The origin of new alleles

I don't understand how "wild digital codes circulate through our homologies" constitutes an "editing mistake." That's a statement that doesn't make any sense whatsoever. It's not a grammar error; it's a nonsense statement, an empty utterance akin to "colorless green ideas." Please do. Your single attempt to do so as yet revealed nothing but your own ignorance of English grammar.Am I perfect? Of course not. But when I make mistakes I accept correction. When I'm ignorant I accept instruction on a subject.I don't accuse people who know more, or are more perceptive than myself, of being "pedantic" or "picayune" as a smokescreen to avoid culpability for my errors.You know, like you do. No, HM, but it is a place where serious people come to talk about science issues, and when you refuse to accept any kind of correction when you're in error, and accuse others of failings to distract from your own, you stink up the place. You crowd out more interesting discussions with your nonsense, like the one I was having with Hawks. It's amazing but he was infinitely better than you at presenting your side of the discussion. He actually convinced me, contrary to your assertions that I'm some kind of dogmatist who can't ever change his mind. Maybe instead of excoriating those who point out your copious errors, you could learn something? I'm not familiar with a single instance where Gould proposed that "homologies" were something that "wild digital codes" could "circulate" through, like veins, as you did. I challenge you to supply such an instance. At best, that's a metaphor, not a statement of reality; and it's not one that I think is especially apt. For one thing, all the digital codes I'm familiar with are binary; whereas, the genetic mechanism is at least a quaternary code (possibly pentinary if you choose to count uracil, but that might be a little pedantic.) Moreover, a code is a rule for converting information into another form, but that's not what DNA does at all.DNA simply catalyzes the formation of specific polypeptide sequences. We choose to represent and model that activity in the form of codes, because that's a metaphor that most people can understand. But only a great neophyte would make the mistake of concluding that DNA is really a digital code located in our cells, like a computer.That's not what's going on, and superfluous metaphor can disguise what's really going on in the cell. That's great, but to do you you need to understand that you're entering a debate that did not begin with you, isn't about you, and doesn't have any responsibility to make allowances for your own private idioms. The responsibility to ensure your meaning is clear rests with you, and your smokescreen of blame and counter-accusations is not an effective strategy to discharge that responsibility.It's nobody's job here to figure out what the hell you're trying to say, and if you're intent on obscuring your meaning with nonsense, be prepared to be rather quickly ignored. I imagine not, since I still don't know what the hell you're trying to say. I imagine, though, that it probably has quite a bit to do with the fact that some of Archie Manning's genes were transmitted to his offspring via his own sperm.

That wouldn't have made you any more right. You associated a whole class of genetic sequences, transposons, and the the genes which modulate their movement, transposases, with one specific family within that class, the Mariner like transposases and transposable elements. You are just as wrong to use Mariner as a generic name for all transposable elements as you were to use it as a generic name for all transposons.TTFN,WK

Actually I think that DNA is technically a digital code, at least if you only consider the primary sequence, I'm not sure how epigenetic phenomena would affect that classification. I think all that is required is for the code to consist of discrete units, i.e. the four basic nucleotides, rather than being from an analogue spectrum.TTFN,WK

Well, I disagree. A digital code would be one that uses digits, that is, discreet numbers, to represent analogue data.DNA doesn't do that; doesn't even come close to doing that. DNA specifies amino acid sequences by means of chemical interactions between nucleotides, not by a numeric, serialized representation of the spacial configuration of the protein (as we might, for instance, if we were modeling the protein on a computer.)The "digital code" idea is an analogy, nothing more. It isn't actually a digital code in reality. And I think it's a poor analogy because it leads to precisely this sort of confusion.

WK said,"technically."The whole issue of using "language" to try to gain biological insight expanded (the development of "theoretical biology")after the notion of "the code"(triples per amino) and I think it was in this latter time (late 60s and early 70s) when for instance Kaufmann got his begining motivation about biology by lights that turn off and on digitally(pre auto-catalytic thought etc)and such that was but certainly since Wolfram there is a very precise tendency NOT to go back to the differences that say seperated the mathematician Rene Thom and Francis Cricks ideas on morphogenesis.Your word "analogy" and WoundKing's "spectrum" seem to be dissonantly resonating becuase they may refer to different periods in the history of biology, yes?Did you not simply misread WK?When he said,

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I'm not sure how epigenetic phenomena would affect that classification.

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Is that not the same as your questioning a "reality"?But look as soon as one starts to think about DNA computers, which as an idea have at the present little to do with extant physiology per say ,may(have true physiological connections).... later. The discrete nature of DNA may be used to write an algorithm that time releases drugs in th soma etc, future, yes, but thought today- yes, also.Yes, there is some issue using "language" and discrete ideas about "letters" (A,C,G,T) discreetly but this notion of disjunction does proceed from the time of the "code" rather than the digital reductionism from the 70s to us, and we have in the latest fad of nanotechnology, seems to me.Edited by Brad McFall, : grammer/languageEdited by Brad McFall, : precisionEdited by Brad McFall, : claification

WK, I’m not clear about what you are criticizing here: I don’t believe I did what you are accusing me of: “wrong...use [of] Mariner as a generic name for all transposable elements . ” Where did I do that?Perhaps, for my education, you would critique this description of “jumping genes,” posted on the National Health Museum website:

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Mariner transposable elements, more popularly known as jumping genes, appear to jump from species to species, not randomly but as a fundamental means of survival, reported University of Illinois researchers at the annual meeting of the American Association for the Advancement of Science.

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Transposable elements are fragments of DNA which appear to migrate from species to species by an as yet little understood mechanism through a process known as horizontal transfer. Mariner elements, which have been identified in many different species of insects are among the smallest of the jumping genes so far identified.

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So what do you make of that last sentenece (the one I've bolded)?”Hoot Mon

Holy smoke, crashfrog, did you say “spacial configurations”? That doesn't make any sense. Did you mean to write “special” or “spatial”? Do you even know what you’re writing about? (I have an idea: Let's move beyond this pedantic bullshit.)Well, on this matter of genes as digital code, maybe I can help. Richard Dawkins, in his book River Out Of Eden (1995, p. 19), has this to say about digital genes:

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Genes are pure information”information that can be encoded, recoded and decoded, without any degradation or change of meaning. Pure information can be copied and, since it is digital information, the fidelity of the copying can be immense.

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Missing this point does not help to support your self-proclaimed expertise in these matters.”Hoot Mon

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Genes are pure information”information that can be encoded, recoded and decoded, without any degradation or change of meaning.

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Dawkins seems to be very deterministic when it comes to the phenotypic effects of a particular (expressed) DNA sequence - and because of this he is also wrong (I don't have the book available, so I'm just going with what is written here). Try to insert a eukaryotic gene containing introns into a prokaryote and you will quickly realise that the meaning of the DNA sequence will now most likely have changed. However, I will agree with the statement that as far as DNA ability to transmit it's own information goes (i.e. it's ability to act as a template for copying purposes), it is for all intents and purposes digital.

Lol! Yes, I did mean "spatial", thank you. I'm not missing the point; I'm explaining it to you, if you'll stop and listen for a minute. Dawkins is making an analogy. (Did they teach you about analogies in school?)

I don't see what that has to do with being digital. Even an analogue recording can be duplicated. For instance, an LP record is made by pressing a reverse master onto the vinyl record. That's an example of an analogue "code" acting as a template for copying purposes.Digital codes are codes that use discreet numerical values to represent analogue signals; like the way the datastream coming off of an audio CD represents analogue signal waveforms. To assert that DNA is a "digital code" is to be making an analogy, not stating a fact. It's like digital codes, sure; but it's also like a stock market ticker, or a busy file clerk, or any number of alternate analogies could be made. And to assert that DNA is literally a digital code is as nonsensical as asserting that DNA is really a tiny little file clerk living inside our cells.

It was in Message 28... They are only referred to as "mariner genes" when they are of the Mariner family as opposed to the PiggyBAC, Minos, Hermes or Sleeping beauty Families or whatever other families remain to be discovered.And they really aren't plasmids! That it agrees entirely with what I said, that the Mariner elements are a family within the larger class of transposons/jumping genes and not a suitable generic term for all jumping genes. What I would say is sloppily worded is the first sentence which make it ambiguous whether it is 'transposable elements' or 'Mariner transposable elements' which are popularly known as jumping genes.It is like deciding that since cats are mammals we can call all mammals cats. Since Mariner genes are a type of jumping gene all jumping genes can be called Mariner genes.TTFN,WK

1. Whoever said a digital code has to be composed of numbers? What about the English langauge; it's digital by way of its letters, is it not?2. Those coded sequences on DNA”the genes”can outlive their material nucleotides by many, many years. Molecular nucleotides are mundane, perfunctory, and ephemeral to those digital genes of pure information. The meaning of a gene, of course, is in the coded arrangment of those nucleotides on DNA. (I'm sure you know that.)”Hoot Mon

I don't see you addressing my points. Isn't this the "ankle-biting" you keep referring to? I'm still waiting for you to show how anything can "circulate" through the "veins" of a "homology", as was your claim.Edited by crashfrog, : No reason given.

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I don't see what that has to do with being digital. Even an analogue recording can be duplicated. For instance, an LP record is made by pressing a reverse master onto the vinyl record. That's an example of an analogue "code" acting as a template for copying purposes.

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Digital codes are codes that use discreet numerical values to represent analogue signals; like the way the datastream coming off of an audio CD represents analogue signal waveforms. To assert that DNA is a "digital code" is to be making an analogy, not stating a fact. It's like digital codes, sure; but it's also like a stock market ticker, or a busy file clerk, or any number of alternate analogies could be made. And to assert that DNA is literally a digital code is as nonsensical as asserting that DNA is really a tiny little file clerk living inside our cells.

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Just like the discrete signal found on a CD, nucleotides form a similarly discrete signal. And since when do digital signals have to represent analogue ones? You ask the question if something analogue can be copied? Yes, of course. But that is not interesting, as the signal being copied is not discrete. (as a side note: given that our DNA sequencing methods are "crude", our ability to detect said sequence relies on the use of millions of DNA copies - this helps reduce the noise inherent in the signal. The signal WE receive is effectively analogue for each and every nucleotide).So when I claim that "DNA's ability to act as a template for copying purposes, is for all intents and purposes digital." I think that I am right, since it is a discrete signal that is being copied. Pretty good analogy, I would say.

Well, OK, you win. My grasp of the operative terms is not quite up to speed. I don't believe I know as much as you about these matters. It could well be that I have my terms mixed up.But I also posted this in Message 28: You didn't respond. Any disagreement with this statement? (I notice it doesn't mention plasmids, which was probably my biggest mistake.)”Hoot Mon