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Author
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Topic: Common descent
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James A. Barham
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Member # 50
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posted 28. April 2002 12:38
NYWG:
I completely agree with your last remark about the analogy between the way that Newtonian mechanics was superseded by the quantum revolution and the way that the Darwinian viewpoint is now in the process of being superseded by a dynamical revolution in biology (or so I believe). I guess our positions are now very far apart, after all. I am probably guilty of some rhetorical overkill which led you to misunderstand me. In general, I think there are serious problems with semantic issues in this whole debate. But I guess that is inevitable whenever things are moving fast on any frontier of science.
Just two little clarifications: On Behe, I meant only to say that from my perspective it would be more sensible to interpret his work as I said---not as denying smooth evolutionary transitions, but as denying that the Darwinian mechanism, unguided by any sort of internal teleological principle, can EXPLAIN the transitions. I don't suppose that Behe himself would want to retreat that far, and I'm sorry if I seemed to be saying that I thought he himself would agree to my interpretation of his work. I doubt that, although of course he would have to speak for himself.
The other issue is speciation. When I say we don't understand it at the genetic level, I just mean that we don't understand how small genetic differences can translate into loss of ability to interbreed. The issue is that there seems to be no correlation between even gross morphological changes (the classic example is of course dogs) and ability to interbreed.
There seems to be some piece of the puzzle missing here (I mean, in addition to the problem of adaptation in general). My own favorite theory is Hugh E.H. Paterson's "recognition" idea (Evolution and the Recognition Concept of Species, Johns Hopkins UP, 1993), which seems to sit well with the general dyanmical approach I advocate. Namely, it is coordinated changes in higher-level physiological, immunological, and even cognitive (sensory) systems that create barriers to interbreeding. Of course, this is highly speculative, and even if it is right, the question remains, as with all adaptations, How is such coordination possible at the genetic level? Certainly not by "chance." And "selection" doesn't solve the problem, it merely labels it.
The real problem, from my perspective, is explaining how the myriad microprocesses in the cell cohere into functional order in the first place. Once we understand the synchronic coherence of the cell, I suspect that the nature of diachronic change will be a relatively easy problem.
I like to draw the analogy between chemistry and astrophysics, on the one hand, and physiology and evolution, on the other. We could hardly explain how gold, say, was created through the process of stellar nucleosynthesis until we first understood how matter itself worked at the quantum mechanical level. Of course, we could always say that each heavier element in the periodic table was "selected" inside the star, and that each "selection" supplied the basis for the next-higher level. That would be a Darwinian model of the "evolution" of the chemical elements, and it is not wrong so far as it goes. It just does not go very far.
I think (or maybe "hope" is a better word) that we are on the verge of developing a real physical understanding of the functional processes in the cell. If and when we do, then the mystery of evolutionary transitions between dynamically stable states of functional systems will hopefully be cleared up, but not before.
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New York Wiseguy
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Member # 210
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posted 29. April 2002 05:55
To James A. Barham:
You said:
"I guess our positions are now very far apart...."
Was that a rather extremely misleading typo? I hope "now" should have been "not", because that is the way I am seeing it now.
Especially after seeing, in the "chance" topic you opened, this:
"I have become convinced that a physical approach is the only one that makes sense."
"...serious problems with semantic issues..."
Here too, our hearts beat as one.
"I don't suppose that Behe himself would want to retreat that far..."
No, I believe you have not unfairly paraphrased him, and he would in fact agree. Although, in agreeing, he would certainly follow up with a speech elaborating on his views. I can cite a statement from Behe which I regard as very significant, in response to a comment by Kenneth Miller. Miller, and this is partly a paraphrase, suggested that quantum mechanics suggests the possibility that God could operate on the world at (paraphrasing) the photon level in such a way that His influence would be "scientifically undetectable to us". Meaning, of course, that no miracles occur and, ultimately, that all evolution is a "natural" process as far as methodological naturalism will permit us to observe it. Behe indicated his agreement with Miller on this point several months ago, and as recently as April 23 in a panel discussion in New York he reiterated this and even showed a slide quoting Miller during his presentation.
"The other issue is speciation.....we don't understand how small genetic differences can translate into loss of ability to interbreed."
I still do not understand why this is considered such a mystery. But also, I wonder if the Harrington paper you cited on the "chance" topic is addressing the question from a viewpoint that I will now try to state simplistically. Whether two forms can interbreed depends not on their morphology (except insofar as mechanical problems might pertain, as in the case of dogs of much different size), but on the design of their DNA. The mechanics of interbreeding is a strand of RNA from each parent joining to form a new DNA. If the two parents' RNAs do not share a sufficiently common pattern, they cannot unite to form a functional DNA. Except for the problem of scale, it should be logically possible to examine drawings of two RNAs and to make a judgment as to what will be the consequence of their attempting to join as a DNA. Is that, in the final analysis, the same question that Harrington is asking?
With respect to interbreeding in dogs, I wonder if anyone has ever attempted to crossbreed a Chihuahua with a St. Bernard by artificial insemination. IF it has been tried, I hope they used a St. Bernard as the female.
I like your analogy between astrophysics and evolution. However:
".....on the verge of developing a real physical understanding of the functional processes in the cell...."
You're better qualified than I am to say "on the verge", but my gut feeling that there is still a long, long way to go. That only the surface is now being scratched. But, in contrast to my general leaning that the origin of life might be a problem that is inherently inaccessible to the human mind, I do not have the same feeling about knowledge of cell processes, and have a confidence that biologists are going to "get there" eventually.
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James A. Barham
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posted 29. April 2002 08:24
NYWG:
Oops! Sorry about that typo. Yes, I did indeed mean to type "not," not "now." (I don't know why I can't make myself proofread these postings more carefully before I hit the "post" button. I'll try to be more careful in future.)
I have to run right now, but I wanted to let you know that that was indeed a typo. I will try to address some of your other concerns this evening.
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James A. Barham
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posted 29. April 2002 15:09
NYWG:
After reading your last posting more carefully, I continue to think that our approaches are convergent, but there are still significant differences between us (which is as it should be).
I think the biggest difference is my relative optimism that we may already be able to see the way forward to a robust physics of functionality via condensed matter physics (i.e., the approach taken by Robert Laughlin, Giuseppe Vitiello, and others), along with nonequilibrium thermodynamics. But since this is optimism is largely a matter of intuition or "faith" or temperament, I wouldn't want to push it too far.
On the speciation question, I have been reading some of Lynn Margulis's recent writings in the past few days, which have driven home to me the fact that speciation is a relatively specialized phenomenon---basically, restricted to multicellular organisms. The vast amount of adaptation already manifest in prokaryotic life has nothing whatever to do with speciation. So the more basic question is that of functional integration, and the ability for functionally integrated systems to undergo spontaneous rearrangements in such a way as to find a new dynamically stable state. If this were well understood at the prokaryotic level, then the special case of speciation in higher organisms would be clearer, presumably.
Basically, it seems to me that reproduction should be viewed as a specialization of the overall functional integration of the cell ("metabolism" in a loose sense), rather than as the defining characteristic of life. If that is so, then speciation is just a transition to a new dynamically stable state in the reproductive system, analogous to, say, acquisition of a new vision system or a new respiractory system. In short, the real problem is not speciation in particular, but adaptation in general. (I assume you will agree with this?)
There was one other point I wanted to touch on. You say that the origin of life may forever remain a mystery, but that the functional integration of the cell may soon be figured out. I see the two as very closely tied together. In one sense, we already know a hell of a lot about the functioning of the cell: we know thousands of details about the molecular structures and the biochemical interactions involved. In another sense, we know very little at the fundamental level (or so I believe), because we cannot explain how such a mind-bogglingly complex set of structures and processes can cohere together in space and be coordinated in time in order to achieve a particular goal---namely, the self-maintenance of the whole. It is this functional aspect that escapes us, and that selection theory and molecular biology both simply take for granted.
But if we really understood the massive coherence and coordination of the cell in a physical sense, I believe that ipso facto we would understand how life began, and would moreover be able to create life ourselves (assuming the conditions required are not too exotic). From what I'm hearing you say, I gather you would not want to go with me this far. But, in that case, what for you would constitute "understanding the cell"? That is, what do you believe is missing from our current understanding of biological functional coherence?
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Evan
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posted 30. April 2002 21:41
I have been reading this and other threads on related topics these past two weeks. At this point I want to add a few comments.
1) The conversation seems to inevitably percolate downwards to the origin of life, which, as I said two weeks ago, does not seem very relevant to the topic of common descent in the more recent past: for example, the question of whether there is a chain of ancestor relationships between humans living today and pre-hominids living five million years ago.
There seems to be a agreement that the idea of a single, solitary common ancestor is in doubt, but some of the arguments for that seem to imply, as NYWG pointed out, that perhaps life arising naturalistically is more likely than we might think, not less.
It has also been pointed out that the conditions under which life arose and expanded in the world of one-celled organisms were different in many ways from those that came later, and that once life started, those conditions could not be duplicated. Extensive genetic interactions among simpler organisms, the nature of early conditions on the earth, and the absence of higher life forms could have made the vast period of one-celled organisms one in which life intermingled in a hopelessly bushy tangle. In such a world, (as someone pointed out) the concept of common descent, much less species, might not be at all applicable.
However, these mechanisms and events that might have applied to the world of one-celled organisms just don’t seem to apply to large organisms such as us. None of these considerations, it seems to me, has any bearing on any alternative to there being a direct chain of common descent between humans and pre-humans (and for that matter back to the start of mammals.) In the absence of any other evidence, or reason to doubt common descent, I don’t see how the discussion on the origin of life bears on common descent as it applies to humans.
2) A topic that arises regularly in this discussion is the topic of “miracles.” This word is being used in two different ways. To say that the emergence of life was miraculous in the sense that it was an extremely unlikely occurrence is different than saying it was miraculous in that it happened by abrogating some aspect of the laws of nature. The first is a matter of probability - a fiddling with chance, as it were; but the second is a matter of fiddling with natural law, which is a different matter. It is one thing to fiddle with chance, which by definition is malleable and expressed as a probability, and another to fiddle with laws which would involves breaking what would otherwise be an inviolable move from one moment to the next.
It is this distinction that I invoked way back in the “Evolution and Design: A Synthesis” thread, and I got the distinction from Dembski.
Let me summarize from Dembski (from “ID Coming Clean.”)
quote:
For instance, what is “extra-natural assembly” (the term is Van Till’s)? It is not what is customarily meant by miracle or supernatural intervention.
Miracles typically connote a violation or suspension or overriding of natural laws. To attribute a miracle is to say that a natural cause was all set to make X happen, but instead Y happened. As I’ve argued throughout my work, design doesn’t require this sort of counterfactual substitution (cf. chapters 2 and 3 of my book Intelligent Design). When humans, for instance, act as intelligent agents, there is no reason to think that any natural law is broken. Likewise, should a designer, who for both Van Till and me is God, act to bring about a bacterial flagellum, there is no reason prima facie to suppose that this designer did not act consistently with natural laws.
If miracles don’t happen, then what does?
Dembski writes,
quote:
But how does an unembodied intelligence interact with natural objects and get them to exhibit specified complexity. ...
6. How Can an Unembodied Intelligence Interact with the Natural World?
In a series of paragraphs too long to quote here (see Articles by Dembski at www.discovery.org/crsc/fellows/WilliamDembski/index.html), Dembski explains that a reasonable hypothesis (and the one I am adopting) is that the designer manipulates probabilities (chance events.) The key idea is that we don’t live in a completely mechanistically determined universe - truly random events happen. Therefore, probabilities exist at some fundamental level, and those probabilities can be manipulated by the designer to cause events to go in a certain way that might be statistically improbable enough to create specified complexity without having anything “miraculous” happen in the sense of breaking any natural law.
We might, in a colloquial way, call such an improbable event “a miracle,” but that would be an improper use of the word in this context. Dembski has already defined complexity to be synonymous with very small probability (less than 10^-150), but he specifically claims that such highly improbable events do not come about by miracles.
3) Now how do these two ideas - common descent and miracles - tie together.
Well, it seems to me that in the beginning, at the origin of life, all the interactions are such that manipulating quantum probabilities can be quite effective, because the designer is basically working at the biochemical level. However, as organisms become not only multi-cellular but in fact as complex and large as a human, the ability of the designer to work with the organism as a whole becomes vastly less possible because small quantum fluctuations at the microcosmic level are overwhelmed by the macrocosmic size and integrity of the organism as a whole.
Hence the designer (maybe as far back as the emergence of sexual reproduction) now works through the reproductive system, because at the cellular, biochemical level of the genome the power of manipulating probabilities is still as viable as it was throughout the whole world when one-celled organisms were all that existed.
The conclusion I reach then, is that common descent is in fact a vital and central aspect of the vehicle by which the designer accomplishes his purposes. The designer does not miraculously create new creatures at any time, but rather builds them from successive modifications of old ones. The methods he uses have been the same since the beginning of time - the manipulation of chance (but not law) at the level where quantum events can be effective; but as time has progressed, he has shifted the locus of such manipulations from a vast world of one-celled organisms (hence the bushy nature of the bottom of the tree of life) to the reproductive nature of sexual organisms (hence the branch and twig nature of the rest of the tree of life.)
[ 30 April 2002, 21:42: Message edited by: Evan ]
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James A. Barham
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posted 01. May 2002 07:57
Evan:
Your point about the difference between the violation of a law and the occurrence of an event with very small probability is well-taken---except that there are cases where the probability is so small that we cannot help but feel that the occurrence of such an event would amount to a suspension of the "laws of nature" in the sense of the way the universe works in general. (And what are the "laws of nature," after all, except our effort to codify the way things seem to work?) So, I don't think the distinction you make is absolute; it is more a matter of degree.
If that is so, then everything turns on defining the threshold beyond which a merely improbable event becomes effectively impossible. Intuitively, it is not really a problem. According to statistical mechanics, there is no reason why all the water molecules in the Red Sea might not accidentally move in a seemingly coordinated way in opposite directions from a given point. That would not violate any known law of nature in your sense---it is merely extremely improbable. But I think it is safe to say that if we actually witnessed the Red Sea parting (in the absence of a tsunami or some other natural explanation), then we would all rightly say we had witnessed a miracle.
Walter Elsasser has written most illuminatingly on this subject (Reflections on a Theory of Organisms, Johns Hopkins UP, 1998). He does some math and comes up with what he calls an "immense" number, which is defined in relation to the number of quarks in the universe and the number of nanoseconds since the Big Bang, or something like that. By this definition, the parting of the Red Sea and the spontaneous self-assembly of a protein molecule by pure chance, with no lawlike guidance, are both "immense." (I probably have some of the details wrong, but you get the idea.)
[ 01 May 2002, 08:01: Message edited by: James A. Barham ]
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New York Wiseguy
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posted 01. May 2002 23:11
To James A. Barham:
'....we may already be able to see the way forward to a robust physics of functionality via condensed matter physics...."-----
"Condensed matter physics" wasn't very familiar to me, so I just did some research. I see that Laughlin is a physicist Nobel prize winner, from work in the quantum-related work within the realm of Physics, and Vitiello works on application of quantum concepts to the brain. I guess it still escapes me how this becomes related to the more general problems in biology, such as explaining cell functions.
"nothing whatever to do with speciation"----
Knowing, James, that you are sensitive to questions of semantics, I should ask if we mutually are proceeding from a common definition of "speciation". As I have been using the term, it would be inapplicable not only to unicellular life, but also to asexual multicellular life forms, such as some lizards, small fish, etc. Although the term species is probably applied to these asexual forms, since, obviously, an asexual lizard and an asexual fish would belong to not only different species, but different classes as well. But I have been using the word as applicable only to bisexual life, and to two related forms which have diverged to the point where interbreeding no longer can occur. My question is: Are Harrington and Margulis analyzing speciation of this type, or in some sort of broader sense?
"the real problem is not speciation in particular, but adaptation in general. (I assume you will agree with this?)"----
Yes, I would. I think we got onto the subject of speciation only because some ID proponents (although not necessarily all) regard speciation as belonging to the domain of macroevolution requiring intervention by an Intelligent Designer. I think all ID proponents accept adaptation which stops short of speciation as belonging to the domain of microevolution, whose causes are agreed to be completely "natural".
"But if we really understood the massive coherence and coordination of the cell in a physical sense, I believe that ipso facto we would understand how life began.." + "....what for you would constitute "understanding the cell"?......"-----
There are what I see as some separate and distincts gaps in knowledge. The first would be just what gaps there are in understanding all of the mechanisms which occur internally within the cell itself. The second would be the mechanisms by which the functionality of cells as units determines the morphology of the biological object. And to relate this to an important semantic question, I believe we need much more knowledge in both areas before we can say we are properly dealing with the concept of "biological information".
"...ipso facto we would understand how life began..."----
Here we definitely part company. To cite an example, the "poster child" of design theory is the bacterial flagellum. Its design and functionality is fully understood, and that knowledge has provided Michael Behe with his perhaps most effective argument for irreducible complexity. The point being that understanding all of this extremely complex detail does not tell us how it was created, and to the contrary can mystify us even more as to how all this wonderful complexity was ever created. Studies of comparative cell morphology across a wide variety of species can give us hints as to how the complexity might have developed (as has been done both for the flagellum and for blood clotting), but the ID proponents still can argue that there are too many large "gaps" and no "proof".
"...moreover be able to create life ourselves....."----
That strikes me as a far-out conjecture. It's very difficult for me to conceive any possible means for that. It would appear to require tools that would permit atom-by-atom assembly operations. My conjecture is that life could only have generated itself from non-living matter by processes which involved (as in the previous discussions with Paul Nelson) up to a thousand steps each taking a long, long time (measured in millions of years), and each requiring its own set of environmental conditions. But I'd also conjecture that given a planet in a solar system environment similar to ours, the odds of life so developing would be very good. Hence my feeling that "we are not alone in the universe".
Despite these thoughts, I do not by any means have a nihilistic attitude toward the goals of complexity and information theory, as I do believe that they can become an important element in expanding our knowledge of the history of life.
To Evan:
"percolate downwards to the origin of life..."..."...not seem very relevant to the topic of common descent in the more recent past..."
In full agreement, and I've been trying to keep these two issues separate and distinct from each other. As in the conversation I'd had with Paul Nelson, this relates to the concepts of polyphyly vs. monophyly, and whether polyphyly was more the rule in the earlier unicellular era of life's history, and monophyly has largely prevailed in more recent times, i.e. even as far back as the end of the Cambrian explosion, much less back to the origin of the human species.
Re the "miracle" discussion:
Dembski's suggestion that "the designer manipulates probabilities" reads directly on Kenneth Miller's concept that God can operate at the quantum level to produce effects which are "scientifically undectable to us". A same concept which I previously indicated was accepted by Behe. I've been told that Dembski very recently (the date was April 23, at a panel program at the American Museum of Natural History), in response to questioning, said that it was "possible" that the Designer injected all of the information into the structure of the universe which was required for life to develop at the time of the Big Bang. That would appear to me to be totally counter to any notion of a Designer who intervenes or has intervened in the history of life since its origin on Earth. And also, from a theological point of view, would appear to be closer to Deism than to Theism.
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James A. Barham
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posted 02. May 2002 19:37
NYWG:
Yes, I agree with your analysis of speciation, and also agree that it is not really the heart of the matter. If "natural genetic engineering" occurs, then I don't see the species boundary in higher animals as posing any special explanatory difficulty beyond that of explaining the natural genetic engineering in general.
As for my comment that an deeper physical understanding of the coherence and the coordination of the processes in the cell (i.e., of the immanent teleology manifest in the cell) probably constituting at the same time the key to the understanding of the origin of life and giving us the insight necessary to create life in the test tube: What I am saying is that, by hypothesis, in that case we would understand the physical principles underlying the coherence, so that it would not be necesary to assemble the cell or the flagellum or any of its other parts molecule by molecule. Somehow, these things must have self-assembled, and if we understood how they did, then I don't see why, at least in principle, we could not replicate the conditions necessary to make it happen artificially.
Perhaps you are right that there are too many steps involved for it to ever be practical to replicate the whole process in the laboratory. Not knowing what the process consists in, that is hard to say a priori, although a physical viewpoint would certainly lead one to predict a much shorter time scale than the Darwinian viewpoint. But if we could even see how the thing could get started, and replicate that much in the test tube, that would be a major breakthrough.
Besides, once we understand a thing, we can always find ways to speed up the natural process. For example, it takes I don't know how many millions of years to produce gold in stars, but we could do it much faster using linear accelerators, if we wished, since we do understand how the trick is accomplished.
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New York Wiseguy
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posted 03. May 2002 10:50
To James A. Barham
"I don't see the species boundary in higher animals as posing any special explanatory
difficulty"
Then, may I take it that the analysis done by Harrington and Margulis, in which they are discussing "speciation", we are assuming to be actually targeted at adapation in general?
"Somehow, these things must have self-assembled, and if we understood how they did, then I don't see why, at least in principle, we could not replicate the conditions necessary to make it happen artificially."
I'd agree, "in principle", the question being one of practicability, especially as regards the time-scales involved, which might not be so easily compressible, as you suggest with reference to such matters as transmutation into gold.
As a general comment, I have a definite feeling that we are here discussing what is and will continue to be the most exciting frontier of science, I daresay equally as exciting and dramatic as has been astrophysics and particle physics over the past century. And, further, I will add that design theory, despite its lack of direct acceptance in the scientific community in general, is making a substantive contribution to the advancement of that science by posing the challenging questions that it does.
I think you and I have probably reached something close to a consensus of our mutual attitudes here, and I am thinking I might shift my attention to another topic in which you have been engaging, that of complex's "What is Intelligence?".
Re this particular topic, there is some "unfinished business" in that Paul Nelson has not yet favored us with his analysis of polyphyly as applied to the "recent" stages of evolution among the higher animals.
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James A. Barham
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posted 03. May 2002 17:05
NYWG:
As far as I recall, Harrington et al. do not directly address any of these questions. I am placing a spin on the significance of their work on proteins that I doubt they have even thought about, much less would be prepared to agree with. But of course that is sheer speculation. I really don't know.
As for Margulis, her work is all over the map---from some very strong anti-neo-Darwinian statements to some more mainstream, irenic-sounding statements. I have the impression that she feels she is revolutionizing biology with her emphasis on the role of endosymbiosis in evolution; however, I am not sure that she would be prepared to enter into the "vitalist" sort of speculation that I am interested in. I rather suspect not. In short, I don't think she is directly addressing the foundational issues of physics and teleology that we are concerned with here. So I just don't know how she would react to your question (about speciation being a special case of adaptation in general). But as for me, yes, I would say that that is true.
I agree that we might as well wrap up this particular thread. We have wandered pretty far from the theme of common descent, anyway.
I am glad that we seem to have arrived at a sort of consensus view. That is a rare experience for me!
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London
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posted 06. January 2004 13:47
Is there any evidence that life evolved from non-life more than once on Earth?
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