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Author
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Topic: Sources of Randomness in Natural Selection
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Irving
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Member # 535
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posted 12. January 2003 11:38
Gedanken
quote:
Erasures are simply pruning of the branching tree. There is nothing here to suggest that there are insufficient probabilistic resources to account for the successful branches in evolutionary progress.
Nothing probabilistic other than say time. The issue with erasures comes into play when the parent node is erased. From that point on the chain can no longer traverse the tree. There is now a limit on just how much can be erased.
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gedanken
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posted 12. January 2003 12:32
Irving, of course each death terminates all possible offspring, and thus is a pruning of tree branches therefrom.
But Scott’s example of “erasure” was clearly meant as a reference to failure of an organism to reproduce (as possibly by the death of the organism or other mechanism leading to failure to reproduce), in a scenario of evolution. Once again the Talk Origins discussion of mutations might be of some interest with regard to this question. There was clearly no intention of the term “erasure” to mean an act that works backward in time to previous branches of an existing tree structure of evolutionary progress -- and in that sense the “erasure” is limited to the current node. In other words selection is a local operator in the evolutionary model -- though it has global effects.
By the way, a Markov model of state transitions would be a difficult undertaking because of the huge number of possible states makes the arrays virtually impossible to manage unless one uses very abstracted state classes. But a Markov chain representing the pruning or death of an organism line (state) would be represented by state transition probabilities of 0. This is simple and causes no problems.
There is considerable danger that reintroducing Dawkins’ “Methinks” algorithm example will be misinterpreted. (Remember that it is focused on demonstrating only an abstracted part of evolutionary theory. The example to follow is worded in terms of a “target”, but that “Methinks” is targeted to a specific string is irrelevant because it is not the issue that the algorithm was designed to illustrate.) Here is an interesting discussion of Dawkins’ “Methinks” example from the perspective of cognitive psychology and cognitive research, with links to other sites. With regard to the specific issue of pruning of the tree, we see that early pruning does not stop the evolution of complexity. And it relates the discussion of nature as exhibiting intelligent behavior. (And I warn that it is important to distinguish philosophical questions of ultimate causation and ultimate purpose from questions of local mechanisms of the physical world. This essay takes a position on local mechanisms as having no “purpose” from the perspective of that physical mechanism -- and is an example of what many ID promoters object to in science, that it cannot identify a “designer’s” purposeful intent.)
[ 12. January 2003, 12:54: Message edited by: gedanken ]
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rafe gutman
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Member # 134
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posted 12. January 2003 19:57
this discussion would be easier if we had a better analogy than monkeys typing shakespeare or dawkin's "methinks" program, both of which in some form involve the interaction with an intelligent agent. it seems that no matter what kind of analogy we come up with, it will either beg the question or be loosely connected to a human designer.
the immune system is a perfect example of a system that can receive input from the environment and use the same principles as evolution to produce an appropriate reaction. if a mammal or some other higher vertebrate were to come in contact with a virus, they would soon produce antibodies that could specifically bind to molecules on the virus. the host organism doesn't know ahead of time what antibodies it needs to combat the virus, those antibodies that have even a weak affinity for the virus are soon selected for and begin to proliferate. furthermore, they are stimulated to mutate their antibody genes, and with several rounds of mutation and selection, cells producing high-affinity antibodies are generated.
with the monkey-shakespeare example, an intelligent agent is erasing the bad prose. in the "methinks" example, an intelligent agent is inputting the desired outcome. so where does the intelligence come from in the immune system? does an intelligent agent rest inside each of our immune systems, instructing which antibody-producing cell to select for and which antibody genes to mutate accordingly? that would be the equivalent source of intelligence.
from the original post:
quote:
Return to Eugenie's mistake-correcting helper. If the helper is not a designing intelligence, then that helper is him/her/itself going to need some help in knowing what to erase. There is a regress here, and it confronts natural selection operating in biology as well.
in the immune system, the helper would be the pool of antibody-producing cells. there are about a billion antibody-producing cells in the average adult mammal at any given moment. each of these cells produces an antibody molecule with a different specificity, and around 10,000 of these molecules are attached to the surface of each of these cells. if a cell comes in contact with a virus that can bind to it's antibody, it will be stimulated to proliferate. this is like saying that if a monkey produces an error-free sentence of shakespeare, the sentence will be saved and distributed to each monkey, and typing will continue starting at the next sentence. the difference here is that the immune system does not require an input of intelligence.
the obvious retort is to suggest that the immune system was itself designed by an intelligent agent. however, this argument is equivalent to saying that the "methinks" analogy is invalid because computers were designed by humans. that is not the issue here. dembski's main point in his original post was to suggest that the source of information that determines which organims are to be selected for is intelligently-derived. at least it is in the two analogies he mentions. in the immune system, there is no such intelligence, just the presence of foreign molecules.
so who's whispering in the immune system's ear?
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Irving
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posted 12. January 2003 20:05
Gedanken,
quote:
Irving, of course each death terminates all possible offspring, and thus is a pruning of tree branches therefrom.
Quite true, no arguement there. I was also considering the example where the parent dies, but the offspring can still reproduce. The offspring overrun the population eliminating the parent. From this point on, all future changes are based on the offspring, since the parent state can't be returned to. The offspring must then be on a direct line to solution. If the offspring were better suited to the current environment, but misaligned to the solution state, then the offspring would be chosen over the parent, yet the solution state could never be arrived at.
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andyg
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Member # 415
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posted 12. January 2003 20:08
Mike Gene writ:
quote:
Andy: Again, the interaction between the genotypes in a population and the environment determines what is "fit" in a particular instance. In an ampicillin-containing medium, ampicillin-resistant bacteria will be more "fit" than kanamycin-resistant bacteria.
MIKE: Yes, but this is incomplete. How does the medium come to contain ampicillin?
The experimenter put it there. The experiment I described was a simple demonstration that "fitness" is a product of both the organism and the environment.
I really hope you're not going to argue that because the experiment above was "designed" then it doesn't provide a good model of natural selection - or worse still, that the experiment argues that selective environments in nature are also designed!!
That argument is just as fallacious as the one that says that Thomas Ray's "Tierra" program can tell us nothing about evolution because the program itself was designed.
AndyG
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Cre8ionist
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Member # 140
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posted 12. January 2003 20:12
Hello again gedanken,
quote:
The answer is clearly that bacteria which exist in nature are seen to regularly reproduce, bacteria that have the flagellum structure. So nature clearly produces the flagellum, you can put out food and starter bacterial and wind up with a very large number of flagella
created in nature. So the flagellum is clearly part of the “vocabulary” of nature.
This could be a simple miscommunication. There are two meanings competing here it appears, on the one hand when speaking of vocabulary we could be referring to a language user's ability to use words, or we could be speaking of the entire lexicon. One's ability to use the English language does not necessarily reflect accurately the size of the language. Certainly in nature we could find all we need to build a flagellum, if we knew how, that's not in question. The question here though is does Mother Nature (MN) have the ability to use the vocabulary to originate biological SC?
If I may, there is quite a big difference in copying and originating. When you say "you can put out food and starter bacterial and wind up with a very large number of flagella created in nature", it should probably read "replicated in nature." But we're really trying to solve origins questions here. Given the right conditions, MN can replicate flagella, she has not been shown to originate them, one could say every flagellum from a flagellum, though I realize the relationship is not as easy to see as the cell's.
Let me offer an analogy, in the vocabulary of the programming language Java, there exist variables, methods etc...to help someone write java programs. Methods for copying, pasting all are within the language. So we can confidently, though needlessly, assert that the vocabulary of Java will suffice to write every Java program. What is missing from the language itself is the ability to originate the multitude of complex java programs which you find on the web, in hand helds and the like. It still lacks know-how. So even if MN has the vocabulary (granting for arguments sake, the human spirit comes to mind as a possible exception), it may lack the know-how to "whisper" the correct pathway.
I'll let you have the final word if you'd like.......................................................................Cre8
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RBH
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Member # 380
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posted 12. January 2003 22:08
Irving wrote quote:
Quite true, no arguement there. I was also considering the example where the parent dies, but the offspring can still reproduce. The offspring overrun the population eliminating the parent. From this point on, all future changes are based on the offspring, since the parent state can't be returned to. The offspring must then be on a direct line to solution. If the offspring were better suited to the current environment, but misaligned to the solution state, then the offspring would be chosen over the parent, yet the solution state could never be arrived at.
I fail to see that this is a problem. That's the way it is in any sort of evolutionary system: in each generation, all future possibilities are based in the then-current population. If some future change in the selective environment cannot be coped with by the offspring, then they go extinct.
There is also a presupposition in the quotation from Irving that there is a "solution" out there somewhere that is being sought. That's not the case. Evolution is local in time and space. A population is not trying to get somewhere; at any given time it is where it is, sitting on some high enough peak on its particular fitness landscape. (If it weren't high enough up on some peak or other it would not exist.) Should that landscape deform (as all biological fitness landscapes do sooner or later), then the population must adapt or die. If it has sufficient variability (initially pre-existing in the population and then generated via mutations) to track a dynamic fitness landscape, and if the landscape is deforming slowly enough, then it has a chance to adapt. If it does not, it will go extinct. And that happens a lot. The fossil record is littered with the remains of species that arose, flourished for a while, and then failed to adapt sufficiently quickly to changing selective circumstances and therefore went extinct.
RBH
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Nel
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Member # 614
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posted 12. January 2003 23:27
Andy wrote:
The experimenter put it there. The experiment I described was a simple demonstration that "fitness" is a product of both the organism and the environment.
Nelson:
But how did the ampicillin-resistant bacteria get there? Were any found when they were assayed for resistance before the experiment (if they were at all)?
[ 12. January 2003, 23:27: Message edited by: Nelson_Alonso ]
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yersinia
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Member # 324
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posted 13. January 2003 03:25
quote:
Nelson:
But how did the ampicillin-resistant bacteria get there? Were any found when they were assayed for resistance before the experiment (if they were at all)?
It is a common myth, perpetuated by Phil Johnson among others, that bacterial resistance is always a result of pre-existing resistance in the population.
It is not true, because you can start a colony from a single bacterium from a non-resistant population, let it grow to a few billion(s), hit it with an antibiotic, and then see the few dots of new colonies regrowing, each descended from the "one in a billion(s)" descendent bacteria with the resistance mutation(s).
Whether or not this particular experiment was such a type, I don't know, but they do exist.
[ 13. January 2003, 03:26: Message edited by: yersinia ]
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Cre8ionist
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Member # 140
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posted 13. January 2003 08:00
Just a side note to you in the bacterial resistance portion of this thread. Spetner cited several
instances where the resistance was due to a loss of specificity/information. In fact he claims that none he knows of are due to an increase in information.
One example is:
"streptomycin and other mycin drugs keep bacteria from growing, and how a point mutation makes bacteria resistant to the drug.....A point mutation makes the bacterium resistant to streptomycin by losing information."
I wonder if anyone thinks that random changes cannot lose information?
I thought the real issue was about the random changes giving an increase. Or is the argument here that this particular example increases information? And if so why? ![[Confused]](confused.gif) ......................................Cre8
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Moderator
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Member # 1
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posted 13. January 2003 08:11
Let's make sure this thread stays on topic: "sources of randomness in natural selection."
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andyg
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Member # 415
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posted 13. January 2003 12:32
quote:
Nelson:
But how did the ampicillin-resistant bacteria get there? Were any found when they were assayed for resistance before the experiment (if they were at all)?
The resistant bacteria were introduced at the start of the experiment by the experimenter. Once again, as with Dembski and Mike Gene you are missing the point. Dembski was asking if selection itself was random. I was replying that it isn't. The genotypes that the environment selects for can be random. The environment can change randomly. But the interaction between a genotype and the environment is not random.
As I mentioned in a previous message - and to get back on track as suggested by the moderator - the source of mutations that can confer resistance can be due to random mutation. It doesn't have to be (as in the example above), but it can occur randomly. As I pointed out before, this was demonstrated over 50 years ago by Luria and Delbruck in their fluctuation test. Here is another URL for that
Fluctuation test
AndyG
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Nel
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Member # 614
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posted 13. January 2003 12:35
Yersinia:
It is a common myth, perpetuated by Phil Johnson among others, that bacterial resistance is always a result of pre-existing resistance in the population.
Nelson:
Reference?
Yersinia:
It is not true, because you can start a colony from a single bacterium from a non-resistant population, let it grow to a few billion(s), hit it with an antibiotic, and then see the few dots of new colonies regrowing, each descended from the "one in a billion(s)" descendent bacteria with the resistance mutation(s).
Whether or not this particular experiment was such a type, I don't know, but they do exist.
Nelson:
AFAIK, evolving resistance as a result of mutation and selection is a phenomenon known as adaptive mutagenesis, which has vitalistic connotations, and is a furious debate within the biological community. If you would indulge me, I think this can illuminate one of the points by Dembski.
For example, Stephen J. Gould stated:
quote:
First, variation must be random, or at least not preferentially inclined toward adaptation. For, if variation comes prepackaged in the right direction, then selection plays no creative role, but merely eliminates the unlucky individuals who do no vary in the appropriate way.
[ 13. January 2003, 18:30: Message edited by: Nelson_Alonso ]
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Frances
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Member # 169
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posted 13. January 2003 12:46
Nelson:
AFAIK, evolving resistance as a result of mutation and selection is a phenomenon known as adaptive mutagenesis, which is a furious debate within the biological community. If you would indulge me, I think this can illuminate one of the points by Dembski
One should be careful to differentiate between adaptive mutatagenesis as a specific example of mutation and selection.
While there were some initial research findings that suggested that some mutations indeed arose preferentially adaptive it now has been shown that these examples are due to a hyper-mutation response by the bacteria followed by selection.
So while there was some initial excitement, it seems that it in the end came down to random (hyper) mutations and selection after all.
Steven J. Gould was correct and so far it seems the evidence for truely adaptive mutations seems to be lacking.
What is important to remember is that mutations may not be random wrt for instance location or time or external stimuli but they seem to still be random wrt environment/fitness.
As far as Spetner's comments and losing information, I have yet to see Spetner show any quantitative examples. Since it is obvious that beneficial depends on the environment, the suggestion that mutations are always reducing information goes against 1. common sense 2. actual simulations that show that information (Shannon) actually increases.
Since one could also show that a 'reverse mutation' would lead to an increase in information there obviously exist mutations which increase information.
Looking at a reduction in specificity only is not very useful a measure of 'information'.
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Janitor@MIT
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posted 13. January 2003 12:55
Uninterpreted results are the results of an experiment that has never been performed. But the fact that results are interpretable represents a problem in science (and is not simply one of its strengths). Scientists arriving at a consensus interpretation must have objectifiable or at least rationalizable criteria for such agreements. It can’t be that we simply compare an interpretation with received theory (consensus) to see if they accord, because that makes of theory doctrine or covering law. It is after all our interpretations that are being tested by interpretations, isn’t it? But that’s a complicated issue.
If we’ve rejected Lamarck’s interpretation (and I know I do), are their possible alternative interpretations of Luria & Delbruck that account for the results? I’ve offered before a “bounded rationality” interpretation of the Luria & Delbruck results, and even indicated that it had a distinct advantage of not requiring the impossible of a petri dish full of bacteria.
Does received theory expect of a bacterial culture what no human culture, including science, can do? Doesn’t it really expect that the bacteria with some high precision predict the changing conditions of its existence and pre-adapt specifically to those changes? Does theory expect bacteria to do what even Luria & Delbruck, for all their Nobels, can’t do?—predict the future.
I suppose as a test for Lamarck, or a test for some involved and omniscient divinized interventionist, the standard interpretation suffices. But as a test confirming Darwin it simply reveals an absurdity in our expectations informed by that theory. Consider the possibility of a counterfactual. (If even the very thought is not too heretical.) I might interpret such a result as evidence of telepathic powers in bacteria! Or certainly cognitive/predictive powers and abilities that far exceed those of the brightest scientific minds!
Maybe the mind rebels at attributing any kind of “rationality” to bacteria or their evolution. In which case how is biology a science if evolution is not rationally comprehensible?--If there isn’t a rationale to it? My, my, my, we certainly are coming dangerously close to anti-scientific and anti-rationalistic thinking here, aren’t we? (E.g., when biologists make a distinction between “rational” and “evolutionary” design—a distinction, I dare say, that no engineer would accept.)
Dr. Dembski is quite wrong. The force of Darwin’s argument from design (his analogy, “natural selection”) is exactly because what is selected is rationalizable and intelligible. And that only on a priori design principles! That’s what makes it a theory of design.
I think that the question might be fruitfully explored by Dembski et al. Seems to me that the fact that evolution is in no wise or in any significant way, shape, or form “random,” might serve as the basis for a powerful argument from design—following Darwin’s own precedent, ironically enough.
Maybe the real rub here is the “panselectionist” habit of thought of biologists to dump all selection into the environment, like their physicist counterparts dump all energy into the virtual vacuum. (Actually, I don’t know if this habit is so much “panselectionist” as it is “pan-Lamarckism.” But that’s another question.) Biologists might consider where exactly this approach has taken the physicists and reconsider.
Just my interpretation.
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