A software engineer on convergent evolution

_{Denyse O'Leary

September 7, 2013

Convergent evolution}

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Further to “Convergent evolution seen in 100s of genes,”

I’m a software engineer, and we re-use components all the time for different programs that have no “common ancestor”. E.g. – I can develop my String function library and use it in my web application and my Eclipse IDE plug-in, and those two Java programs have nothing in common. So you find the same bits in two different programs because I am the developer of both programs. But the two programs don’t extend from a common program that was used for some other purpose – they have no “common ancestor” program.

Now with that in mind, take a look at this recent article from Science Daily, which Mysterious Micah sent me. …

“We had expected to find identical changes in maybe a dozen or so genes but to see nearly 200 is incredible,” explains Dr Joe Parker, from Queen Mary’s School of Biological and Chemical Sciences and first author on the paper.

High rates of convergent evolution are only “incredible” if we simply assume as an article of faith that there is no design, and that therefore there is nothing to research. It shall remain then, forever, incredible. No matter why the design exists.

A price paid, shall we say, for dogmatism killing curiosity.

Comments

You have absolutely no intentions whatsoever of acknowledging any artifact of design found in nature, regardless of the type or quality of that artifact. And if something is presented to you that the mechanism of Darwinian evolution could not have possibly created, you can then defend your position by demanding an impossible standard of evidence far beyond anything you would apply to your own position. In other words, you have deliberately insulated yourself from any contradictory evidence. And since I am not even needed for that type of exchange, I will deplane the conversation and leave you the last word.
I'll happily accept design if and when all possible unguided, natural causes have been eliminated. Since that has not yet been done (regarding DNA) then I'll not yet accept the design inference. That includes the discovery of something that is irreducibly complex. I am frequently asked on this forum to be impossibly specific on historical matters. I expect that ID proponents should at least be able to (roughly, I'm not talking about a particular year) say when design was implemented. And I think if you can't give some idea of what designs were implemented then ID really has no teeth whatsoever. It doesn't explain what we see in the fossil record. It doesn't explain the bio-geographic diversity we observe. It doesn't explain the existing genomes. And it doesn't cast any light on aspects of existing morphologies. Any problems with evolutionary theory aside, ID really has no central, coherent, explanatory hypothesis. All you all seem to be able to agree on is: Design happened. You can't even agree on when or what. (I've stopped asking for how and why.)Jerad_{September 10, 2013
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Jerad: Saying, believing or wishing does not make things so. In the case of evolutionary materialism and associated scientism, the evidence is, that the mechanisms put forth have no empirically undergirded capacity to account for origin of FSCO/I, in particular origin of life and of body plans. As has already been summarised repeatedly. Similarly, the Nobel prizes you list constitute a case of subject switching, i.e. irrelevancy by strawman fallacy joined to elephant hurling. KFkairosfocus_{September 10, 2013
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Occam’s razor is not an excuse to ignore evidence, as there is a world of difference between being simple while coherently addressing the facts in evidence and being simplistic while suppressing or ignoring material but inconvenient facts.
Obviously you apply Ockham's Razor after looking at all data. And you try and find the most parsimonious model/explanation that invokes the fewest assumed causes. Evolutionary theory explains the data, is not contradicted by the data and assumes no processes that we cannot be sure were in existence at the pertinent time. ID is happy to assume there was an unspecified, undetected intelligent designer around . . . at what time was it? Who did . . . what was it ID is saying the designer did again? You can't inferred design without invoking a designer. And you can't even specify when design was implemented or what designs were implemented. So, at this point, ID assumes an agent/cause which evolutionary theory does not invoke. And ID cannot even account for the actions of this assumed intelligent designer. I'd say evolutionary theory is the better model. Recent Nobel Prizes for Chemistry 2012 - "for studies of G-protein-coupled receptors" 2010 - "for palladium-catalyzed cross couplings in organic synthesis" 2009 - "for studies of the structure and function of the ribosome" 2006 - "for his studies of the molecular basis of eukaryotic transcription" 2005 - "for the development of the metathesis method in organic synthesis" 2004 - "for the discovery of ubiquitin-mediated protein degradation" 2003 - "for discoveries concerning channels in cell membranes [...] for structural and mechanistic studies of ion channels" 2002 - "for the development of methods for identification and structure analyses of biological macromolecules [...] for his development of nuclear magnetic resonance spectroscopy for determining the three-dimensional structure of biological macromolecules in solution" 1997 - "for their elucidation of the enzymatic mechanism underlying the synthesis of adenosine triphosphate (ATP)" 1993 - "for contributions to the developments of methods within DNA-based chemistry [...] for his fundamental contributions to the establishment of oligonucleotide-based, site-directed mutagenesis and its development for protein studies" 1990 - "for his development of the theory and methodology of organic synthesis" 1989 - "for their discovery of catalytic properties of RNA" 1980 - "for his fundamental studies of the biochemistry of nucleic acids, with particular regard to recombinant-DNA" 1972 - "for their contribution to the understanding of the connection between chemical structure and catalytic activity of the active centre of the ribonuclease molecule" And now I'm bored. Perhaps none of these directly, specifically address whatever issue you think is not being studied. But it does show that the Nobel committee has recognised, many times, outstanding contributions to the understanding of how molecular biology works with their prize in chemistry. And the Nobel prize is the smallest tip of a giant iceberg.Jerad_{September 10, 2013
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Joe (122):
Yes design has been detected.
Well, better get busy trying to figure out when that happened then eh?
There isn’t any evidence that accumuylations of genetic accidents can produce proteins, let alone multi-protein configs. Just because you accept hearsay and speculation as science that doesn’t mean the rest of us have to be so gullible. And if you stopped lying and started presenting some actual evidence, my tone would change. However when all you do is lie and deflect then I will respond accordingly.
Well, what many, many, many intelligent, educated people who have worked decades in biology find to be evidence isn't good enough for Joe. Oh well, I guess some people will just get left behind. Joe (124):
You have no idea if they are all random or not. The evidence says they are not all random, just ask James Shapiro.
Are you sure he's right? Is your mathematical skill up to the task of evaluating his argument? What if he's wrong? Has his work been reviewed and verified and built upon by others? Is it your contention that all mutations are not random, most mutations are not random, some mutations are not random or a select few mutations are not random? Or are you just trying to sew doubt and avoid making a stance yourself?
Changing what exists does not account for the origin of the body plan being changed. Also ID is OK with change, so is YEC.
Body plans are derived from previous body plans by a step-by-step process of modification. Hey, if you're okay with change then you must be okay with evolution! Cool.
Changing eye color does not account for the eye. Nor does it account for the organism.
What do you get if you cumulatively select hundreds, thousands, millions of years of small changes? Why do you think there is some magical boundary beyond which such accumulations cannot step? You seem to agree that we've observed 'micro' evolution. What do you think prevents 'macro' evolution from occurring?Jerad_{September 10, 2013
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Sigaba at 156,
The problem is your argument at 109 is fine, I was working from this account of it I read last year, which I would hold has a faulty premise at 4. Your argument has significantly changed in the last year.
I have no problem with that, after all, that’s what arguments are properly supposed to do – improve. The issue with #4 is that not all material representations present an arbitrary component to the system. Some do, and some don’t. All semiotic systems function via the three dimensional recognition of the representational objects given to them. Most systems produce their effects directly from that recognition. A pheromone is a prime example. Other systems however, vastly rarer in number, have an added dimensional component to their operation. Some systems recognize the three dimensional structure of a representational object but do not immediately produce an effect from that recognition, instead they operate in a single dimension to recognize another object (and perhaps another after that) before producing an effect. In order to function, such systems require systematic protocols to establish this dimensional quality in both in the medium and in the translation apparatus producing effects from that medium. So while all semiotic systems demonstrate a physicochemically arbitrary relationship between the arrangement of the medium and the effect it evokes in the system, this extra dimensionality does indeed present a physicochemically arbitrary component to the system (i.e. the dimensional quality of the system is not locally derivable from physical law). My #4 from last year did not properly reflect this distinction. As it happens, genetic information systems are in this second group of systems, and given that they are the general focus of the argument being presented, this may explain why I did not catch the distinction. In any case, dimensional semiotic systems demonstrate the added quality of being able to encode virtually any amount of information of any kind – maintaining a physically economical store of representational objects. The only other examples of dimensional semiotic systems are mathematics and language.Upright BiPed_{September 10, 2013
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The problem is your argument at 109 is fine
Yup. That's the problem. We agree. I couldn't have said it better myself.Mung_{September 10, 2013
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Upright BiPed:
Describe a sign that does not have a mapping or does not require translation.
The sign of Jonah? The sign of the son of man? Great question. Let me know if it's ever answered.Mung_{September 10, 2013
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Is Jerad now willing to discuss "the Origin of Life," a topic he so assiduously avoided (feigning complete ignorance/incompetence) in his first foray here at UD? Or is he now just trolling?Mung_{September 10, 2013
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Upright BiPed @102 Just want to thank you for that concise historical review. Bookmarked. p.s. May be the basis for a new thread. (hint hint) The Relevance of Semiotics to Biology (or some such high falutin soundin monicker).Mung_{September 10, 2013
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Upright BiPed @100 lol. thanks! Nice to see that wit and sarcasm still thrive.Mung_{September 10, 2013
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I was looking for Convergent Evolution in my "Design Patterns" book. =PMung_{September 10, 2013
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If I present an argument where it’s blatantly obvious that the argument is falsifiable, and someone tells me that it’s non-falsifiable sophistry, then I feel completely validated in pressing them on a question to measure their balance on the issue.
The problem is your argument at 109 is fine, I was working from this account of it I read last year, which I would hold has a faulty premise at 4. Your argument has significantly changed in the last year.sigaba_{September 10, 2013
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Larry,
Regardless of my definition, I wonder what your response is to my earlier point, “by definition a semiotic system requires a decoding mechanism, someone or something to assign a specific value to the material signal or inscription.”
Yes, of course it does - and every semiotic system (including the genetic system) has a material protocol(s) to accomplish just that. The material protocol establishes a mandatory physicochemically-arbitrary relationship between the arrangement of the medium and the physical effect the system will produce from that arrangement. Your question illustrates exactly why you should set aside the anthropocentric view, and analyze these systems from their material consequences alone. The interesting thing about the genetic system is not only does it contain the protocols to establish the required relationships within the system, but also has the additional systematic protocols to establish the dimensionality of the genetic code.Upright BiPed_{September 10, 2013
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No need to worry about it sigaba, I am sure these are just differences in personality. If I present an argument where it's blatantly obvious that the argument is falsifiable, and someone tells me that it's non-falsifiable sophistry, then I feel completely validated in pressing them on a question to measure their balance on the issue. There is also no need to assume my argument is based on the faults in other arguments. I am fairly capable of defending my position, and I would have lost it long ago if my position were based on such obvious faulty reasoning.Upright BiPed_{September 10, 2013
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Why does it matter if my position is falsifiable? Such a thing would have no bearing on your argument. If your entire defense of your theory is "everyone else's is faulty," that's not really valid.sigaba_{September 10, 2013
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segaba: Your position is non-falsifiable! UB: It can be immediately falsified by experiment, Is yours falsifiable? segaba: Let me restate your argument. UB: You just said it was non-falsifiable. So is yours falsifiable? segaba: Actually your argument is fine if we use your definitions. UB: So is yours falsifiable? segaba: I must confess, I don’t like your argument style.
:|Upright BiPed_{September 10, 2013
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I confess I find your mode of debate far from irenic, let alone persuasive.sigaba_{September 10, 2013
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So, per 146, you are unwilling to subject your position to the same scrutiny as you subject mine
I don't have a position at this time... Are you trying to weasel out of qualifying yours?sigaba_{September 10, 2013
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So, per 146, you are unwilling to subject your position to the same scrutiny as you subject mine. Fine. We needn't go any further. cheersUpright BiPed_{September 10, 2013
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Actually your argument at 109 seems fine if we accept all your definitions. I don't think it gets you anywhere, it certainly doesn't get you to supernatural causation, but it's fine. If you take my general definition of semiotics it becomes unfalsifiable. I still don't think you need the semiotics stuff, it just complicates the argument -- evolution has many necessary parts, and the informational parts are only one of them. We can just as easily say that evolution requires reproduction, or death, thus reproduction or death must be established before the onset of evolution, and that evolution thus cannot create reproduction or death per se. It really does feel like you're just trying to make the reasoning harmonize with the information complexity literature.
Given these observations, a mechanism capable of establishing this semiotic state is necessary prior to the onset of Darwinian evolution and information-based organization.
Did the "onset of Darwinian evolution" happen at one or a few remote times in the past, or all the time? I don't understand what you mean by something being the "source" of evolution, this should be more carefully qualified. Can mechanism be stated as simply "conditions," or is there the necessity of some previous other thing?sigaba_{September 10, 2013
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I'm off for a short while for lunch. I'll return later.Upright BiPed_{September 10, 2013
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sigaba at 143 My comment in #131 is not strictly about acceptance of the semiotic argument, and even if it was, at this point it does not matter. The simple fact is that you’ve already accepted its content for argument sake and made a direct and unambiguous assessment against it (i.e. I’m sorry UB but I think it’s all sophistry, even if it’s logically consistent, it’s not empirically falsifiable). So now I am asking you to direct your attention to your accepted alternative. Here again is the question I am asking you to respond to:
A claim against the rise of a semiotic system from inanimate matter is immediately falsifiable by a demonstration of the rise of a semiotic system from inanimate matter – or was that not already obvious? On the other hand, how would you falsify a claim that a semiotic system arose from inanimate matter if that claim is forever made in debate, but never put to a test? It would seem (per rational observation) that the first claim is immediately falsifiable through experiment, while the second is ultimately non-falsifiable by any means whatsoever. Do you disagree? If so, then describe your reasoning.
You will either address the accepted alternative in the same vein as you did my argument, or you will refuse to do so. If you refuse to do so, then you will have accepted the content of my argument long enough to make an unambiguous claim against it, then upon my direct response, refuse to address it again as a means to protect your alternative from the same scrutiny you afforded my argument. It’s your call. Accept the content as you did in order to disparage it, and answer the question. Or, refuse to accept it, and protect your alternative from the obvious outcome of your own critique.Upright BiPed_{September 10, 2013
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That cannot be because by definition a semiotic system requires a decoding mechanism, someone or something to assign a specific value to the material signal or inscription.
Right, that's basically my position, but he seems convinced he has an objective (or as he'd say, "rational") justification. His program seems to be about using a physical properties of a system to decide if it uses signs or not. If he can prove it does, then he believes he can use certain assumptions from more humanistic semiotic disciplines to prove his point.sigaba_{September 10, 2013
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UBP @40, How is the etymology of the word 'information' of use for the technical sense in which we want to use the term? But to answer your question very broadly, I would would say information is the result of material in motion and/or interacting. Regardless of my definition, I wonder what your response is to my earlier point, "by definition a semiotic system requires a decoding mechanism, someone or something to assign a specific value to the material signal or inscription." After all, the term under discussion is "semiotic system," not "information." Right?LarTanner_{September 10, 2013
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sigaba, do you plan on responding to my post at 131 ?
I did at 133, to which you responded. Let me restate how I understand this: My gloss of your argument is that if something is translated, it necessarily is a sign; signs have meaning; certain organic molecules are translated, thus these organic molecules have meaning; meaning cannot exist with prior context, thus these organic molecules could not create themselves?sigaba_{September 10, 2013
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Larry, may I offer you something, then ask you a question?
The general etymology of the word “information” suggests that information gives “form” to a subject of interest. This definition originates from Greek precursors, and leads to the Latin verb informare; to “in-form”. This is the standard description that virtually all people would recognize in common use. Information informs us of (or gives form to) the things we speak, write, and think about. When we say “the sky is blue” we are giving form to our perception of the sky - it’s blue. Likewise, the recipe for an apple pie gives form to the way in which an apple pie is made, just as the code that passes through our computers gives form to the programs we run. This is a purely anthropocentric view of information, but it is no stretch to also recognize that other living things have their own methods of communicating form. The ant's pheromones give form to the coordinated response of the other ants (i.e. they attack, they follow, they gather food, etc). In the same way, the bee's dance gives form to the response of the other bees (i.e. they fly off in the right direction to their feeding grounds). From direct observation of the living world, information gives form to the various effects it evokes within the systems where we find it.
Here is the question: From a purely material perspective (i.e. without regard to its source) what do you think "information" is?Upright BiPed_{September 10, 2013
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Sigba @136,
I think it’s his position that his definition is the criteria for an objectively semiotic system.
That cannot be because by definition a semiotic system requires a decoding mechanism, someone or something to assign a specific value to the material signal or inscription. So it makes no sense to call something a semiotic system and not identify who or what performs (or could perform) the decoding. Same thing at the encoding end.LarTanner_{September 10, 2013
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DNA codons represent amino acids, they do not become amino acids via some chemical reaction. That the codons represent amino acids means the codons are symbols in the process.
I'm not sure there's a difference between representing and becoming in this instance. A lot of physical processes The magnetic field of the earth shifts occasionally, and these changes are recorded in bands on oceanic ridges, but neither the Earth nor the magnetic field "become" the bands, and we don't say that the alternating bands are "symbols." We can say that the bands "represent" the magnetic field at such-and-such an epoch. We can add the qualification that such recordings don't qualify as semiotic in this sense, unless they act on further phenomena. Would you like to do that?
And it bothers you that unguided proceses cannot account for that.
We haven't even gotten there yet, I'm still stuck on this whole "semiotic" formalism...sigaba_{September 10, 2013
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sigaba, do you plan on responding to my post at 131 ?Upright BiPed_{September 10, 2013
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Sigaba,
I’m not sure your definition of a semiotic system is particularly rigorous
Every element in my argument is described at the material level, without anthropocentric ambiguity.
it’s significantly different from the philosophical one in that you seem to state that a signer and a signed can be molecules
There is no sign in existence that is not embedded in a material medium of some kind, regardless of its origin.
when the social science definition requires them to be thinking agents.
That view is over half a century old and serves no purpose in science. The entirety of the semiological community has moved on, based on rational observation.
I mean your argument has a very thorough account of how information is reified in matter
Reified? Information requires a medium. If you cannot demonstrate an instance of information without a medium, then your words are rather inconsistent with reality.
but that doesn’t get you to a “sign,” which has semantic meaning independent of itself or any mapping or translation.
Describe a sign that does not have a mapping or does not require translation.
That’s a big issue — DNA can be translated a dozen ways into different media, producing different molecules, but at no time does it become a collection of “signs"
Describe how a set of nucleotides can specify something in translation, without representing that something to a system capable of producing it.
I think your information theory stuff is completely beside the point, and probably is an atavism from previous versions of your argument, when you incorporated more CSI-conservation language
Who even knows what this means? It seems to have come from a grab bag. My argument has never been about the measurement of content.
Also you’ve introduced a new term here, “inanimate matter,” which I don’t quite see — you need a clear distinction between living and nonliving.
A rational observer hardly has a problem with such concepts. A quick search of Google Scholar produces roughly 100,000 references to papers from across the physical sciences spectrum. Apparently, people are able to communicate with such terms. Frankly, this again seems like another pull from the grab bag.Upright BiPed_{September 10, 2013
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