A software engineer on convergent evolution

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September 7, 2013

Convergent evolution

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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

UBP, This will be my last post on the matter, not because we're resolving issues or flagging on interesting topics but simply because I have professional and personal obligations that need my mindshare. You say:
Biological systems are chemo-physical systems.
I agree. In fact, I have already said the same thing myself, but we also need to allow a certain distinction by saying that biological systems form a certain class of chemo-physical systems. All biological systems are chemo-physical, but not all chemo-physical systems are biological. So, again, we agree on this point. Now, I don't exactly understand your meaning with this next bit:
The issue here is that information recorded in the arrangement of a material medium, which is then translated into a material effect, has a physical fingerprint with real-world physical requirements.
You seem to be talking about a code (i.e., "information recorded in the arrangement of a material medium") that then gets translated/transformed into something else ("a material effect," which could be another substance or some work, I suppose). If so, at bottom what you are talking about is life; this translation/transformation is what life does. In other words, this is biochemical evolution, the systematic mechanism for translating matter to energy to different matter(s). The "physical fingerprint" of recorded information is the physical process, the work, of decoding. It takes work to convert something into something else. I must be misunderstanding your point, however, and this is the main reason you should consider using an illustrative example that lines up all of the different pieces of the semiotic system and allows people to see where exactly your terms are being applied across the semiotic process. If you already have an illustration that uses your terms, then I'm happy to take a look. Otherwise, I don't see how we are supposed to achieve clarity. Next, this:
If those physical requirements are not met, then there is no such thing as information-based anything. Whether we call it biochemical or just chemical doesn’t matter. So… you are simply wrong about this.
Wrong about what? I agree that information has physical requirements and also that translation/transcription has physical requirements. I do not think there are biological or chemical reactions without physical preconditions and consequences. The work of information transfer happens in a physical context. If it did not, we would have a very hard time looking back in cosmological time for example. How do you think we would learn anything about the early universe if the universe itself did not contain physical clues to what happened long ago? Then, this:
There are no pre-biological instances of “information-based chemical and physical organization” recorded anywhere in the physical record.
Perhaps the sticking point is "information-based." So, let's put this term aside for now and focus on the rest. Thus, what exactly is planet or a star if not an organization of chemicals conforming to physical laws in a physical reality? If a rock is made of a chemical, the rock also contains information. The information about the rock drawn out depends on what comes into contact with it. If a larger, rock smashes it, the arrangement of smaller rocks will conform to the nature of the impact and the circumstances of the environment. And if a rock is in motion, the character of that motion gives clues to some physical attributes of the rock. But when you say "information-based chemical and physical organization," you are not talking about a rock or a rock in motion; you are talking about a living thing. So my question to you is why there would be any "pre-biological instances of 'information-based chemical and physical organization'" when this organization actually is itself biological? Your reasoning seems circular, as if you were asking why there were no pre-human instances of rational animals.
We can, of course, equivocate on what information is, and we can force fit some alternate conception of “information” which will fundamentally differ from every instance of translated information we observe in nature – but to what end? It would inescapably have nothing whatsoever to do with the physical process of translating form from a medium into an effect.
Well, you were the one who asked -- out of the blue -- for my definition of information. The only definition you gave was one based on the etymology of the word, which isn't what you want, right? In any case, you haven't made it satisfactorily clear to me what the technical meaning of information is, so I cannot gauge what a standard or 'alternative' definition might be to you. You now tell me that the meaning of "information" is irrelevant. So it goes. Finally, this:
Physical reality exists? Sure. The process of translating form from the arrangement of a material medium exists as well. It has unique physical requirements found nowhere else in the physical world. Can it occur in the absence of the material conditions that make it possible?
I agree with everything here. Yes, life -- the process of translating form -- "has unique physical requirements found nowhere else in the physical world." Life cannot occur without specific material (pre)conditions. I suppose I should ask how any of this points to an ID.LarTanner_{September 11, 2013
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Jerad @181:
ncluding ‘possible’ was a poor choice of words on my part. ... I should not have included the word ‘possible’. I meant that all natural explanations should be exhausted before the assumption of some unobserved, unmeasured and undefined cause should be made.
lol. All natural explanations, now extended to included both the possible and the impossible.
ncluding ‘possible’ was a poor choice of words on my part. ... I should not have included the word ‘possible’.
Perhaps you had in mind some relevant natural explanations of the impossible, or some impossible natural explanations of the possible?Mung_{September 11, 2013
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Larry,
UB: That is the condition prior to the onset of information-based biological organization. Larry: But not prior to information-based chemical and physical organization.
Biological systems are chemo-physical systems. The issue here is that information recorded in the arrangement of a material medium, which is then translated into a material effect, has a physical fingerprint with real-world physical requirements. If those physical requirements are not met, then there is no such thing as information-based anything. Whether we call it biochemical or just chemical doesn’t matter. So… you are simply wrong about this. There are no pre-biological instances of “information-based chemical and physical organization” recorded anywhere in the physical record. Does material evidence matter? We can, of course, equivocate on what information is, and we can force fit some alternate conception of “information” which will fundamentally differ from every instance of translated information we observe in nature - but to what end? It would inescapably have nothing whatsoever to do with the physical process of translating form from a medium into an effect. We would then have two conceptions of information; one requiring translation via a physicochemically arbitrary relationship (universally observed throughout the living kingdom) and then another conception having absolutely nothing in common with the first. Do we then pretend among ourselves that these two entirely unrelated physical processes are the same thing?
The mechanisms of chemistry and physics are there, and they must be there co-extensive with the material state.
Physical reality exists? Sure. The process of translating form from the arrangement of a material medium exists as well. It has unique physical requirements found nowhere else in the physical world. Can it occur in the absence of the material conditions that make it possible?Upright BiPed_{September 11, 2013
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That is the condition prior to the onset of information-based biological organization.
But not prior to information-based chemical and physical organization. The mechanisms of chemistry and physics are there, and they must be there co-extensive with the material state. Of course, you anticipate the above:
You may then wish to suggest chemical evolution, however, there is nothing whatsoever (a massive understatement) in the literature about inanimate chemistry establishing relationships between disparate material objects and instantiating those relationships into a system consisting of two irreducibly complex arrangements of matter.
I think you are quite wrong here. Chemistry and physics seem to be pretty good at establishing all kinds of relationships between disparate objects. Such objects and phenomena include discrete planets and stars, atmospheres and weather patterns, starlight, spacetime, gravity, orbits, atomic elements. The objects, particles, and waves of the universe relate to one another often in very regular, predictable -- and dare I say, systematic -- ways. It seems to be that our fundamental disagreement concerns whether biochemistry is an extension of chemistry or a radical break from it. If the latter, there remains the question of whether such a departure can occur by the mechanisms already present in the universe or require some additional, outside force as a necessity. And I think at this point, we can go round and round the mulberry bush on metaphysical outlook and baseline conceptions of what is chemistry and what is biochemistry -- but we are now at the point where experimentation and observation must settle the questions.LarTanner_{September 11, 2013
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Larry,
I see what you are saying but it would seem that evolution is the mechanism, or chemical evolution, if you like. In the realm of biology, evolution establishes “physicochemically arbitrary relationships,” as you call them, and uses them to build and perpetuate life.
I am unsure you are grasping the full weight of the issue. 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. You may then wish to suggest chemical evolution, however, there is nothing whatsoever (a massive understatement) in the literature about inanimate chemistry establishing relationships between disparate material objects and instantiating those relationships into a system consisting of two irreducibly complex arrangements of matter. And yet, that is exactly what must happen in order for biological organization to occur. There is no alternative. The existence of recorded information, and its translation into material effects, have distinct physical requirements. They are both coherent and identifiable.Upright BiPed_{September 11, 2013
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Jerad:
I don’t think I am trying to prove a negative.
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’ll happily accept design if and when all [...] unguided, natural causes have been eliminated.
And then complaining that the only thing you are hearing is a negative argument.
All I hear is a negative argument from ignorance (natural processes aren't up to the job)…
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.
Do you think that because I won’t accede to your view I’m being unreasonable and biased?
No. I only think it is unreasonable to require a negative argument and then complain that all you are hearing is a negative argument.
Do you envision a conspiracy against ID promulgated by materialist zombies who have been brainwashed into supporting the party line?
Brainwashed zombies? No. I envision that any conspiracy against ID has nothing to do with either brainwashing or zombies.
Can it not be possible that someone disagrees with you without being a shill, a ideologue or an idiot?
Of course it is possible, though certainly not guaranteed. Still, I am very willing to give folks the benefit of the doubt. Have I said something to imply otherwise?
I’ve been called brain dead, a liar and a hyper-skeptic amongst other things on this very thread. Do you think those are fair statements?
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.Phinehas_{September 11, 2013
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Any scheme in origins science that claims a general basis but cannot provide empirical warrant for the powers of its claimed key mechanisms, is in serious trouble. And, if it is backed up by obvious ideological, worldview level question begging, that gets much more serious. Multiply by slanders, career busting and the like, and things are worse than just serious.
ID has no independent evidence that there was an intelligent designer around . . . when was it? And what did they do exactly. I have slandered no one. I have hampered no one's career. If you didn't mean to include me in your diatribe then I'd like that stated.
And that is the state of the evolutionary materialist orthodoxy in our day. It is high time for some serious rethinking.
Do you think it's possible to disagree with you and still be an intelligent, caring, non-hyperskeptic, non-biased person? You seem to label people based on their relationship to your view.Jerad_{September 11, 2013
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Have you noticed that the negative argument that you are decrying appears indistinguishable from the one that you are requiring in order to be moved off your current position? Again, it looks like you are (unconsciously?) protecting your position to an unreasonable degree. Why do you suppose you feel the need to protect it like this?
I don't think I am trying to prove a negative. I'm saying that be very, very, very sure that you cannot account for a phenomena with known existing causes before hypothesising a new one. It seems to me that ID is jumping the gun and claiming that natural causes can't do the job despite all the evidence that they can and before all explorations of their abilities are exhausted. Do you think that because I won't accede to your view I'm being unreasonable and biased? Do you envision a conspiracy against ID promulgated by materialist zombies who have been brainwashed into supporting the party line? Can it not be possible that someone disagrees with you without being a shill, a ideologue or an idiot? I've been called brain dead, a liar and a hyper-skeptic amongst other things on this very thread. Do you think those are fair statements?Jerad_{September 11, 2013
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jerad, Any scheme in origins science that claims a general basis but cannot provide empirical warrant for the powers of its claimed key mechanisms, is in serious trouble. And, if it is backed up by obvious ideological, worldview level question begging, that gets much more serious. Multiply by slanders, career busting and the like, and things are worse than just serious. And that is the state of the evolutionary materialist orthodoxy in our day. It is high time for some serious rethinking. KFkairosfocus_{September 11, 2013
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I see what you are saying but it would seem that evolution is the mechanism, or chemical evolution, if you like. In the realm of biology, evolution establishes "physicochemically arbitrary relationships," as you call them, and uses them to build and perpetuate life.LarTanner_{September 11, 2013
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...the conclusion of the argument presented in #109:
"[So] in order to translate any form of recorded information, the process fundamentally requires two arrangements of matter operating as an irreducible core within the system. And because Darwinian evolution requires the transfer and translation of recorded information in order to exist itself, it cannot be the source of this system. Given these observations, a mechanism capable of establishing this semiotic state is necessary prior to the onset of Darwinian evolution and information-based organization.
A mechanism capable of establishing physicochemically arbitrary relationships is required prior to the onset of Darwinian evolution and information-based biological organization.Upright BiPed_{September 11, 2013
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Yes, understood. Go on.LarTanner_{September 11, 2013
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Larry, Perhaps you just read to fast. I specifically state what sets the protocol in protein synthesis.
the relationship is established by the protein aaRS.
This isn't controversial.Upright BiPed_{September 11, 2013
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But UBP (#179):
The function of the protocol is to establish a physicochemically arbitrary relationship between the arrangement of the medium and the production of a physical effect. The establishment of a local relationship is fundamental to the operation of the system. It is required in order to allow the input of recorded information to constrain a deterministic system. Without the establishment of this relationship, the effect would have to be locally derivable from the arrangement of the medium (by inexorable law alone).
You have not here identified what it is that actually acts as the protocol and establishes the local relationship. I'm looking for you to make the identification.
During protein synthesis, the arrangement of DNA is transcribed into an arrangement of messenger RNA. That mRNA is then transported to the ribosome and used to order transfer RNA molecules in the sequence as originally prescribed by the DNA. That entire process is controlled by the purely deterministic forces of base pairing. But such forces cannot establish the required relationship within the system. Instead, the relationship is established by the protein aaRS. The aaRS charge the tRNA with their proper amino acids prior to the tRNA ever entering the ribosome. The establishment of the code (the relationship) is therefore realized in both temporal and spatial isolation from the medium, thereby establishing the physicochemically arbitrary relationship required for the system to function.
The above also does not identify what it is that actually implements the protocol and establishes the local relationship. But this is your semiotic theory; you should be able to make the identification readily. Try looking at it from the other end of the semiotic process: what is it that does (or allows) transcription of the arrangement of DNA into an arrangement of mRNA? Part of the issue is that many semiotic operations are in play simultaneously. For one thing, we are grafting our own sign encoding and decoding abilities onto what we see (or believe we see) happening at the gene level. For another thing, at the gene level, our use of semiotics-laden terms like "transcription" are accurate and helpful to a point. For a third thing, ultimately what's happening in the genes amounts to life using energy to make organized structures. Now, I don't disagree that what we're talking about is a semiotic system, yet not only life but the universe and everything in it seems to be semiotic, at least potentially. So, the semiotic argument, to the extent it works, doesn't make a case for an ultimate ID behind the secenes/signs: it provides a different way of seeing and understanding information gets trafficked in life and the universe. This was why I was curious about your response to my definition of information -- admittedly, I suspect it's too broad or inadequate a definition in some ways. As I see it, though, information necessarily inhabits a universe of things and things in motion. Does this make the semiotic system of life any less remarkable or awe-inspiring? I don't think so. All it does is put life along a continuum of different types of interactions, reactions, and relationships between entities and groups of entities in the universe.LarTanner_{September 11, 2013
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Jerad:
I should not have included the word ‘possible’. I meant that all natural explanations should be exhausted...

I’ll happily accept design if and when all [...] unguided, natural causes have been eliminated.

All I hear is a negative argument from ignorance (natural processes aren’t up to the job)...
Have you noticed that the negative argument that you are decrying appears indistinguishable from the one that you are requiring in order to be moved off your current position? Again, it looks like you are (unconsciously?) protecting your position to an unreasonable degree. Why do you suppose you feel the need to protect it like this?Phinehas_{September 11, 2013
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Look, any new, controversial idea that is severely different from the accepted paradigm is going to have massive amounts of opposition. You can see that in many scientific controversies of the last century. The successful ideas find evidence, define their proposals and do research no one else has done. Except for finding new gaps to point to in evolutionary theory ID has somewhat stagnated. Dr Dembski is seemingly no longer doing ID research. Dr Behe's ideas have been roundly dismissed. Dr Meyer does no research of his own. Dr Miller . . . I'm not sure what Dr Miller does but it's not research. Dr Gauger as well doesn't seem to do much original research. Dr Gonzalez had his moment in the sun and now . . . You can't just keep finding fault with evolutionary theory. Even if you manage to make some valid points you still haven't pushed ID forward. At best that will just point out places where more work needs to be done. That doesn't give you a designer. That doesn't prove ID. Many of you will have read Holy Blood, Holy Grail or are familiar with some of the claims therein via some other source like a Dan Brown novel. Do you buy those ideas? They're pretty . . . far out there. There's lot of speculation and maybes and could be's and . . . that's it. I'm guessing that most of you, like me, find the ideas interesting but unproven. Maybe all the evidence for the ideas has already been found. If so then they've got to remain speculation. (In fact several of the assumptions have already been punctured.) What about those who claim to have been abducted by aliens and 'tested'. Is there any hard evidence? Nope. IF someone can show me some physical evidence, preferably lots of physical evidence then I'll start paying attention. I'm not hyper-skeptic, I'm realistic. You have to have a very, very strong case to get me to give up ideas that have great explanatory power, are currently parsimonious and invoke no undefined and unproven causes. And the scientific community, which is actually very conservative, is going to smoke test any claims that don't match the current consensus. As it should. You don't throw out old ideas until you're damn sure the new ones are better. That just makes sense. It's a hard row to hoe but . . . that's the way it should be.Jerad_{September 11, 2013
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All possible unguided, natural causes? Could you please elucidate all possible unguided, natural causes for us so that we can understand exactly what it will take to falsify your position that only unguided, natural causes are responsible for all of life?
The currently understood laws of physics, chemistry, biology, etc. Including 'possible' was a poor choice of words on my part.
And if you cannot provide us with a list of all possible unguided, natural causes, will you concede that it would be unreasonable to expect us to provide what you cannot? And if it would be unreasonable to expect us to provide such a list, will you concede that it would be even more unreasonable to expect us to eliminate as a possibility that which cannot even be provided as a possibility? In other words, isn’t it abundantly clear at this point that you’ve protected your beliefs with an unreasonably high barrier? What then distinguishes such beliefs from dogma? And why do you think these beliefs need to be so well protected?
I should not have included the word 'possible'. I meant that all natural explanations should be exhausted before the assumption of some unobserved, unmeasured and undefined cause should be made. And, as in the example of relativity and quantum mechanics, when new laws or causes are hypothesised they need to be backed up with empirical data. In the last 100 years someone proposed that continents move! Absurd some said. Ridiculous!! How could that be? But evidence piled up and then the hypothesis became a theory. If you want your idea accepted then you have to find the evidence. Maybe there is/was an intelligent designer. It's possible. It's impossible to prove there wasn't. But, so far, there's not enough evidence to suggest there was/is. Get the evidence. Define what it does and what it doesn't do. Measure it, study it, give the scientific community something to work with. All I hear is a negative argument from ignorance (natural processes aren't up to the job) and a jump to an assumption (a designer did it) with no clear claim or specifics. You don't have to get it all right at first. But you have to present something that has some teeth and can explain the data. You can't just say: that's the way the designer wanted to do it without defining the designer somehow.Jerad_{September 11, 2013
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Cuz a scientifically illiterate Jerad sez so?
How else do expect to be taken seriously?
LoL! They haven’t found anything that demonstrates unguided processes can produce a multi-protein complex. IOW you are just a bluffing liar and a gullible sad-sack.
If you want to come up with a better model then by all means do so. Do you have such a model?
Strange that you cannot name once instance of micro-evolution that can exttrapolated into macro. Beak sizes do NOT explain the bird. Moth coloration does not explain the moth. Antibiotic resistance does not explain prokaryotes.
Why do you think there is some undefined limit to evolution? The evidence seems to suggest that you're wrong.
That is your opinion. However you can’t link to this alleged theory nor can you produce a testable hypothesis for unguisded evolution. So obviously you have no idea.
I'm not a evolutionary biologist. Your queries have been addressed if you could be bothered to look for the answers. But you think if I don't provide them for you your case has been proven.
You can’t even produce a testable hypothesus wrt unguided processes producing, say, a bacterial flagellum. Heck you can’t even determine if all mutations are random as you don’t have any methodology to do so.
The default, parsimonious assumption is that they are random until proven otherwise. You've got some work to do aside from being a merchant of doubt.
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.Jerad_{September 11, 2013
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Hello Larry,
Right, but if you classify what you call the “genetic system” as a semiotic system, then what specifically acts as the “material protocol”?
The function of the protocol is to establish a physicochemically arbitrary relationship between the arrangement of the medium and the production of a physical effect. The establishment of a local relationship is fundamental to the operation of the system. It is required in order to allow the input of recorded information to constrain a deterministic system. Without the establishment of this relationship, the effect would have to be locally derivable from the arrangement of the medium (by inexorable law alone). During protein synthesis, the arrangement of DNA is transcribed into an arrangement of messenger RNA. That mRNA is then transported to the ribosome and used to order transfer RNA molecules in the sequence as originally prescribed by the DNA. That entire process is controlled by the purely deterministic forces of base pairing. But such forces cannot establish the required relationship within the system. Instead, the relationship is established by the protein aaRS. The aaRS charge the tRNA with their proper amino acids prior to the tRNA ever entering the ribosome. The establishment of the code (the relationship) is therefore realized in both temporal and spatial isolation from the medium, thereby establishing the physicochemically arbitrary relationship required for the system to function.Upright BiPed_{September 11, 2013
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You are unable to provide a single of blind chance and mechanical necessity producing any example of FSCO/I in our observation.
How about the development of life on earth? :-)
It seems to me that you find yourself advocating for a mechanism not shown to have the required capability to create FSCO/I on an empirically plausible basis, in the teeth of one that has abundant such evidence, and to do so, you complain of demanding more than is deliverable while projecting a demand that amounts to a turnabout attempt, demanding what science does not normally address, logical impossibility.
'Not shown' only if you are denying the theory of evolution.
The second law of thermodynamics is not at the logical impossibility level. In short, it looks like you are being selectively hyperskeptical, while projecting that inappropriately to those who are saying, if you claim blind chance and mechanical necessity are capable of creating FSCO/I including coding systems, codes in string data structures, algorithms and associated co-ordinated, organised execution machinery, at least show us capacity to create FSCO/I.
It only looks like that to you because I disagree with you. You are so convinced by your own argument that you think people who don't see it the same way are deluded or idealistically motivated.
SETI is the clincher on this, as it seems that it is acceptable — to the point of expending cumulatively quite impressive taxpayer-funded sums across decades — to infer design on signs, save where the a priori commitment Johnson objected to is at stake.
Isn't the point that we don't know if there is 'anyone out there' and some people think it's reasonable to look? I don't mind you looking for a designer. The search might be scientific. But claiming there is one is not until you find the evidence. And inferring design means you are inferring a designer.
Here, you seem committed to the proposition that molecular scale coding systems, codes, algorithms and implementing machinery assembled themselves out of molecular chaos, by chance and necessity. That is a very strong claim or implication, and it is reasonable to expect that you will show empirical warrant of such capacity.
OR I just use the scientific method and I adopt a model which is the most parsimonious. All scientific knowledge is provisional. Someday you might prove that your intelligent designer exists. Good luck. You've got a lot of work to do. But until then I'll stick with a theory that has gotten stronger and stronger over the last century and a half.
You are free to hold a materialist ideologically driven view on origins, but you have no right to then dress it up in a lab coat and demand a monopoly on science or science education.
Except it's not idealogical. You say so because you can't imagine how anyone could disagree with you.
We know per massive observation that chance [whatever gives rise to random distributions etc], necessity and intelligence exist as empirically warranted causal factors. They have characteristic signs, and these are distinct. So, we may infer freely from circumstantial evidence of causal factor to its empitically warranted, inductively grounded source.
Human intelligence. Anything beyond that? Many people would argue with you that DNA shows the characteristic signs of human intelligence. There's junk, there's broken bits, there's repeated segments. it's a mess.
Which of the above Nobel prizes demonstrates the capacity of blind chance and mechanical necessity to generate FSCO/I in particular codes, code systems (a linguistic phenomenon), coded data structures beyond 500 bits of functionally specific info stored integrated with algorithms and algorithm implementing machinery?
I admitted that I was just showing that lots and lots of recognised research was going on regarding fundamental biology. Part of the reason no one has been awarded prizes for studying mechanical necessity, blah, blah, blah is because very few people find it an interesting topic. The ID community pretend like it's a critical topic and then try and show that ID is not taken seriously because no one is working on their subject.
Have you considered the fine tuning implications of actually showing that the laws and circumstances of physics and chemistry have “life” based ob carbon chemistry in cells written into them?
You don't even know if the constants of the universe are tuneable.Jerad_{September 11, 2013
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Jerad:
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?
I was going to attempt to answer these questions, albeit admittedly from a layman's perspective, but then I read this remarkably candid admission:
I’ll happily accept design if and when all possible unguided, natural causes have been eliminated.
All possible unguided, natural causes? Could you please elucidate all possible unguided, natural causes for us so that we can understand exactly what it will take to falsify your position that only unguided, natural causes are responsible for all of life? And if you cannot provide us with a list of all possible unguided, natural causes, will you concede that it would be unreasonable to expect us to provide what you cannot? And if it would be unreasonable to expect us to provide such a list, will you concede that it would be even more unreasonable to expect us to eliminate as a possibility that which cannot even be provided as a possibility? In other words, isn't it abundantly clear at this point that you've protected your beliefs with an unreasonably high barrier? What then distinguishes such beliefs from dogma? And why do you think these beliefs need to be so well protected?Phinehas_{September 11, 2013
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UBP @ 155:
every semiotic system (including the genetic system) has a material protocol(s) to accomplish just that [i.e., decoding].
Right, but if you classify what you call the "genetic system" as a semiotic system, then what specifically acts as the "material protocol"? There is an answer, and I am not posing a trick or 'gotcha' question. But I think it is important to be able to say what's performing the decoding in the genetic system. I don't want to presume what your answer is or should be, so I'd like to know what you think on this. Also, you seemed to be driving me to something earlier when you asked me for a definition of information. Yet you did not comment on what I offered. Can you please do so now?LarTanner_{September 11, 2013
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Jerad:
I’ll happily accept design if and when all possible unguided, natural causes have been eliminated.
You can't even produce a testable hypothesus wrt unguided processes producing, say, a bacterial flagellum. Heck you can't even determine if all mutations are random as you don't have any methodology to do so. 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.Joe_{September 11, 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. sigaba:
I’m not sure there’s a difference between representing and becoming in this instance.
Then you do not belong in this discussion.
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.”
Umm the earth does become the bands. What do you think the bands are made of if not the earth? They don't just hover above the earth in the ocean.Joe_{September 11, 2013
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Jerad:
Evolutionary theory explains the data,
That is your opinion. However you can't link to this alleged theory nor can you produce a testable hypothesis for unguisded evolution. So obviously you have no idea.
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”
Nothing there that has anytrhing to do with unguided evolution. Jerad is either really ignorant or very dishonest.Joe_{September 11, 2013
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Yes design has been detected.
Well, better get busy trying to figure out when that happened then eh?
Cuz a scientifically illiterate Jerad sez so?
Well, what many, many, many intelligent, educated people who have worked decades in biology find to be evidence isn’t good enough for Joe.
LoL! They haven't found anything that demonstrates unguided processes can produce a multi-protein complex. IOW you are just a bluffing liar and a gullible sad-sack.
Body plans are derived from previous body plans by a step-by-step process of modification.
That is the bald assetion. However there isn't any evidence to support it. Also you make it sound as if Lamarkiam is the ruling paradigm.
Hey, if you’re okay with change then you must be okay with evolution!
So you are ignorant as to what is being debated. Cool.
What do you get if you cumulatively select hundreds, thousands, millions of years of small changes?
No one knows. However throwing father time at an issue is NOT science. But then again you have no idea what science is.
Why do you think there is some magical boundary beyond which such accumulations cannot step?
You seem to think there are magical mystery mutations that can do things when we aren't looking.
You seem to agree that we’ve observed ‘micro’ evolution. What do you think prevents ‘macro’ evolution from occurring?
Strange that you cannot name once instance of micro-evolution that can exttrapolated into macro. Beak sizes do NOT explain the bird. Moth coloration does not explain the moth. Antibiotic resistance does not explain prokaryotes.Joe_{September 11, 2013
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Jerad: Which of the above Nobel prizes demonstrates the capacity of blind chance and mechanical necessity to generate FSCO/I in particular codes, code systems (a linguistic phenomenon), coded data structures beyond 500 bits of functionally specific info stored integrated with algorithms and algorithm implementing machinery? The answer is obvious, none. In short, you are partly swi\tching topical focus [essentially any prize for molecular biology related topics] -- a red herring led away to a strawman, and you are partly elephant hurling by way of literature bluff -- implying a proof in a body of work where bno such actual proof is on the table. In short, you are showing, more and more, the lack of evidence. Worse, there is another side to the story. Have you considered the fine tuning implications of actually showing that the laws and circumstances of physics and chemistry have "life" based ob carbon chemistry in cells written into them? Don't forget, there is a whole other side to design theory. KFkairosfocus_{September 11, 2013
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Jerad: The design inference is both modest and well grounded. We know per massive observation that chance [whatever gives rise to random distributions etc], necessity and intelligence exist as empirically warranted causal factors. They have characteristic signs, and these are distinct. So, we may infer freely from circumstantial evidence of causal factor to its empitically warranted, inductively grounded source. That holds when we cannot explain why the world so often shows lawlike patterns like F = m*a, or why molecules follow particular statistical patterns, or quantum processes such as RA decay, or when we do not have separate evidence of a particular designer at work in a given case. KFkairosfocus_{September 11, 2013
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Jerad: something is wrong. Even posts in this thread provide cases of FSCO/I coming from design, it is that ubiquitous. You are unable to provide a single of blind chance and mechanical necessity producing any example of FSCO/I in our observation. Just one solid case would suffice. But after years of suggestions that have repeatedly failed, that is hopeless. For the same reasons why we will not observe a significant macro-scale "exception" to the second law of thermodynamics. You full well should know the difference between an abstract logical possibility of "anything" -- any config -- emerging by chance, and a reasonable empirical plausibility. The underlying application of inductive reasoning to traces of the unobservable past of origins, is just as straightforward: like causes like, and circumstantial evidence is in many cases just as decisive as eyewitness testimony. It seems to me that you find yourself advocating for a mechanism not shown to have the required capability to create FSCO/I on an empirically plausible basis, in the teeth of one that has abundant such evidence, and to do so, you complain of demanding more than is deliverable while projecting a demand that amounts to a turnabout attempt, demanding what science does not normally address, logical impossibility. The second law of thermodynamics is not at the logical impossibility level. In short, it looks like you are being selectively hyperskeptical, while projecting that inappropriately to those who are saying, if you claim blind chance and mechanical necessity are capable of creating FSCO/I including coding systems, codes in string data structures, algorithms and associated co-ordinated, organised execution machinery, at least show us capacity to create FSCO/I. You need to think again, on whether Lewontinian a priori materialism is driving your judgement and leading to a situation as described by Johnson:
For scientific materialists the materialism comes first; the science comes thereafter. [[Emphasis original] We might more accurately term them "materialists employing science." And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) "give the appearance of having been designed for a purpose." [Emphasis added] . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [[Emphasis added.] [[The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]
SETI is the clincher on this, as it seems that it is acceptable -- to the point of expending cumulatively quite impressive taxpayer-funded sums across decades -- to infer design on signs, save where the a priori commitment Johnson objected to is at stake. And indeed, as I already pointed out, we routinely do things like inferring to arson on signs, even in absence of other direct evidence of an arsonist. Here, you seem committed to the proposition that molecular scale coding systems, codes, algorithms and implementing machinery assembled themselves out of molecular chaos, by chance and necessity. That is a very strong claim or implication, and it is reasonable to expect that you will show empirical warrant of such capacity. And, it is precisely why the first main point in the pro-darwinism essay challenge was to address this, A challenge that you ducked a year ago, and which no serious and cogent effort from your side has come forth since. (And BTW, you will notice that Wiki was stood in for an attempt and addressed, as was the talk origins 29 evidences claim. Both were found wanting, for cause.) You are free to hold a materialist ideologically driven view on origins, but you have no right to then dress it up in a lab coat and demand a monopoly on science or science education. KFkairosfocus_{September 11, 2013
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Saying, believing or wishing does not make things so.
Quite true. Are you sure your own position is not just wishful thinking? You have no proof that body plans exist on isolated islands of function. Are you sure design has been detected? Your metric is not verified by empirical application to borderline cases. Are you sure design was implemented? No one seems able to point to any case of when it happened. Casting doubt on evolutionary theory does not fill in the huge blank spaces in the design inference.Jerad_{September 10, 2013
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