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

UPB, Up in comment 215, I had a message for you that I hope you now have the time to respond to. Here's what I said, slightly edited:
UBP @ 203, At last I might grasp the core of your semiotic argument. If I understand you, you ultimately claim that an arbitrary yet also systematic relationship exists between raw physical phenomena, on the one hand, and the biological processes used by organisms to translate perception of phenomena into specific “neural” configurations, on the other hand. I put “neural” in quotation marks because your point goes beyond what might physically happen in a human brain; your point is that any biological form must have a physical way of “knowing” the thing it perceives, and then responds to. I understand you have follow-on points from this one, but have I captured the central part of what you are arguing?
LarTanner_{September 19, 2013
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If you have something typed up, you can send it to the contact at complexitycafe.
postedMung_{September 17, 2013
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Teaser: Optimal foraging Strategies: the honeybees As von Frisch had taught us, at the start of a foraging period some individual honeybees go out foraging on their own ('proactive' search) and some ('reactive' searchers) stay in the hive awaiting information from returning foragers that is conveyed by the famous 'bee dance' (von Frisch, 1967). The issue to be solved was: which optimal percentage of individuals should go out and forage and which correspondingly optimal percentage should wait for information?Mung_{September 15, 2013
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Hello Mung. No regretfully I haven't read it yet. If you have something typed up, you can send it to the contact at complexitycafe. I'm always happy to read more.Upright BiPed_{September 15, 2013
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Hi Upright BiPed, Have you read What Darwin Got Wrong yet? Interesting section on bees. If you haven't read it yes I'll think about typing it up. Seems they "just happened" to have "evolved" an optimal strategy for foraging.Mung_{September 15, 2013
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How life originated directly impacts how it evolved.
How exactly? Once you have a viable population of basic replicators how exactly does the way they came into being affect how they develop via natural processes from that point on? As little handwaving as you can manage please.Jerad_{September 14, 2013
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Unguided evolution doesn’t have a model.
It does. You deny it does. Your choice. But it does make you look ignorant. What's ID's model then? You never seem to get around to elucidating one. Actually, no one ever seems to get around to it. Funny that. Can't you guys agree on what you're saying?
Why do you think there is some undefined limit to evolution?
The evidence-> just look at Lenski’s experiment with well over 50,000 generations and no new proteins.
But new traits. So, let me get this straight . . . if you don't observe something in a certain time then it can't/won't happen? Or . . . What is your 'best by date' for allowing natural processes their chance?
I have looked, Jerad. Your position has nothing but mental midgets supporting it.
There's no need to be rude. I know you enjoy that but it does make you sound like a primary school bully.
The default, parsimonious assumption is that they are random until proven otherwise.
LoL! “We don’t know” is the default, Jerad.
Is that your opinion about coin flipping as well? Or rolling fair dice? We don't know if the results are random? Do you not understand the mathematical tests for randomness then? I guess you don't.
I’d say unguided, natural processes. As is supported by several lines of data.
Then please present that evidence or admit that you are lying.
Have you got evidence of another cause? Evidence independent of the artefact in question? If you don't then . . . how do you know the 'cause' exists? AND, what if you're wrong and natural processes ARE capable of everything evolutionary biologists claim. Does that mean we can junk the idea of an intelligent designer?Jerad_{September 14, 2013
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We are dealing with a toxic, ideologically charged situation with an overbearing orthodoxy that has imposed questionable a priori materialism on science and has resorted to tactics that have unjustly harmed a lot of people.
You are entitled to your opinion. But just because I disagree with you (as do many, many, many people) does not mean I subscribe to any invented conspiracy you envision. I still do not concede that there has any been a need for biological systems to search a large configuration space. AND that's not the argument that evolutionary biology makes. Why you keep bringing it up is a mystery to me. If you had some academic credence behind the idea . . . have you tried to publish it? And, no matter what you think, there is no materialist/atheist plot to keep down the truth. If you want to discuss science, fair enough. But if you're going to make up paranoid plots then I'm bailing.Jerad_{September 14, 2013
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Me neither. I don’t think I implied otherwise. You are simply requiring that others provide a negative argument if you are to be moved off your current position.
I don't see what's wrong with being very, very sure that natural processes can't explain a situation before assuming an unmeasured, unobserved and undefined cause. But, whatever floats your boat.
And then complaining that the only thing you are hearing is a negative argument.
I could have phrased my statements more better. :-)
So, we need to prove to you that natural processes aren’t up to the job before you’ll consider design, but you want us to do so without arguing that natural processes aren’t up to the job? Again, your position would seem to be very well protected.
Obviously you can't PROVE natural forces couldn't do something or other. But you can pretty damn sure. And I don't think that's the state of our knowledge at this point. You disagree.
No. I only think it is unreasonable to require a negative argument and then complain that all you are hearing is a negative argument.
Well, hopefully I've qualified my previous statement enough.
As I’ve said, you appear to be protecting your position to an unreasonable degree. I’ve asked several times why you would do this. I think this is a fair question, but it is only one that you can answer. I do think it would be unfair for me to assign motives or to move from talking about what you’ve said to who you are. If you ever feel I am doing so, please point it out to me, because that’s not what I want to be about.
I am not 'protecting' my position. I am confident it is correct but I am open to new data. But to overthrow the current model is going to take some a damn strong case against it. Especially one that hypothesises an undefined, unobserved and unlimited cause.Jerad_{September 14, 2013
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Alan, didn't you previously admit that you were incapable of comprehending the argument that Upright BiPed makes and thus are unable to provide any relevant commentary on it? Since that still seems to be the case, why not just remain silent? If you have questions, UBP has been very gracious in answering.Mung_{September 13, 2013
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Alan Fox:
I’m glad that you are now stating clearly that your argument is intended to refute a “natural” abiogenesis, an issue on which the theory of evolution can have nothing to say.
Yeah Upright BiPed! Thank you for finally making it clear that you're describing what must actually be in place prior to the onset of Darwinian evolution. And thanks to Alan as well! For exposing, once again, for all to see, your complete ignorance of the argument put forth by Upright BiPed.Mung_{September 13, 2013
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sigaba,
UB: The observations are made at the material level; the words are merely descriptors. Consequently, they are quite defensible. sig: I would agree they’re defensible philosophically
I’m glad of that. However, when a representation is described as an arrangement of matter that evokes a functional effect within a system, where the arrangement of the medium is physicochemically arbitrary to the effect it evokes – then I have described a physical thing that can be identified and modeled within a particular material system.
“Relationship” in this argument is referring to a “protocol,” an abstract concept which is germane to a discussion of communications systems but not to chemistry.
I don’t refer to a protocol as an abstract concept. Like the other elements of the system, it is described materially so that it may be identified within the system. In the case of the protocol, it is described as an arrangement of matter that physically establishes the otherwise non-existent relationship between the arrangement of the medium and the effect it evokes in the system. As far as the language of communications being relevant to chemistry; you show me a communication system, and I’ll show you a physical system (matter = chemistry) containing a local relationship creating unambiguous function in the living kingdom. Marshal Nirenberg used radioactive phenylalanine to establish its relationship to the input of polyuracil into the ribosome. He did so because that local relationship could not be established from the mere chemistry of the polyuracil. As the investigator, he did not impute that relationship on the system, he observed it in reality. If he had ignored those relationships, we would not know the genetic code today. But he wasn’t doing the experiment to ignore the relationships, he was doing it to discover them. That’s the point. Ignoring the relationship is an obvious non-starter; superseded in its ignorance only by overlooking the fact that if those relationships had not been instantiated in a physical system 3 billion years ago, we would not be here to ponder whether or not they’re anthropic projections.Upright BiPed_{September 13, 2013
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UBP @ 203, At last I might grasp the core of your semiotic argument. If I understand you, you are ultimately claiming that an arbitrary yet also systematic relationship exists between raw physical phenomena, on the one hand, and the biological processes used by organisms to translate perception of phenomena into specific "neural" configurations, on the other hand. I put "neural" in quotation marks because your point goes beyond what might physically happen in a human brain; your point is that any biological form must have a physical way of "knowing" the thing it perceives, and then responds to. I understand that you have follow-on points from this, but have I at last captured the central part of what you are arguing?LarTanner_{September 13, 2013
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Alan Fox wallows in his willful ignorance:
I’m glad that you are now stating clearly that your argument is intended to refute a “natural” abiogenesis, an issue on which the theory of evolution can have nothing to say.
How life originated directly impacts how it evolved. If the OoL = design then it is evolution by design. IOW Alan loves his ignorasnce so much he refuses to listen to reason.Joe_{September 13, 2013
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Oops ...a material universe, [in which] it is not possible...Alan Fox_{September 13, 2013
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Upright Biped in 193
To put it into perspective, you must return to the time on Earth when it was completely barren of the even a microbe of Life. That is the condition prior to the onset of information-based biological organization. From that material state, a mechanism is required to establish the physicochemically arbitrary relationships required for the translation of recorded information. Obviously, the mechanism cannot be Darwinian evolution, because it does not yet exist.
I'm glad that you are now stating clearly that your argument is intended to refute a "natural" abiogenesis, an issue on which the theory of evolution can have nothing to say. Your argument therefore should be directed to those proposing ideas, mechanisms and scenarios that might explain (at least partially) how life on Earth may have come about. It would be a kindness to let them know they are wasting their time on such research. With your emphasis on "...a material universe, it [which] is not possible to transfer any form of recorded information into a material effect without using an arrangement of matter (or energy) as an information-bearing medium", I wonder where you go after insisting on such a material universe, having ruled out non-material effects in your argument. I mean, what is the ID explanation for the origin of life on Earth, if we turned up in a solely material universe? That's curtains for the cosmic designer according to Upright Biped, apparently!Alan Fox_{September 13, 2013
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LarTanner:
Can you please give some different examples of information-based effects in the sense you define above?
Flipping a light switch. Hitting keys on a keyboard. Punching in a phone number on a cell phone and hitting the send button.Mung_{September 12, 2013
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sigaba:
Protocols and symbols are things people use, things that we push through communications networks and computers. I’m not sure it’s warranted to apply our understanding of these terms to pheromones or kinases. We can talk about them as “signaling” or “messaging,” and these metaphors are common, but aren’t they just metaphors?
Wetware: A Computer in Every Living Cell People are beginning to notice. :)Mung_{September 12, 2013
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sigaba:
You can’t suppose a “protocol” in the semiotic sense without teleology.
so? :D
“Relationship” in this argument is referring to a “protocol,” an abstract concept which is germane to a discussion of communications systems but not to chemistry.
Fine. So cells aren't just bags of chemicals undergoing chemical reactions. You'll get no argument from us ID'ists about that. But given physics and chemistry alone, how do systems of communication arise?Mung_{September 12, 2013
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The observations are made at the material level; the words are merely descriptors. Consequently, they are quite defensible.
I would agree they're defensible philosophically, however I'm not sure you're using these terms merely descriptively. Like up at 198 you say:
When I refer to an “information based” effect, I am talking about an effect that is originated by the local translation of an arrangement of matter, where the effect produced is physicochemically arbitrary to the arrangement. Let that sink in. This translation cannot occur without a relationship instantiated in the system.
"Relationship" in this argument is referring to a "protocol," an abstract concept which is germane to a discussion of communications systems but not to chemistry. We can't really say something like this unless we say that, for example, it's DNA's "purpose" to make tRNA or copies of itself. You can't suppose a "protocol" in the semiotic sense without teleology.sigaba_{September 12, 2013
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sig, The observations are made at the material level; the words are merely descriptors. Consequently, they are quite defensible. If you believe there is an overgeneralization, you can point to it in detail, and I'll respond later.Upright BiPed_{September 12, 2013
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Sorry, further:
The answer must surely be that the brain is causally connected to the mind and the mind contains and processes information. That is, a conscious subject has knowledge, memory, perception, and the power of reason—I have various kinds of information at my disposal. No doubt I have this information because of activity in my brain, but it doesn’t follow that my brain also has such information, still less microscopic bits of it. Why do we say that telephone lines convey information? Not because they are intrinsically informational, but because conscious subjects are at either end of them, exchanging information in the ordinary sense. Without the conscious subjects and their informational states, wires and neurons would not warrant being described in informational terms.
sigaba_{September 12, 2013
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On this matter of overextending metaphors of "purposefulness" to biological entities, Colin McGinn wrote a very insightful review of Ray Kurzweil's last book that makes this point better than me:
Presumably (I am not entirely sure) Kurzweil would agree that such descriptions cannot be taken literally: individual neurons don’t say things or predict things or see things—though it is perhaps as if they do. People say and predict and see, not little bunches of neurons, still less bits of machines. Such anthropomorphic descriptions of cortical activity must ultimately be replaced by literal descriptions of electric charge and chemical transmission (though they may be harmless for expository purposes). Still, they are not scientifically acceptable as they stand. [...] Here I must say something briefly about the standard language that neuroscience has come to assume in the last fifty or so years (the subject deserves extended treatment). Even in sober neuroscience textbooks we are routinely told that bits of the brain “process information,” “send signals,” and “receive messages”—as if this were as uncontroversial as electrical and chemical processes occurring in the brain. We need to scrutinize such talk with care. Why exactly is it thought that the brain can be described in these ways? It is a collection of biological cells like any bodily organ, much like the liver or the heart, which are not apt to be described in informational terms. It can hardly be claimed that we have observed information transmission in the brain, as we have observed certain chemicals; this is a purely theoretical description of what is going on. So what is the basis for the theory?
sigaba_{September 12, 2013
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UB: Aren't you concerned that there's a bit of overgeneralization in this argument? Protocols and symbols are things people use, things that we push through communications networks and computers. I'm not sure it's warranted to apply our understanding of these terms to pheromones or kinases. We can talk about them as "signaling" or "messaging," and these metaphors are common, but aren't they just metaphors?sigaba_{September 12, 2013
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Larry, I am challenged on time as well. I will have to cut and paste:
When you see an apple hanging from a tree, light waves are converted by the specialized organization of your eyes into a neural pattern. That pattern is a mechanically transcribed representation of the image before you. It is information (form) recorded into a material medium. It will then be sent to your visual cortex where it will be translated into a functional effect via neural (material) protocols that are already established there. There is no inexorable relationship between the pattern of impulses traveling through the optical nerve and the cognitive effect of "Hey it’s an apple". In other words, there is no measurement you could take of that neural pattern and derive "apple". The relationship between the representation and its effect is physicochemically-arbitrary, requiring the protocol in the visual cortex and brain to establish that relationship.

If an ant colony should come under attack, the ants will produce an "alarm" pheromone to signal a coordinated response in the defense of their mound. The pheromone is a specific arrangement of matter which will evoke a functional effect within the ant's sensory system. But the defense of an ant colony is not derivable from the chemistry of a pheromone; the relationship between them is context specific, requiring the receptors in the ant's sensory system to recognize the individual pheromone and produce the response specified by that recognition. The proximate constraining factor on the system is not inexorable law alone, but the recognition of a specific arrangement in the signal medium, followed by a systematic protocol mapping that recognition to the effect it specifies.

Another example might be non-biological, such as an information processing system created by intelligence. For instance, the first automated fabric looms used an arrangement of holes punched into paper cards as a means to control the patterns in the fabrics being produced. The holes in the cards served as a physical representation of the desired effects in the fabric. Sensors and pins within the machine would sense where the holes were punched, and it would use that information to change and control the colors of threads being woven into the fabric. In this instance, the configuration of holes served as the representation, and the configuration of sensors served as the protocol, leading to specified effects in the fabric. These three things (the holes in the cards, the configuration of the sensors, and the resulting effects in the fabric) are three entirely separate things, sharing a relationship not derived from inexorable physical law, but established locally by the protocol within the system.
Upright BiPed_{September 12, 2013
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UPB @ 198, I have a few minutes before a 1:00 meeting, so I wanted to ask you about this:
When I refer to an “information based” effect, I am talking about an effect that is originated by the local translation of an arrangement of matter, where the effect produced is physicochemically arbitrary to the arrangement.
Can you please give some different examples of information-based effects in the sense you define above? This is related to my earlier request for a visual (illustrative example) in which your terms point to specific areas of the diagrammed system.LarTanner_{September 12, 2013
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Jerad:
If you want to come up with a better model then by all means do so.
Unguided evolution doesn't have a model.
Why do you think there is some undefined limit to evolution?
The evidence-> just look at Lenski's experiment with well over 50,000 generations and no new proteins. Obvioulsy it is very limited.
Your queries have been addressed if you could be bothered to look for the answers.
I have looked, Jerad. Your position has nothing but mental midgets supporting it.
The default, parsimonious assumption is that they are random until proven otherwise.
LoL! "We don't know" is the default, Jerad. And finally you have no idea what makes an organism what it is. That means you have no idea what it would take to make one.
I’d say unguided, natural processes. As is supported by several lines of data.
Then please present that evidence or admit that you are lying.Joe_{September 12, 2013
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Jerad: We are dealing with a toxic, ideologically charged situation with an overbearing orthodoxy that has imposed questionable a priori materialism on science and has resorted to tactics that have unjustly harmed a lot of people. We cannot by ourselves end that. But, we can be reasonable and ask for reasonable standards of scientific warrant and serious answers on empirical support for driving dynamics for pivotal points such as OOL and OO body plans. That means, showing empirically backed cause that FSCO/I is capable of coming from blind chance and mechanical necessity. Until and unless that happens, the empirical evidence is plain on billions of cases: FSCO/I comes from design. The needle in haystack search challenge analysis on solar system or observed cosmos scale backs that up, once we see that specific function resulting from multiple, correctly arranged and coupled parts leads to narrow zones in the space of possible configs. What is happening is that in the teeth of such, you have been insisting on sticking to party line by exerting a glaring inconsistency on warrant. For the party-line, promissory notes and/or just sos on why we cannot observe the dynamics are okay. For the challenger, you demand not just normal inductive inference but independent evidence on an unobservable deep past. In short, you are demanding a standard that you know is unlikely to be met on inductive reasoning. This inconsistency can properly be described as selective hyperskepticism, and beyond a certain point where there is a willful disregard for duties of care to accuracy, truth, materiality and fairness, one is guilty of speaking with disregard to truth, hoping to profit by that which is misleading being perceived as truth, or even indulging in a continued misrepresentation under the like disregard of duty. (And note, I am NOT asserting that you have crossed this second threshold; I am pointing out that it is there as a moral hazard in the situation.) You may find such an analysis harsh, but please look above. I call attention back to the focal issue, inductive warrant in light of inference to best, empirically grounded explanation, of FSCO/I especially codes, coded string structures, algorithms [which, being goal directed are strongly associated with action towards intent], and associated organised implementing machinery. The DNA --> mRNA --> Ribosome + tRNA etc --> AA cahain --> protein system is a capital example. It is time for a rethink without a priori materialist ideological blinkers. KFkairosfocus_{September 12, 2013
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edit: "...in order to constrain a system capable of producing an effect specified by that form".Upright BiPed_{September 11, 2013
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Larry,
This will be my last post … because I have professional and personal obligations that need my mindshare.
Believe me, I completely understand. I’ve read through your comments. There is only one thing to address at this time.
Perhaps the sticking point is “information-based.” So, let’s put this term aside for now and focus on the rest.
No can do. Everything turns on it. Like any physical thing we might choose to describe, these systems can be described mechanistically, but there is also an organizational description which is fundamental in accounting for the operation of the system. When I refer to an “information based” effect, I am talking about an effect that is originated by the local translation of an arrangement of matter, where the effect produced is physicochemically arbitrary to the arrangement. Let that sink in. This translation cannot occur without a relationship instantiated in the system. That relationship is a physical necessity, allowing the input of form to harness inexorable law in order to constrain a system capable of producing that form. If we remove the relationship, then we might as well be talking about oxygen reacting with iron to cause rust. Take care Larry.Upright BiPed_{September 11, 2013
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