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DLL Hell, Software Interdependencies, and Darwinian Evolution

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In our home we have six computers (distributed among me, my wife, and two daughters): two Macs, two Windows machines, and two Linux (Unix) machines. I’m the IT (Information Technology) or IS (Information Systems) guy in the household — whatever is is.

A chronic problem rears its ugly head on a regular basis when I attempt to update any of our computer systems: Software programs are often interdependent. DLLs are dynamic link libraries of executable code which are accessed by multiple programs, in order to save memory and disk space. But this interdependence can cause big problems. If the DLL is updated but the accessing program is not, all hell will break loose and the program will either severely malfunction or suffer an ignominious, catastrophic, instantaneous death. On the other hand, if the program is updated and the DLL is not, the same thing can happen.

I’m still trying to figure out how the circulatory avian lung evolved in a step-by-tiny-step fashion from the reptilian bellows lung, without encountering DLL hell, and how the hypothesized intermediates did not die of asphyxia at the moment of birth (or hatching), without the chance to reproduce.

Of course, we all know that this kind of challenge — no matter how obvious or compelling — presents no problem for the D-Fundies (Darwinian Fundamentalists), who are true believers in the clearly impossible, based on materialistic assumptions in which design could not possibly have played a role.

Comments
Hi Paul, I'm going to be addressing Behe's book (which I own and have read, btw) in stages.
It looks like we agree that there is an edge beyond which evolution cannot reasonably be expected to go (I suspect that we agree that the edge moves with time, and varies somewhat depending on the environment).
Actually, it varies a lot depending on both the environment and amount of variation and potential variation possessed by the population in question. It is therefore highly contextual.
That means that the underlying premise behind Behe’s attempt to find an edge is valid; there is an edge somewhere.
I think it is far more fruitful to look for an ‘edge’, if you want to call it that (though I think everyone here knows what is really meant by ‘edge’ is ‘limit’) on a case by case basis.
You seem to strongly disagree with Behe’s attempt to find an edge. For reasons we discussed, it can’t be that an edge doesn’t exist.
For reasons we have discussed, it is clear that any limits are dependent on a lot of variables.For instance, how much variation does the population possess at the outset? What is the mutation rate? How much variation is generated by recombination? What is the strength of selection for the adaptive problem at hand? Is the adaptive value of the genotype in question constant or variable? And that is just for one population. If one were trying to establish some general limit, given the large number of variables, then it seems reasonable to examine limits over a wide variety of taxa,environments,and adaptive problems. That, unfortunately, is not what Behe has done.
with what in his strategy and/or tactics do you disagree? I’m not necessarily trying to defend him (although, if it seems to me that he is right on a point, I will), but primarily trying to understand why you think his procedure is “arbitrary and pointless . One point that, IMO, needs to be considered is that the limit that Behe sees is not primarily a problem with natural selection. It is a problem of how fast mutations can create the genetic code for a given structure if there is no natural selection for the intermediate steps, or if the intermediate steps are selected against. In other words, the problem limiting the speed of evolution is not so much what mutations can do assisted at each step by natural selection, as what it can do without the assistance of natural selection.
Behe is looking only at the limits on multiple mutations occurring simultaneously to solve a particular adaptive problem. We know this because the example from which he derives his limit is one of an extremely harsh selective regime. Under the selective pressure of chloroquine, the only way an organism can adapt is for both required mutations to occur at once: any organisms that possess only one of them are eliminated. The adaptation cannot, therefore, occur in steps. So, can we derive any general principles about evolution from Behe's example? Well, the most pertinent question is, are most selective regimes in nature as harsh as this? Do most of the adaptive problems in nature require multiple specific mutations to occur simultaneously in one step? If the answer is “no”, then all Behe has done is find a limit for a very small subset of the kinds of adaptive problems organisms face. Literature on the strength of natural selection in the wild tells us that the strength of selection can vary widely, with very harsh regimes such as chloroquine being on the extreme end of the distribution. So Behe's limit is inapplicable to most situations in nature. That would rule it out as some metric by which to judge evolution in general, in my opinion. I'll comment later on other aspects of Behe's book.Dave Wisker
June 27, 2009
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Hi Paul, Just a note to say I haven't forgotten our discussion, just haven't had time to work on it. Probably this weekend.Dave Wisker
June 25, 2009
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Dave (#249, #251), It looks like we agree that there is an edge beyond which evolution cannot reasonably be expected to go (I suspect that we agree that the edge moves with time, and varies somewhat depending on the environment). That means that the underlying premise behind Behe's attempt to find an edge is valid; there is an edge somewhere. You seem to strongly disagree with Behe's attempt to find an edge. For reasons we discussed, it can't be that an edge doesn't exist. So with what in his strategy and/or tactics do you disagree? I'm not necessarily trying to defend him (although, if it seems to me that he is right on a point, I will), but primarily trying to understand why you think his procedure is "arbitrary and pointless." One point that, IMO, needs to be considered is that the limit that Behe sees is not primarily a problem with natural selection. It is a problem of how fast mutations can create the genetic code for a given structure if there is no natural selection for the intermediate steps, or if the intermediate steps are selected against. In other words, the problem limiting the speed of evolution is not so much what mutations can do assisted at each step by natural selection, as what it can do without the assistance of natural selection. I can think of three reasonable ways to attack Behe's theory for where the edge of evolution is located. First is to show that his calculations are off given his premises. One is to show that his premises are faulty, for example by showing that there are no pathways that require long strings of non-selected or deleterious mutations. And one is to show that experimentally we can routinely exceed what he says is the edge, in terms of neutral or deleterious mutations. I gather that you are not particularly challenging the calculations themselves. So the challenge has to be to the premises, either theoretically or experimentally. It is important to note what is not a legitimate challenge. It is not legitimate to say that natural history demonstrates that evolution has progressed much faster than Behe's proposed edge, and that therefore he has to have made some mistake. That argument can only be made with the assumption that no design input happened at any stage, and that therefore earth history is a natural experiment demonstrating that Behe is wrong. That argument begs the question. The whole point of intelligent design is that we see in nature things that are inexplicable on the basis of natural law and chance and their various combinations alone, that are explicable if there is a designer. Evidence that experimental evolution is not as fast as natural history requires is evidence for some other kind of process, which could be directed intervention. The only way one can trump this evidence is to assume, on a theological basis, that either there cannot be a God, or that God would never act in nature except in accordance to laws which are impersonal and which we understand. Those are theological positions. (One must also assume that intelligent aliens are not an option. But while the ID position may not necessarily entail a pro-God position, the anti-ID position necessarily entails an anti-interventionist-God position.) I assume, since previously you have allowed for ID as a theoretical possibility, you are not prepared to give a challenge of the sort that "evolution has been demonstrated to work much faster in the fossil record than Behe's edge, so he must be wrong somehow." So do you have experimental evidence that he is wrong, or do you find that in multiple cases his premises are wrong, specifically with regard to the need for neutral or deleterious mutations in a given pathway, or do you live by faith that one or both of these will happen without having proof yet?Paul Giem
June 23, 2009
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Mr ScottAndrews, Yes, that is why i said i had Googled all those pictures. I was pretty confident I could get to Hiroshima on that basis. The pictures are analogy to the fossils we have been talking about. I have no evidence I can walk to the Moon, or even San Francisco. So I don't think I can. ;)Nakashima
June 22, 2009
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Mr. Nakashima: It's easy to follow that we can infer one possibility from a very similar possibility. But that's not what we're talking about. Rather than waste time on an elaborate analogy, a better comparison is this: If you can walk to Hiroshima, can you extrapolate that one could walk to any place where people have ever been, and beyond? I'm not saying it's a pointless hypothesis. But it's up in the air. It is nowhere near to being established.ScottAndrews
June 22, 2009
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Mr ScottAndrews, If I live in Tokyo, I can walk across my apartment, I can walk across town, I can walk to Mt Fuji. I can walk up Mt Fuji. I can walk to Hiroshima. I can Google hundreds of pictures of people walking between those places. So even if I haven't personally walked all the way to Fuji-san, I can extrapolate based on evidence that it is possible. If you want to have a fuller discussion of macro-evolution and speciation there are some good online resources, even books such as Levinton's Genetics, Paleontology, and Macroevolution, 2nd Edition.Nakashima
June 22, 2009
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After an unexpected and long delay, I have returned to answer a claim that was made earlier in this thread. To recap: I had made the comment that the genetic code was “physically inert”. Mr. Hunt chimed in with the familiar refrain that stereochemistry provided a reason to believe otherwise. He stated there “is a decided and demonstrable chemical basis for this code”. To which I replied that there was an overwhelming amount of information which “fundamentally dispute(s)” his claim, and also, that the “nature of the patterns within nucleic sequencing did not come about because it physically had to.” He then replied that “Nothing has to occur. But it is hard to make an evidence-based argument that the genetic code is entirely arbitrary and disconnected from the chemical properties of RNA.” I know the conversation has moved on, and I see that Paul Giem, KF, and others have responded to the issues, but I would like to reply anyway. Mr. Hunt, the bottom line of your position equates to the inevitability of life existing in an environment such as that provided by the Earth (which by the way, exists in a scientifically inexplicable Universe). You seem certain of this because you are just as certain that Life is a property of matter itself. Apparently Life is inevitable because (given enough time in the right environment) the matter that makes up living things will become functionally organized into living things by means of the containment and transfer of symbolic information (which is what we observe today). Your explanation will never vary from what can be explained by the properties of matter, along with the influence of chance. In other words, it would happen anyway. Your position is an unjustifiable abrogation of empirical evidence (as has been pointed out). In questions such as these, science and scientist have a public obligation to speak within respectfully modest boundaries as to what is actually known. Suggesting that stereochemistry supports the idea that Life is an inherent and inevitable chemical property of matter (acted upon by chance) is a suggestion that flies in the face of reason (and a mountain of contrary evidence). Such claims are based on prior assumptions which are ideologically motivated at their core. They are not a manifest part of the institution of (S)cience itself. The fact that (S)cience allows, and indeed perpetuates, such misleading public claims is an indictment of an institution that is ignoring its responsibilities in the same way it ignores the contrary evidence. Stereochemistry has absolutely nothing to do with the actual sequencing of the nucleic acids in DNA. Why? Because it provides no explaination along the linear axis of nucleic sequencing (where the information and organization is). But we need not dottle over science shucking its public responsibilities; we can just address your claim instead. You say “nothing has to occur”. I don’t wish to take any big issue with this statement; however it is completely and utterly wrong. The fact that things must occur is the bedrock foundation of empirical science. We rely on it. A dropped apple must fall to the ground on earth, starlight must bend around the sun, and Miller-Urey must create amino acids. To suggest anything different is to instantly remove our ability to know anything at all. You then say “it is hard to make an evidence-based argument that the genetic code is entirely arbitrary and disconnected from the chemical properties of RNA.” What I find interesting in this sentence is the choice of the words “entirely arbitrary”. No one is suggesting that the genetic code is somehow divorced from the physics that underlies its function in biology – no more than anyone is suggesting that the radial tires on your car are entirely arbitrary and disconnected from the chemical properties of rubber. Why should we make radial tires out of water, or light bulbs out of peat moss? What stereochemistry tells us is that the design (strongly inferred by the ignored but logical evidence of agency involvement) appropriately works with its constituent parts - however, that fact does not negate the evidence of agency involvement (no more than the properties of rubber lends doubt as to where radial tires come from). I am tickled to death that there are men and women who make it their concern to study stereochemistry and its associated studies, but the suggestion that the findings explain the source of the genetic algorithms and organization inherent in living systems is so far off the mark it does little more than illuminate how ideological assumptions can pollute the claims made by science.Upright BiPed
June 22, 2009
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Nakashima, I'm glad, because I couldn't be that precise. Macroevolution, as I understand it, means that all birds are descended from something that was not a bird. Or that the giraffe, with all its physiology enabling it to survive with a long neck, had as its ancestor a creature with neither the a long neck nor the giraffe's vascular system. Rather than harp on my own disbelief that microevolutionary changes add up to such distinctions over time, I'll just point out that extrapolation is only hypothetical. No one knows if lots of A gets us B.ScottAndrews
June 22, 2009
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Mr ScottAndrews, i'm not trying to begin a definitional red herring with this question, but what are you holding to as a definition of macro-evolution? Micro-evolution doesn't scale to macro-evolution in the sense that one day a jellyfish gives birth to a lobster. There is only speciation, happening further and further in the past. We've talked recently on several threads about speciation, whether from reporoductive isolation, or from small genetic changes leading to larger phenotypical changes.Nakashima
June 22, 2009
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Dave, Zing! You got me. That's a nice diversion from the question of how we know that microevolution scales to macroevolution. How does one test if A scales to B, when one has never seen B, and one isn't even sure what A is made of? That's why I derive amusement from paragraphs that describe how factor X and factor Y are likely to cause evolutionary effect Z, unless mitigated by circumstance Q. Someone reading them might think they are drawn from repeated observations. They would never guess that it's all speculation extrapolated from instances of microevolution. Your inference is so weak it can only loosely be called such.ScottAndrews
June 22, 2009
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Scott, An extrapolation is an inference.Dave Wisker
June 22, 2009
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Dave Wisker:
There is no good scientific reason to deny inferring that the capabilities for variation and forces rthat mold it occurred to organisms in the past.
What you are describing is not an inference, but an extrapolation. We all know that small things don't always scale. You can't build the Empire State Building out of Legos. You assume that microevolution scales, but how could you possibly know that? What is your test? Add that to the uncertainty over which mechanisms may or may not effect such changes and there's not much left to be hyperskeptical about. I respect everyone's right to put faith in whatever they wish.ScottAndrews
June 22, 2009
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Mr Nakashima, I liked it for the exact same reasons you did.Dave Wisker
June 22, 2009
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Mr Wisker, Did you really like Barlow's Ghosts of Evolution? I liked the exposition of the material on the megafauna and the relationship plants can have with animals to accomplish seed dispersal. Even the work on how modern animals introduced by humans (cattle and pigs) could substitute for extinct species. But a lot of the intervening material about ghosts seemed to go to far to be just literary affect. And it got boring.Nakashima
June 22, 2009
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Mr ScottAndrews, It’s entirely possible that the explanation is there and I’m just missing it. But when chance leads to extinction and species go out, why do multiple species of whales remain while any speciations from their transitional predecessors do not? I think this issue is developed nicely at the end of Gould's Wonderful Life. There he is treating it at the level of entire taxa, but the form of the argument is the same. I will try to catch up with the thread!Nakashima
June 22, 2009
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Scott, We have plenty of observed evidence from numerous taxa that even large morphological changes are possible by very few corresponding genetic changes. We have extensive evidence that landscape (i.e., ecological) and competive forces change the gentic structure of populations and, coupled with reproductive isolation, result in divergence and increased diversity. There is no good scientific reason to deny inferring that the capabilities for variation and forces rthat mold it occurred to organisms in the past. An educated inference is not a guess. And to deny that such an inference can be reasonably made suggest two things: 1) That the body of evidence we see in extant populations is anadequate to explain the diversity of life, and thus 2) Other mechanisms and forces were involved. You seem completely comfortable with 1) & 2), despite the fact that actual empirical evidence supporting either one is almost negligible. I think that more than qualifies selective hyperskepticism on your part.Dave Wisker
June 22, 2009
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Dave Wisker @254:
What strikes me more odd, is that one can observe all of these factors in extant populations, and somehow assume, just because we can’t observe the actual factors at work in the fossil populations, that they didn’t apply then.
There are no observations of macroevolution resulting from landscape changes or competition. So when you use such factors to explain past evolution, it's a guess. And to list those factors and then use expressions like "expected variation" is a bit ridiculous. Refusing to accept a guess as fact is not hyperskepticism.ScottAndrews
June 22, 2009
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Scott, What strikes me more odd, is that one can observe all of these factors in extant populations, and somehow assume, just because we can't observe the actual factors at work in the fossil populations, that they didn't apply then. Must we assume they had different genetics? That mutaions occurred any more or less different,y than they do today? That they didn't sexually reproduce? That they didn't have ancestors or leave descendants? That they didn't have to adapt to environmental changes? This is selective hyperskepticism, in my opinion.Dave Wisker
June 22, 2009
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Dave Wisker:
How much variation does the subject population possess? How much of a role does natural selection vs genetic drift take in influencing gene frequencies? What about landscape features, mating strategies, levels of intra-and inter species competition, geology, etc?
What strikes me as odd is that one reading such factors listed might conclude that their effect on major evolutionary changes had been observed and documented. In fact, when looking at fossils, we can only guess at what effect the landscape or competition may have had. There isn't any real observation that we could apply to any forward speculation.ScottAndrews
June 22, 2009
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Hi Scott, If the lack of specific information available precludes understanding the limitations of evolution, wouldn’t it also preclude understanding its capabilities? If we haven’t considered the variables, isn’t it also arbitrary and pointless to conclude what natural evolution can accomplish? Scott, we actually know quite a bit what evolution can and cannot accomplish (see my examples as just a small subset of what we do know). Coming to very general conclusions-- as in setting some overall limit, or declaring there is no limit at all-- is pointless and arbitrary if one has not considered the variables involved. Many topics of current evolutionary research (a simple browsing of some journals like Evolution or Molecular Ecology will show you) involve establishing just what limits evolution in populations. How much variation does the subject population possess? How much of a role does natural selection vs genetic drift take in influencing gene frequencies? What about landscape features, mating strategies, levels of intra-and inter species competition, geology, etc? On the other hand, we have a growing evidence base for the generation of variation, and how little genetic change can produce dramatic phenotypic change. We also see how much variation can be generated by mobile genetic elements (such as retrotransposons). Just browse a few issues of the journal Molecular Biology and Evolution for a tiny fraction of the work being done on that front. Or consider the variation that can occur in "promiscuous" proteins, that is, proteins with additional activity and functions that can absorb many mutations without affecting the primary function of the protein. Mutations affecting these promiscuous functions have been observed to generate novel functionality. The bottom line is, we are seeing more and more evidence for sources of variation. Additional sources of variation only increase the capabilities of evolution, in my view. Does it make the capabilities endless? No, I don't think so. But it certainly damages the arguments I've seen trying to establish a general limit.Dave Wisker
June 22, 2009
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Paul, To clarify a bit more, I my original point was that "establishing" a general limit is arbitrary and pointless, mainly because much of what limits a particular lineages is due to unique circumstances. We might be able to attempt establishing what we may or may not expect a particular lineage will be able to accomplish in terms of adaptations, and even come to some broad conclusions. For example, we might be able to predict the fate of an orchid pollinated only by a species of hawkmoth with an extremely long proboscis if the hawkmoth suddenly becomes extinct. If the range of variation in the width and length of the nectary isn't enough to attract and allow another insect or bird access, then the fate of the plant may very well follow the moth. There are some interesting examples of plant species today that may have depended on the Pleistocene megafauna to disperse their seed, and which now face an uncertain future since the extinction of those animals. An interesting popular book on the subject is The Ghosts of Evolution by Connie Barlow. Obviously, for these plants, the limits to what they can do are different from those plants who don't specialize. In addition, for plants who don't specialize, they present challenges to the different organisms that must compete for the fruit or nectar, adding even more variables to consider when establishing limits for them. The challenge to establishing a general limit are enormous, but maybe not insurmountable, given enough paleoecological, current ecological, and genetic research, and especially with a very broad base of data from many taxa. I don't see anybody even approaching that depth of research and analysis yet. And there is always the question, "how much is enough?", coupled with "what exactly does a 'general limit' tell us" To be honest, I don't know the ultimate answer to either one. But I'm pretty sure (for the above reasons) it will take far more than what I've seen presented by Behe.Dave Wisker
June 22, 2009
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Dave Wisker:
So, deriving a general limit when so many variables haven’t even been considered makes it arbitrary and pointless, though you may not realize it.
If the lack of specific information available precludes understanding the limitations of evolution, wouldn't it also preclude understanding its capabilities? If we haven't considered the variables, isn't it also arbitrary and pointless to conclude what natural evolution can accomplish?ScottAndrews
June 22, 2009
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Paul, Actually, my point was, determining this "edge of evolution" using Behe's criteria is arbitrary and pointless. I'm not saying a limit to what evolution can do does not exist. That one exists is intuitively obvious: the paths evolution takes in lineages is primarily determined by historical contingency, that is, the adaptive challenges and how they were solved in the past often limit what future changes in the lineages can be. Some can be irreversible: highly specialized coadaption, as we see in some plant species and their animal pollinators. So, deriving a general limit when so many variables haven't even been considered makes it arbitrary and pointless, though you may not realize it.
And the argument about environmental influence is a smokescreen. One can postulate all environments, or all reasonable environments, and find the maximum expected variation, and that would constitute the edge of evolution. We could be fooled into thinking that the edge is smaller than it is by failing to take the environment into account. But that does not demonstrate that the limit does not exist, or that attempting to find it is, ” in the end, a pointless arbitrary exercise.”
Again, jumping to a general conclusion without taking the time and effort to actually consider such vital variables is arbitrary and pointless.Dave Wisker
June 22, 2009
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Whoops! In #244, I should have referred to #231 rather than #237.Paul Giem
June 21, 2009
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Hi Dave, In #237 you clarify that you did mean beginning in the way with which I disagreed. It looks like this is another area where we disagree. I can live with that. In #238 you argue that there is no such thing as an edge to evolution. Perhaps you misunderstand. The argument is not so much that anything is off limits to evolution given enough time and enough organisms. Rather, the argument is that probabilistic resources make certain transformations for practical purposes impossible given time and population constraints. You actually agree with this, even though you may not recognize it. If you take a Petri dish with E. coli and put it under a hood, and come back the next morning and find a cockroach crawling in it, you do not hypothesize that the cockroach evolved from the E. coli overnight. You assume that it must have gotten in from the outside somehow. In fact, if you started with E. coli, and the next morning you have Serratia marcescens, you assume that someone switched plates. That is, you believe in an edge to evolution also. The disagreement is not over whether an edge exists. The disagreement is over what it is. And the argument about environmental influence is a smokescreen. One can postulate all environments, or all reasonable environments, and find the maximum expected variation, and that would constitute the edge of evolution. We could be fooled into thinking that the edge is smaller than it is by failing to take the environment into account. But that does not demonstrate that the limit does not exist, or that attempting to find it is, " in the end, a pointless arbitrary exercise." That way of arguing seems anti-scientific, of the same kind that ID adherents are accused of when they suggest that attempts to find a naturalistic origin of life may be ultimately fruitless. Only this time there may be more justification in the charge.Paul Giem
June 21, 2009
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Arthur Hunt (#233)
About my essays:
I looked at his essays. They seem a little short on documented detail.
I’m sorry. This unsupported assertion is just not true. My essays focus on a few interesting aspects of life, and my claims and conclusions are supported by reference to actual experimentation. (I’ll admit that one may have to follow a trail through several essays. But laziness is no reason to misrepresent things so.)
Okay, then I'll support my assertion. In particular, your comments on the protocell mention Nakashima, and didn't have any other references. And most of the assertions don't even claim that Nakashima supported them. I think that qualifies as "a little short on documented detail." Now, if I had said "undocumentable detail", or "false detail", you might have had reason to complain. You may or may not be able to support your claims from the literature, and it would be unfair of me to claim that you could not without knowing all of the literature. But when I read that particular work, I could have done just as well, and possibly better, simply by reading Nakashima, as your synthesis as presented looks like Nakashima warmed over. In that case, why not simply link to Nakashima rather than your own essay, other than self-aggrandizement? This scorn for others, the "look it up yourself and I'm not telling you where I found it, and if you object you're just lazy" attitude, is not calculated to actually persuade those who may disagree with you at present but are open. It would be much more helpful if you were clearer about what authority stands behind your statements. This gets into the philosophy of science. Science usually claims that there is no pope, or college of cardinals, who can discover scientific truth infallibly, and that the only true authorities are experience, including controlled experience, otherwise known as experiments, and logical inferences from the data produced by those experiences. Neither one of these sources are in principle reducible to personal authority. This is in contrast to a political authority, where what the king, or the president, or the judge, says, or the Congress votes, goes, and the less challengeable the decision is, the greater the political authority. There are authorities in science. But they are authorities precisely because, and to the extent that, they transmit data accurately and their logic is transparent. Anyone who claims authority in science because "I have studied the situation carefully and I say . . ." is abusing his or her authority. That means that if you want to be truly a scientific authority, and have us take your essays seriously, you will be clear on where you got your data (unless they are commonly known, in which case if someone does not know them you can still show where they came from), and your argumentation will be clear as to how you are using the data and the legitimacy of your inferences. Outside of this kind of support, nothing you say (or I or anyone else says) has any kind of legitimate authority. That means that having to follow a trail through several essays, especially unmarked essays, to understand your support is a defect, not an excuse to blame others for laziness. Be careful here, or this could turn out to be projection on your part.Paul Giem
June 21, 2009
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Arthur Hunt (#232),
Um, the “toddler test” was something that Mike Gene introduced me to. If you don’t like it that this ID tool actually takes one places where one is predetermined never to tread, blame him. Not me, nor our schools.
I gave reasons why your particular "toddler test" was invalid. You fail to challenge any of those reasons, instead resorting to the claim that Mike Gene uses "toddler tests", and therefore so can you. If you don't want to defend against my specific line of reasoning, then at least explain why Mike Gene's use of the "toddler test" was valid, and why your use paralleled his closely enough so that it is reasonable to consider yours as valid as well.Paul Giem
June 21, 2009
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Arthur Hunt (#237),
Fox’s protocells “are able to impose their particular brand of complexity on the relatively simple raw materials they intake”.
Your comment completely misses the point of my comment, and is arguable incorrect as well. First, protocells do not have a brand of complexity. It could be argued that they have an organization, as they form into rough spheres. It could be argued that they have complexity, as the proteinoids (they are not really proteins, for several reasons) do have multiple parts that are not strictly repeating as the parts of crystals or certain forms of nylon are. But the irrregularly recurring repeats have no overall pattern to which they conform, and thus the proteinoidss, and the protocells, do not have a particular brand of complexity. Not having a particular brand of complexity, they cannot impose it on anything. Furthermore, the "raw materials they intake" are not relatively simple. They consist of multiple amino acids linked by peptide and other bonds, and may be hundreds of mers long, with side branching. The protocells simply take these complexes and aggregate them into spheres, with little or no modification. If you wanted to argue that this is a possible first step toward life (not counting the creation, purification, and polymerization of the amino acids themselves), then I might be able to buy it. But arguing that this is a close parallel to what is done by life is a particularly poor example of argument from analogy.
Not that the debate about what is really living is all of what my argument is about. There seems to be a tenuous agreement that the properties I list, that protocells are observed to possess, are also characteristics seen in living cells. What this means is that a DNA code (or whatever “information” the ID proponent wishes to invoke) is quite unnecessary when it comes to the origination and maintenance of these characteristics.
Nobody is arguing that "these characteristics" require DNA, or information, or organization. The question is whether DNA, or information, or organization, are necessary for life. You haven't answered that yet.
Control is an inherent property of chemistry. For example (one quite apart from all that has been discussed in this thread - it’s just a simple illustration), consider a 4-step series of irreversible first order chemical reactions that leads from A to B to C to D to E. It turns out that, no matter how you change the rate constants of the second and third reactions, you don’t change the overall flux thru the pathway at the steady state. That’s quite exquisite control, a simple and strong robustness that we don’t see in engineered systems.
You are using "control" in a way that is novel to me. Control means that some entity, usually the organism itself, decides that (or is programmed to act so that) a process happens in a way, in particular at a rate, that is advantageous for the organism. The lack of change in the rate of formation of the end product is the precise opposite of control. I'm also having trouble understanding your series of "irreversible" reactions. Most reactions are reversible, and most effectively irreversible reactions are degradative, and the ones that are not are almost always catalyzed by enzymes. Whether enzymes are engineered is precisely what is in question. One cannot use them in contrast to engineered systems without begging the question. Perhaps you can give me a specific example of this A to B to C to D to E system so what you mean can be understood better.
There’s no reason to claim that prebiotic chemistry was without control. We’re talking chemistry, not primitive engineering.
From an ID point, I agree. What I don't understand is how you can claim that from a non-ID standpoint. Who or what controlled, and how?
And that is why it is difficult, and may be impossible, for RNA to be the control molecule. One needs a way of clearly differentiating the backup from the working copy.
Why? RNA viruses do this just fine.
Yes, one can use RNA to perform both functions, as long as the need for backup is limited. When one can obtain complex preformed "raw materials" from a cell, such as ribozymes to translate proteins, T-RNA's, aminoacyl transferases, metabolic intermediates, and all the free ATP one wants, one can use a stripped-down version of information and code it all in RNA which will serve both as the information storage device and the working copy. But when one cannot depend on another cell to produce such things, and the first cell could not, then the problem of preserving information while using it becomes much more complex. Presumably this is why we have not yet discovered cells whose information storage function is performed by RNA. The statement that RNA can do this perfectly well is at present a faith statement against the weight of evidence. If that's your faith, fine. Just so we're clear on it.
Life is about RNA, ribosomal RNA to be specific. This is the central player in the cell - the bulk of the RNA is rRNA, most of the rest “services” rRNA, and the majority of cellular metabolism is geared towards rRNA function. . . .
That's a rather parochial attitude. One could just as easily say, "life is about enzymes. RNA is little more than the way the cell produces enzymes." Or, "life is just about DNA. RNA and enzymes are there simply to protect, reproduce, and service DNA." In fact, I think I recall someone talking about selfish DNA. Dawkins or something like that. Life is really a whole coordinated package where all the pieces play their part in a master plan.
I think I told Paul Nelson this fictional anecdote - if a very advanced alien species did a quick fly-by analysis of life on Earth, their conclusion would run along the lines of “well, rRNA sure has found a lot of interesting ways to propagate itself on this planet”.
I am really impressed. You say that you told Paul Nelson a fictional anecdote? How much more authoritative can you get than that! I missed the significance of your last paragraph.Paul Giem
June 21, 2009
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Mr. Nakashima, It's entirely possible that the explanation is there and I'm just missing it. But when chance leads to extinction and species go out, why do multiple species of whales remain while any speciations from their transitional predecessors do not? Those predecessors must have been fit, as they remained long enough to produce the "mitochondrial whale." What line could be drawn that kills off everything on one side and permits the rest to continue? If it were an environmental anomaly, what explains the repetition of that pattern? The environment permits all sorts of creatures in the sea - why not the variations of those intermediates? Thanks for indulging my half-baked question.ScottAndrews
June 20, 2009
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Mr ScottAndrews, What you are describing is a statistical effect. As time goes on, chance leads to extinction, and species thin out. The same thing happens with individuals, families go extinct. That is why "mitochondrial Eve" is so close to the present, why so many of the bauplans of the Burgess Shale are not around, why so many of the original Dow Jones Industrials no longer exist. The pattern of radiation and extinction is seen over and over.Nakashima
June 20, 2009
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