer is displaying when only about 1 out of every 100,000 pixels is lit.3. Modern species are exceptionally complex. There is no danger that one over stresses how complex we are. For all we've learned we still have a very fragmented understanding of how DNA works.4. There is much code reuse in life from the point of view of genetic information. It is very reasonable to use this observation as a way to categorize life forms. And it is reasonable to describe creatures with lots of similarities at a genetic level as being closely 'related' to one another. But it should be stressed aggressively that this idea of 'closeness' is a very relative term. Recently they succeeded in mapping the chimp DNA and the papers were full of comparisons with humans. 99% of the DNA is the same. If they were talking about the portion of the DNA that is replicated (and I think they were) then that’s about 300,000 base pairs that are different spread over 200,000 sites. Whether this is close enough together to expect that it is reasonable for proto-primate (the common ancestor) to become chimps and humans in the time allotted (I’m not sure how long this is meant to be) is Very much an open question. To answer it with any authority we will need a much better understanding of the exact positions of the ”Galaxies in Morph Space’ than we have now. It is possible we will never be able to really work this out. It is a very complex problem in information technology. It is akin to asking what are all of the possible combinations of letters that form viable meaningful books over human history when you do not know all of the languages and we can’t agree on what is and isn’t meaningful. In fact it is a great deal more complicated than this. This difficulty should be stressed.5. The most difficult problem facing an evolutionary theory is NOT where does all of the diversity come from, that’s easy, the problem is where does all of the complexity come from. The second law of thermodynamics is not called a ”law’ for no reason. The basic forces of this universe seem to actively discourage complexity. The standard evolutionary response is to say that it is a natural result of asymmetric copy combined with natural selection and varying ecological pressures. That works for diversity but it falls short of explaining why any creature should every bother to get more complex. Complexity means two things for a strand of DNA. First it takes you longer to reproduce yourself and second it means you require more energy to do it. Simplicity rules. There are a couple of ways to look at this question:
A. Why don’t the bacteria wipe us out? They are millions and millions of times more flexible and adaptable than we are. The stock answer to this is that it is not in their interest to do so, we are hosts to them. If that is so, then why do we need immune systems, which are themselves very complex multi-part machines. I don’t mean this point to be an ”Ah Hah!’ more just a good way to expose the whole issue of complexity verses simplicity and why one can not disregard ”the second law’ when it comes to life.
B. How do you put something as flexible as the simple life forms under the right kind of ecological pressure to make it have to resort to complexity to solve the problem of survival. Why not move laterally across the complexity space to find a solution.
C. OR why not get simpler? No one ever discusses this possibility.It is vital to stress at this point that observing that we are in fact here and that it seems the biosphere got more complex over time does NOT mean that mutation and natural selection must be the motivating force behind this process. In fact I think it can just as easily be argued that those things discourage order, and that the biosphere has found a number of ingenious ways to prevent mutation and encourage a capacity for adaptation within a species.The real question is what promotes order? It can be asked of the universe itself. What defined the set of laws that transformed the ”quantum foam’ into an ordered universe? No one has any idea. Why would life ever bother to form in the first place? And once its there why should it grow into outlandishly complex forms, unless something encourages it to do so?6. Consciousness is the only known force in the universe that does actually promote order. This is readily observable and teachable and no well-taught science class should leave out this point. Science (as well as philosophy and religion) have never produced a good explanation for what it is or how it does what it does. In my humble opinion, it qualifies as a fundamental force in the universe in that it cannot be reduced or predicted by any of the other four basic forces.7. Extrapolating up (or out or back or whatever) from consciousness to a purposeful connected God is an exercise that can be left to the world’s churches and does not belong in science. But I freely admit that the above described points leave the door wide open.Does that make me a creationist?This message has been edited by Thinian, 09-24-2005 05:34 PM

From diversity. If you have a process that increases the diversity of a population over time, then one of the diversities that is going to increase is going to be a diversity of complexity; this will result in organisms that are more complex that what was there before, and organisms that are less complex than what was there before.However, if the organisms that you had were as simple as they could be and still be alive, then their simpler decendants will not live. You will be left with the organisms that were just as complex as the ones before, and the organisms that are more complex than the ones before. Hence, there's your trend towards complexity. How, in your view, is the second law violated by an organism turning energy into work and increasing entropy to reproduce a slightly more complex entity? That just doesn't make any sense to me. How is evolution a process to which thermodynamic concerns are relevant? Indeed it does. As we observe, the majority of living things on Earth are very simple. No one discusses it? Nonsense. You don't do too much reading, do you? How do you think that parasites evolve? By getting simpler. I don't understand the question. Are you ascribing will or thought or something to a consequence of chemistry? Is it your view that freezing water "bothers" to form crystals? Or don't these things simply happen because of physical laws of the universe?These are definately not things to teach in science classes. What you haven't gotten outright wrong is just your own quasi-philosophy of purpose in the universe. Now, perhaps you believe that your philosophy is good enough for the nation's children, but surely you don't believe that our students need to be taught falsehoods about the evolution of life on Earth?

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I'm going to maintain that the mappings we observe are, as much as anything, historical artifacts; that specific synthetases are associated with the charging of specific tRNA molecules with specific amino acids because that is the combination that was stumbled upon by the ancestral proteins of these enzymes, and that a from-the-beginning replay of the history of life forms on Earth might see completely different sets of synthetases using completely different sets of mappings. I'm saying that the constraints to remappings within the present system are not of the nature of 'first-order chemical rules', but are a 'locking-in' on a system of mappings already in use.

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I understand that and agree, but that only explicates the issue of "arbitrary", not "symbolic"."Symbolic" by definitions includes abstraction, that is, no "real" connection to the thing that is being symbolized. I don't see how that is representative of DNA. Can a codon map any amino acid at all, with no constraints? Can a codon even map to a different amino acid? (Assuming only that we are dealing with the RNA system we have, not all potential systems)Going back to my "cat" example, "cat" can map to any number of referents... large yellow earth movers, molesters of dogs, double hulled boats, etc, etc. A particular sign is not anchored to any given referent, because it is purely an abstraction.The reason that this is important to discuss is that Creationists often try to state that DNA is symbolic, usually as a precursor to trying to assert something that requires DNA to also be abstract.

So stipulated. "No constraints" is pretty strong; I don't know that it is clear that there are no constraints, but there may be no fundamental constraints. Another way to look at this is to recognize that a statement that a particular amino acid cannot possibly be associated with a particuar codon is really a statement that the space of all possible proteins does not contain any enzyme that could charge a tRNA molecule bearing that (anti)codon with that amino acid. Yes. In mitochondria, and some microbes, some codons do map to different amino acids, hence TIC references to the "The Almost Universal Genetic Code". For example, in mitochondria, instead of representing a stop codon, UGA codes for tryptophan. Granted, there is not a large enough number of such exceptions (most of which also involve the assigning one or two of the three stop codons to an amino acid instead) to make a strong case on this basis alone. The addition of that qualifier is critical, and I think unjustified in the context of a claim that there is a "real" connection between RNA codons and amino acids.As I mentioned above, the system we observe does involve constraints, but we have no certain way of knowing that those constraints are not primarily an example of the "QWERTY" phenomenon, a locking-in on previous design features that were, initially, arbitrary
(in this case, such a hypothesis, to remain consistent, would have to include the proposition that this locking-in occurred at the very root of the 'tree of life', and its near-universality is due to common descent rather than to fundamental constraints). I think we might find other good reasons for exploring this matter, and I feel that we should continue to seek the most reasonable explanations for the things we observe without regard to the ways in which our conclusions may become tools in the hands of creationists.

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I think we might find other good reasons for exploring this matter, and I feel that we should continue to seek the most reasonable explanations for the things we observe without regard to the ways in which our conclusions may become tools in the hands of creationists.

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I think that it is, however, important to understand what we mean.

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The addition of that qualifier is critical, and I think unjustified in the context of a claim that there is a "real" connection between RNA codons and amino acids.

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In the context of the type of discussions I'm talking about I think it is justified, in that we are talking about evolution, not abiogenesis. It doesn't matter if it is a historical artifact or not. (At least that's the way I see it.) If the discussion is "how things could possibly work" rather than "how things work" then that's different.

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"No constraints" is pretty strong; I don't know that it is clear that there are no constraints, but there may be no fundamental constraints.

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Can any part of the process be replaced with something different - say a salt for a sugar?The discussions that I'm talking about are not about historical potentials, but rather about the current system, such as attempts ot use Shannon IT to demonstrate "no new information".I've just started learning the actual molecular mechanics of DNA etc, most of my interest has been on a gross level up until now. So I appreciate your patience with my questions.For instance this:

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In mitochondria, and some microbes, some codons do map to different amino acids, hence TIC references to the "The Almost Universal Genetic Code". For example, in mitochondria, instead of representing a stop codon, UGA codes for tryptophan.

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... is fascinating.As mitochondria are thought to have originated as symbionts, could this provide a clue to the origins of the Eukaryotes?

You seem to completely misunderstand the concept of time dilation. What you have said here is nonsense. So what gauge boson mediates the consciousness force ? What is its mass? Are there conservation laws and symmetries that apply to this force ? What is its variation over distance ?Please cite appropriate experimental evidence.

Let me quote part of a passage from a book I'm reading now, Matt Ridley's The Red Queen:-------------------------
In physics, there is no great difference between a why question and a how question. How does the earth go arund the sun? By gravitational attraction. Why does the earth go around the sun? Because of gravity. Evolution, however, causes biology to be a very different game because it includes contingent history. [. . .] When a neo-Darwinian asks, "Why?" he is really asking "How did this come about?"
He is a historian.
------------------------- The "how things work" discussion is a journey, not a destination. Having identified a mechanism, the next logical step is to investigate the mechanism(s) underlying the mechanism. The question "is this the only way this could possibly work" is part of that. Assuming that you are referring to a substitution at the level of the 'substrate' (say ribose in RNA), then I would answer: no. I would regard that as a 'fundamental constraint'. But the mapping of RNA triplets to amino acids doesn't have any more to do with ribose in RNA than "Catcher In The Rye" has to do with the paper it's printed on; that's exactly my point. Obviously, if you used battery acid instead of ink... Those discussions are often hampered by the fact that those who would invoke Shannon in order to demonstrate that are often not well enough aquainted with either evolutionary theory or information theory to understand either the argument they are making or its refutation.* The arguments tend to consist of huge gobs of googled text (replete with charts and graphs) interlaced with sententious bits of folk wisdom (often bearing little relevance to the quoted portions). In my view, the teleological assumptions inherent in Shannon (that the message in a communications channel originates with an intelligent and purposeful source) make it a non-starter when applied to biological systems, and this far upstream of the logically outrageous conflation with Kolmogorov. But getting the proponents of such an approach to address that in a meaningful way can be an exercise in frustration, and a questionable use of time. For the most part, ID 'theorists' are like hecklers at a lecture hall; we may not be able to have them removed from the audience, but we don't have to invite them up on to the stage and give them use of the microphone and projector. I still think it is best to try to continue on as best we can despite their efforts to disrupt the proceedings.*The rare exceptions to this seem to fall into two categories: arguments presented by those who, knowing enough to know that their arguments are flawed, package them in ways deliberately intended to disguise this fact; and arguments which ultimately encounter philosophical issues regarded by philosophers as unresolved or unresolvable (in some cases, whether they are unresolved or unresolvable is itself unresolved (and possibly unresolvable).

Boy, this is a tough crowd. Misunderstanding the concept of time dilation is something I can live withHow can two particles traveling at different speeds be the same age?And what is the trick to quoting text?This message has been edited by Thinian, 09-25-2005 02:46 PMThis message has been edited by AdminJar, 09-25-2005 02:04 PM

You almost had it right. You need a forward slash "/" at the end (just before the "qs", not a backslash "\".

Hi Thinian,Welcome to EvC! Glad to see you join the fray.You've got a lot going on in this post, none of which seems to be on topic for this thread. We have a forum for discussing education and creation/evolution; you may want to look at threads in that forum. This is a thread focused on how bacteria can develop immunity to various agents.I'd encourage you to read through some of the education threads and post there, or propose a new topic if you'd like. Let's keep this thread focused and not go so far off topic.Below you'll find some links that may be useful during your stay here. Take a moment to look at them!Thanks, and again, welcome to EvC!

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The mean lifetime of a particle isn't altered by its speed. What is altered (due to time dilation effects) is the apparent lifetime observed in a frame of reference other than the particle's rest frame, if the particle is traveling at relativistic speeds.This has nothing to do with how long something has existed since the Big Bang.

Hi Crash. In Message 97, Faith said That's what gave me the idea that I should have explained that A, G, C and T were abbreviations and not chemical symbols.I've had quite a bit of experience in trying to explain certain aspects of molecular biology to non-biologists and non-scientists and this is one of the more common problems I've come across - mixing up abbreviations and chemical notation.One of the problems that we scientists struggle with is to avoid making assumptions about what people know and don't know. In our everyday lives, many of these terms are used with colleagues without a second thought. When we try to explain to a lay person, we find that nearly every second word we use has to be explained because we use jargon without thinking.To someone with even a passing familiarity with DNA, the A, G, C and T would be obvious (I learned about his when I was 15), but to peole with no knowledge of the subject it can appear that you are claiming that the chemical formula for an amino acid is the codon that you say codes for it.