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Author
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Topic: Testable ID hypothesis
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Berthajane Vandegrift
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Member # 272
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posted 25. September 2002 10:06
Eventually science will find a way to determine where adaptive change takes place - in the genome or the phenotype.
Is adaptive change a rational, intelligent, purposeful interaction between a biological system and its environment -- which eventually becomes encoded into the genome after a number generations of becoming a permanent part of the organism?
Or is adaptive change the result of a series of accidents in the genome -- DNA copying errors?
This is an testable ID hypothesis that science will eventually be able to answer.
Berthajane Vandegrift
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Frances
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Member # 169
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posted 25. September 2002 10:17
Berthajane,
Could you please explain why you consider this to be an ID hypothesis? Both seem to be natural that is regular or in Dembski terminology _chance_ hypotheses. Only through elimination of such hypotheses (and countless others) may one infer intelligent design.
It seems that you are confusing Intelligent design hypothesis with non-Darwinian mechanism but I do not believe that such a use of ID is supportable by reference to the available literature on ID inference.
Epigenetic inheritance is well known for instance as an additional mechanism.
Another example is the Baldwin effect which at first appears to be Lamarckian in nature but which in fact seems to be simply Darwinian.
See Myths
Adaptive mutations, once considered to be a goal driven process now seem to be nothing more than stationary phase hypermutations in cells.
[ 25. September 2002, 10:31: Message edited by: Frances ]
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Berthajane Vandegrift
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Member # 272
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posted 25. September 2002 13:49
Francis wrote: Could you please explain why you consider this to be an ID hypothesis? Both seem to be natural that is regular or in Dembski terminology _chance_ hypotheses. Only through elimination of such hypotheses (and countless others) may one infer intelligent design.
Bertvan: Hi Francis. No adaptive change has ever been documented as occurring in a genome before appearing in the phenotype. It is true that the genome can be damaged (by genetic engineers or other external assaults and accidents), but the theory that adaptive traits appear in the genome before appearing in the phenotype is an undocumented assumption. No "adaptive trait" has been observed appearing in a genome. On the other hand, we are all aware of how individual organisms change and interact in response to the environment during their lifetime and development. Individual organisms’ strive to adapt, teleologically, not "randomly". (Certainly not "random with regard to fitness".) An immune system, the entire complex biological system, strives to increase fitness. Life is more than automatic response to stimuli. Otherwise science could "create" living systems. Life, down to individual cells, possess a degree of intelligence - the ability to make fallible choices, based upon limited information - that science cannot duplicate.
Personally, I see no reason to regard the intelligence inherent in life as "supernatural". Science can neither measure nor predict any creative intelligence. (If creativity were predictable it wouldn’t be creative.) However, science can study the effects of intelligence (or volition) upon physical reality. Such studies include biofeedback and the placebo effect.
If intelligence is involved in the creation of life, life is "intelligently designed". While I view the teleology of life as a natural force of nature, I defend anyone’s right to define the "designer" differently than I do. I should think the only people who would bother to argue with that would someone on an adolescent ideological crusade against religion.
P.S One of my favorite sites demonstrating the intelligence of cells:
http://www.basic.northwestern.edu/g-buehler/cellint0.htm
Francis:{b]Adaptive mutations, once considered to be a goal driven process now seem to be nothing more than stationary phase hypermutations in cells.[/b]
Bertvan: If many, many mutations occur, that increases the odds that "copying errors" might just happen to accidentally organize themselves into complex, adaptive traits in the genome? Perhaps that sounds reasonable top you. Eventually science will figure out a way to determine whether adaptive change originates in the genome or in the complex, adaptive, environmentally sensitive biological system.
Berthajane Vandegrift
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charlie d.
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Member # 159
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posted 25. September 2002 14:10
Berthajane:
you have it all backwards. What has never been shown is that adaptive changes occur first in the phenotype, and are later encoded in the genome. However, adaptive changes occurring by "standard" (non-lamarckian) gene mutation processes have been shown by the dozen, and in many cases have been proven to occur before the onset of selection (thus completely ruling out any possibility of "heuristic solution-searching" and such). Paradoxically, the immune system you mention is a perfect counterexample to your claims: the adaptive immune system works in strictly darwinian fashion, in which variability is generated at random before challenge, and adapted variants are selected from the available pool by strict mechanistic processes (differential affinity for antigen). Even immunological "learning" (the fact that antibodies to an infectious agent improve during the course of the immune response) is due to repeated cycles of random mutation and selection, just like a good, old-fashioned darwinian GA.
You know this very well (or should, at this point) from discussions over at ARN, so I am surprised you keep repeating these totally unfounded statements.
[ 25. September 2002, 14:11: Message edited by: charlie d. ]
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Berthajane Vandegrift
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Member # 272
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posted 25. September 2002 18:16
Hi Charlie,
I must have missed the details. I know you have cited one experiment with bacteria. The interpretation of whether Lactose adaptation occurred in the genome before occurring in the phenotype has been disputed. In any case, adaptive change in bacteria and multi celled organism might not involve the same process. I’m eager to hear the details of all those adaptive changes in multi-celled organisms that have been proven to originate in the genome, not the phenotype.
Thank you,
Berthajane Vandegrift
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charlie d.
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Member # 159
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posted 25. September 2002 20:49
Yeah. The evidence for spontaneous mutations in bacteria derives originally from the work of Luria and Delbruck in 1943 (Luria and Delbruck, Genetics 28: 491-511, 1943), further refined by Lederberg a few years later (Lederberg and Lederberg, J Bacteriol 63, 399, 1952). Those would be good places to start (though it's along way and several hundreds papers to 2002).
As for multicellular organisms, it is unclear to me while you would argue they work any differently then microorganisms from a mutational standpoint. Certainly there is no evidence supporting that view either.
Of course, experimentally assessing the spontaneous vs induced status of specific mutations requires very large populations(billions) of clonal individuals rapidly grown under controlled conditions - as you might understand, rather impractical for elephants, or even sponges. The most large-scale experiments based on lamarckian genetics were conducted in the Soviet Union under Lysenko's guidance, and failed miserably. In fact, for all it's worth, and as far as I know, there are only a few examples of beneficial mutations in metazoa whose origin before or after selection can unequivocally be defined: human mutations that either protect against HIV infection, or delay disease progression. These have all been found to be widely present in populations of healthy individuals never exposed to HIV (indeed, many born before HIV was even present in their population). Thus, if ever HIV mutates into an airborne, influenza-like virus, I think you better count on a protective, randomly generated genome, rather than on the heuristic processes going on inside your cells. But then again, everybody's different.
[ 25. September 2002, 23:06: Message edited by: charlie d. ]
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Berthajane Vandegrift
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Member # 272
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posted 26. September 2002 13:41
Charlie wrote:As for multicellular organisms, it is unclear to me while you would argue they work any differently then microorganisms from a mutational standpoint. Certainly there is no evidence supporting that view either.
Bertvan: Hi Charlie. I’m not assuming anything. You are the one assuming adaptive change in microorganisms and multicellular organisms are identical processes. ID would favor investigating the matter. The Darwinists are also the ones who assume adaptive change is the result of some random, accidental, purposeless change in the genome. ID favors further investigation, just in case a more rational explanation exists - such as “a heuristic process” occurring in the complex biological system.
Your remarks about HIV immunity are anecdotal, and hardly scientific. Perhaps HIV immunity could occur randomly and accidentally, without prior exposure to HIV, but I assure you such immunity could never be verified without an exposure to the disease. And, if an immunity to HIV were spreading through the population, it certainly is not by the mechanism of “natural selection” (people with HIV immunity producing more offspring than those without the immunity)!! The question will not be definitively answered until science establishes whether or not HIV immunity is determined by a specific gene. (I strongly suspect it is not.)
Whether adaptive change occurs in the genome or the phenotype will eventually be determined by studying organisms with a much shorter generation time than elephants or humans. However, our understanding of the details of individual genomes, including the so-called junk, will have to become more complete than at present. But I am confident the question will eventually be answered - by science. In the meantime, lets not discourage anyone from trying to devise a more rational explanation of life than RM&N.
Berthajane Vandegrift
Teleology is a part of nature. Whether that teleology is internal or external is a philosophical choice, and I defend anyone's right to define the "designer" differently than I do.
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charlie d.
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Member # 159
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posted 26. September 2002 14:52
I don't have much time, so this is my last one on this thread.
quote:
I’m not assuming anything. You are the one assuming adaptive change in microorganisms and multicellular organisms are identical processes. ID would favor investigating the matter.
But the matter has been investigated. Basic genetics, mutation mechanisms, DNA repair processes, environmental effects on the genome are by-and-large comparable in uni- and multicellular organisms. If anything, some significant differences are observed at the prokaryote/eukaryote transition, but eukaryotic unicellular organisms amenable to large scale genetic analysis (such as yeast) show spontaneous, non-directed mutations.
quote:
The Darwinists are also the ones who assume adaptive change is the result of some random, accidental, purposeless change in the genome. ID favors further investigation, just in case a more rational explanation exists - such as “a heuristic process” occurring in the complex biological system.
Again, that mutations are random with regard to fitness is not an assumption, it's a verified observation. That adaptive change is the result of the interaction between random mutations and the action of the environment on the differential reproductive success of organisms is an inference based on the above-mentioned observations on the random nature of mutations and the effect of selective environments on differential reproduction. Such inference has been validated empirically in a large number of cases.
quote:
Your remarks about HIV immunity are anecdotal, and hardly scientific. Perhaps HIV immunity could occur randomly and accidentally, without prior exposure to HIV, but I assure you such immunity could never be verified without an exposure to the disease. And, if an immunity to HIV were spreading through the population, it certainly is not by the mechanism of “natural selection” (people with HIV immunity producing more offspring than those without the immunity)!!
"Anecdotal"? "Hardly scientific"? These empirically verified observations are the result of hard, extensive studies by immunologists, virologists, molecular/cell biologists and geneticists over many years. Anecdotal is my sister: there are dozens of papers published in leading scientific journals on the subject!
You don't seem to even fully understand the issue: there are gene mutations that prevent HIV from entering their target cells. Let me repeat: people with certain genotypes get infected by HIV, but HIV cannot effectively grow in them. Did these mutations arise in response to HIV infection, through a "heuristic process" in the infected people's cells? Most definitely not: the same mutations are commonly found in people who have never been exposed to HIV, even born before HIV was around. In fact, these individuals inherited the mutations from their parents, as easily verified and genetically expected.
That's all the issue is about: by the luck of the genetic draw, some people have inherited mutations that spare them from getting AIDS. Should HIV become airborne and aggressive, you bet these people are going to be selectively favored! Indeed, they may be the only survivors of such a pandemic, should it occur.
quote:
Whether adaptive change occurs in the genome or the phenotype will eventually be determined by studying organisms with a much shorter generation time than elephants or humans. However, our understanding of the details of individual genomes, including the so-called junk, will have to become more complete than at present. But I am confident the question will eventually be answered - by science. In the meantime, lets not discourage anyone from trying to devise a more rational explanation of life than RM&N.
And yet, despite all your pronouncements of "confidence" in science, you seem to reject every single conclusion science has reached in the past 100 years. Maybe you are only confident in future science, or maybe only in science that reaches conclusions you already like. That's not how science works, though. Lamarckism has been around longer than darwinism, and has little of consequence to show for it. It ain't likely gonna change any time soon.
[PS: I remembered of another case of spontaneous adaptive mutation in humans: a de novo thalassemia mutation in a Swiss family. Should they migrate to a swamp somewhere, they'd be resistant to malaria, and happily reproduce while their unmutated neighbors are too sick to mate; of course, they have almost certainly never been subject to plasmodium-instructed "heuristic processes" in Bern, and it's unlikely they will ever take advantage of their genotype. Nevertheless, one day under a gray Swiss sky, another random, senseless spontaneous mutation with adaptive value was born, all by itself.]
[ 27. September 2002, 11:06: Message edited by: charlie d. ]
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michaelgoodrich
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posted 27. September 2002 10:13
Berthajane,
Much of what you say sounds familiar with Lee Spetner's conception. Are you familiar with his work?
If so, how would you characterize the basic aggreements or disagreements between the two?
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Frances
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Member # 169
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posted 27. September 2002 12:55
charlie,
I have to agree with you, there are vaste amounts of evidence and research supporting the genotype precedes phenotype pathway. In fact there seems to be little evidence for an opposite route. Bertjane´s suggestion that ID would pursue other natural pathways seems to be contradictory with reality since ID is not about inherent intelligence in cells but about intelligence manipulating and engineering new systems.
Even the Baldwin effect which seemed initially to be Lamarckian has been shown to be Darwinian.
In the end the evidence supporting Darwinian pathways seems far larger than the evidence supporting Bertjane's proposals.
Nevertheless I encourage Bertjane to show evidence of phenotype preceding genotype in support and explain why this would be any evidence of ID?
As I have argued in other forums, Bertjane seems to hold to a very narrow definition of ID which does not even seem to overlap with the ID as proposed by the major design theorists.
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michaelgoodrich
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posted 27. September 2002 13:18
Berthajane,
Much of what you say sounds familiar with Lee Spetner's conception. Are you familiar with his work?
If so, how would you characterize the basic aggreements or disagreements between the two?
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Janitor@MIT
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posted 27. September 2002 15:21
Hi, bert! Your “theory” has already been tested and is true as any in science. Of course, interpreting the results is another matter.
The concept of an “optimal mutation” rate occurs in EC. It also occurs to biologists also, apparently, because the question was asked when I was studying evobiology in college. I don’t know why, even on Darwinian grounds, we shouldn’t expect that populations will, in ~4-billion yrs, have evolved optimal mutation rates and patterns. We expect that birds have evolved “optimal” flight, fish have evolved “optimal” swimming, etc. Just substitute the word “adapted” in those phrases and you have an utterly uncontroversial statement in evolutionary biology: birds are adapted to flight, fish are adapted to swim. Why is it that populations are not adapted to adaptation? Populations are not evolved to evolve?
It’s a matter of perspective or interpretation, I suppose. E.g., rather than saying that mutation is random wrt to effect on fitness, I would say that mutation is optimized wrt to effect on fitness. Of course, my reformulation is consistent with every experimental result I’ve ever heard of. It’s even consistent with a Darwinian outlook, since all evolution-adaptation must occur upon a pre-adapted or adaptable substrate.
Now if we deny that this is possible we come dangerously close to giving Darwin’s theory something of an “anti-evolutionary” interpretation: Populations cannot have evolved to exploit, facilitate, or enhance existing resources to effect. They can’t have evolved to evolve more effectively—even though my argument is simply the kind of “evolutionary advantage” argument that theorists themselves often make. It is to evolutionary advantage for a population to adapt “adaptability,” to evolve “evolvability.”
The spin (“rational reinterpretation”) on Luria & Delbruck, e.g., might look like this: It is always advantageous in the evolutionary sense for any sufficiently large bacterial population to express every possible viable phenotype under existing conditions in an pre-adaptive strategy, in effect “anticipating” any change in conditions. (Given the population’s limited “cognitive” capabilities, its inability to induce or predict specifically what changes will occur in its environment, it uses to maxeffect the resources available to it: an intrinsic and irreducible variability + MPP. Of course, for all our superintelligence we are in the same boat as the bacteria. We can’t predict the weather for three days.)
This gives the population a “running start.” Its always “running in place,” anticipating the starting gun in the race to the evolutionary finish line. Alternatively, it is never to the advantage of a population to suppress this variability. The cost of doing so far exceeds the potential benefit. (It is only under extreme conditions that this cost is ever borne by the population as a whole, that mutation threatens its viability—in a “Vulcan philosophy.”) Rather than a “mutational load” or entropy, this variability is an evolutionary or adaptive potential.
Extending the science fiction analogy to the immune system is clear: The immune system forces its attackers to adapt faster than they can (Kamp, C. & S. Bornholdt, “Coevolution of Quasispecies: B-Cell Mutation Rates Maximize Viral Error Catastrophes,” Phys. Rev. Lett. 88 (6): 068104-1-4.). In the same way that the crew of the Starship Enterprise modulate their weapons to attacks by the Borg (LOL). Now, if those sci-fi fans thought that Capt. Picard was particularly ingenious (intelligent) in choosing this strategy of attack-defense, then why do we discount the same thing as “random” in the immune system? I find it interesting that an alternative spin has been put on an analogous system--stress response in bacteria. We insist that these mutations are “random” when they are the result of a system of response involving the coordinated regulation and expression of upward of ~80 genes (!). This is a strange conception of “randomness.” The very term is rendered meaningless by its overuse and abuse. It ceases to be either ontologically substantive or epistemically warranted and becomes mere "mantra" in the dysteleogical metaphysic.
Continuing the spin: A phenotype is a genotype’s “belief system,” a hypothesis trialing system, a theory of its own evolution-adaptation tested against existing and changing conditions. Many evolutionary theorists have compared evolution to experimentation, learning, and heuristic problem solving (factoring in pre-adaptation, it is, in a sense, only ever “heuristic” problem solving). Do we know enough about genotype <> phenotype mapping to conclude that that it is “random” wrt to fitness? Yes and no. We know that in many populations naturally and in experimental systems, the G <> p mapping is not “random.” A hive of bees refutes this idea. Phenotypes are “selectively” distributed in fixed and constant (and varying) proportions by the genotype in a population fitness enhancing (or maintaining) way.
(This is also a tried and true design strategy: What you can’t change you use to advantage. No life form can change the fact, written into the laws of physics, of random change. But they can use it effect—and do in many instances. E.g., I just read an article on circadian clocks: Vilar, J.M.G., et al, “Mechanisms of noise-resistance in genetic oscillators,” PNAS 99 (9): 5988-5992, April 30, 2002. The authors note that the clocks’ function is “paradoxically” enhanced by intrinsic noise. There is nothing “paradoxical” about it on a design perspective.)
Probably the longest chapter in Origin was entitled “The Laws of Variation.” But Darwin, having demonstrated his mastery of those phenomenological laws (he probably knew as much about the laws of heredity as anyone at the time), then turns around and says that we are largely ignorant of those laws—permitting him to say that adaptive variations occur by “chance.” It may be true, in the middle of the 19th century, we didn’t know enough about the laws of variation to relate them to evolution. But is that still true? Can we confidently state the conclusion that nothing has really changed in the past 150 years? Or are we only repeating the same tired old formulae? Is it possible to “think outside the box” on such matters? Are their any possible scientific advantages to doing so? Of course in a universe sans “determinism,” I suppose “randomness” is one way to “explain” everything. But, of course, that idea tested even the credulity of Darwin (LOL), which is why he included Lamarckian concepts in his theory. Even Darwin did not believe chance and selection was a competent cause.
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Berthajane Vandegrift
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posted 27. September 2002 15:56
Hi Michael,
Perhaps our present technology cannot definitively establish where adaptive change takes place - the genome or the phenotype. Existing evidence can be interpreted differently. Some people interpret it as indicating that biological novelty is the caused by accidental “mutations” in the genome - which “natural selection then, somehow, organizes into complex biological structures. Others believe living organisms adapt purposefully (not randomly with regard to fitness), and such adaptation is later encoded in the genome. I am glad scientists such as Lee Spetner and Eva Jablonski are pursuing such investigations.
My view of ID, that life is designed by an intelligence innate to all life, is not the most common. I regard the creative intelligence of life as a natural force, but I feel no urge to disprove the existence of God. As an agnostic, not an atheist, don’t deny the possibility that someone’s God might play a role in the process. I share a skepticism with all ID supporters that random (with regard to fitness) “mutation” and natural selection is capable of “creating“ biological novelty. However, I am a spectator, not a scientist, and am not going to personally produce any evidence. All I can do is occasionally protest that:
ONE DOESN’T EVEN HAVE TO BE RELIGIOUS TO BE SKEPTICAL OF RM&NS AS THE “CREATOR” OF BIOLOGICAL NOVELTY.
As long as people continue to insist that ID is a form of “creationism”, I suppose I’ll feel compelled to periodically repeat my protest.
Berthajane Vandegrift
Hi Janitor,
I thoroughly enjoy your discussions, which are on a more sophisticated level than I could manage.
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peroxisome
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posted 27. September 2002 20:13
quote:
ONE DOESN’T EVEN HAVE TO BE RELIGIOUS TO BE SKEPTICAL OF RM&NS AS THE “CREATOR” OF BIOLOGICAL NOVELTY.
I think you have had some rather expert tuition here from janitor, charlie d, frances, etc.
However, I cannot resist pointing out that the above is factually wrong in multicellular organisms.
Take the worm C. elegans. You can induce mutations in the genome of elegans by radiation or chemical mutagenesis. This leads to a vast enhancement in the generation of biological novelties. This can be a selection protocol- e.g. enabling elegans to grow in adverse thermal, biological or chemical conditions. These mutants simply are not found in normal populations.
Thus random mutation does lead to the creation of biological novelty.
yours
per
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charlie d.
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posted 27. September 2002 20:28
Janitor:
nice theory: intelligent planning introduces random mutations because that's the best way to cope with unforeseen circumstances. It still means mutations are random though. That's all we can measure with our scientific means: outcomes, not intentions. Similary, of course the stress response is adaptive, and its adaptiveness is in increasing the rate of random mutations. So is the randomness of antigen receptor variability in the immune system, the product of complex adaptive mechanisms.
Alas, bertvan would not like that: she says no adaptation can come from chaos, or randomness, or chance. I suspect most ID theorists would not like that either. It's like saying that God designed the universe to work through entirely natural mechanisms, including darwinian evolution: it's a perfectly plausible, consistent philosophy, but it's still a naturalistic philosophy, in essence. Purposeful randomness is still randomness.
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