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Author Topic:   natural selection is wrong
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 91 of 276 (112462)
06-02-2004 4:36 PM
Reply to: Message 90 by Dan Carroll
06-02-2004 3:45 PM


Well I fear you may have found the one area in which I can find myself siding with Syamsu, the less said about your wang the better as far as I'm concerned.
TTFN,
WK

This message is a reply to:
 Message 90 by Dan Carroll, posted 06-02-2004 3:45 PM Dan Carroll has replied

Replies to this message:
 Message 92 by Dan Carroll, posted 06-02-2004 4:48 PM Wounded King has not replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 99 of 276 (112565)
06-03-2004 3:51 AM
Reply to: Message 98 by Syamsu
06-03-2004 2:35 AM


Syamsu,
How can you have been on this forum for so long without having come across the concept of being able to back up your arguments. Yes the paper suggests that all modern Darwinism is teleological, but it has the same failing you do, it makes absoloutely no effort to back up its statement with any evidence.
Your petulant complaints are rather hollow when all I am asking for is a minimal standard of evidence, i.e. any at all, to back up your assertions.
Once again you showcase your ignorance of evolutionary biology and population genetics when you say there is no literature concerned with the effects of non-selective pressures, just look for genetic drift. In fact to save you some time here is what talk.origins has to say on the subject. I would specifically draw your attention to the second last quote.
In any population, some proportion of loci are fixed at a selectively unfavorable allele because the intensity of selection is insufficient to overcome the random drift to fixation. Very great skepticism should be maintained toward naive theories about evolution that assume that populations always or nearly always reach an optimal constitution under selection. The existence of multiple adaptive peaks and the random fixation of less fit alleles are integral features of the evolutionary process. Natural selection cannot be relied on to produce the best of all possible worlds.
(Suzuki, D.T., Griffiths, A.J.F., Miller, J.H. and Lewontin, R.C. in An Introduction to Genetic Analysis 4th ed., W.H. Freeman, New York 1989)
Please show the teleological bias in this statement.
TTFN,
WK

This message is a reply to:
 Message 98 by Syamsu, posted 06-03-2004 2:35 AM Syamsu has replied

Replies to this message:
 Message 103 by Syamsu, posted 06-03-2004 5:51 AM Wounded King has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 102 of 276 (112571)
06-03-2004 5:25 AM
Reply to: Message 98 by Syamsu
06-03-2004 2:35 AM


Syamsu writes:
Selection does not describe the relationship of the organism to the environment in terms of reproduction. It describes relative reproductive proneness, or whatever, between variants. The two are not the same, unless you want to throw any measure of precision out the window in science, they are demonstrably not the same.
Demonstrate away!
It is statistically descriptive as it is determined as a post-hoc analysis of the populations genetic makeup over generations, therefore it sums the various environmental pressures on the population, both selective and non-selective pressures and allows trends to be determined. It doesn't describe what happens to every specific organism in regards to every specific instance, but then that isn't what statistical methods do.
Precision in science is only neccessary to the level required for a specific task. For example, to apply Newton's laws of motion to a rolling ball you do not have to understand that behaviour of the sub-atomic particles which make up the ball.
In the wild it is impossible to monitor every single individual in a sizeable population and their interactions with the environment. Population genetics is a versatile tool to retrospectively observe the effects the environment has had on the populations genetic makeup.
Your formulation still makes very little sense. It requires a massive amount of observation and produces data which are completely useless, certainly in evolutionary terms, until you start comparing them and factoring in genetic variations.
TTFN,
WK

This message is a reply to:
 Message 98 by Syamsu, posted 06-03-2004 2:35 AM Syamsu has not replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 105 of 276 (112583)
06-03-2004 7:32 AM
Reply to: Message 103 by Syamsu
06-03-2004 5:51 AM


I don't see why you should have thought that if you had actually been reading my posts, I have twice said that my objection was to you presenting the fact that the author of the paper makes an unsupported assertion as supporting evidence for the same assertion.
The teleology is that natural selection is in principle relied on to produce the best of all possible worlds, but that other things inhibit this goal of selection, like random fixatation etc.
And here you are making the same unsupported assertion again. This is certainly an approach suggested by the adaptationist viewpoint, but as has been pointed out this is a strongly contested issue and most modern formulations reject adaptationist approaches specifically due to their teleological nature.
Random fixation [i]is[/is] also a part of this 'force' but you give no evidence for its being an equal part. The distinct contribution of various factors to final population genetic outcomes is in fact the entire point of the paper and the paper comes out saying that you can't determine the exact contributions of various factors, hence its suggestion of the correction analogy for evolution from physics being the probabilistic approach of thermodynamics rather than the deterministic approach of Newtonian mechanics. This doesn't mean that you can't still determine evolutionary trends.
The phrase "the best of all possible worlds" is hardly unique to evolutionary biology and in the quote I gave you where the phrase was used the very specific reason for it was to say that this was not the way evolution operated. I believe it was Liebnitz who coined that particular phrase, and not in any sort of biological context.
As to teleology in biology, I agree that it is still a problem. But it is not a problem introduce by Darwinism, in fact Darwinism was a great leap forward in removing teleological notions from biology.
Some small history of teleology in science is covered in this paper (its a PDF by the way so you need acrobat to view it), once again from a philosophy department just to keep things on an equal footing, which talks about teleology in physics.
You have yet to show any teleology inherent systematically in the way natural selection is approached, all you have shown is that adaptationist interpretations of evolution are teleological, which we already knew.
TTFN,
WK
P.S. You have yet to either show any understanding of Newtonian mechanics place in modern science or alternatively retract your ridiculous assertion that all of science must adhere to Newtonian laws of motion.

This message is a reply to:
 Message 103 by Syamsu, posted 06-03-2004 5:51 AM Syamsu has replied

Replies to this message:
 Message 106 by Syamsu, posted 06-03-2004 11:34 AM Wounded King has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 107 of 276 (112645)
06-03-2004 1:28 PM
Reply to: Message 106 by Syamsu
06-03-2004 11:34 AM


Dear Syamsu,
Thank you for finally something actually resembling a reference, why not just link the URL though and save everybody some time?
I can appreciate the view Wilkin's puts forward of selection as a subset of sampling this doesnt however make any actual difference. You still have exactly the same factors natural selection and genetic drift (GD), the only difference between Wilkins statistical approach and that in the original paper you referenced is what level they decide to put the label Natural selection at. Wilkins decides to leave it seperate from GD and make a higher level called sampling, the original paper just says that since we can't dissect out the specific causes of the exact outcomes we see in the populations genetics we will just stick natural selection as the label at the top for the coming together of all the factors to produce specific trends in the population. The paper concludes that
It follows that natural selection is not just a part of evolution: heritable variation leading to differential retention is all that evolution amounts to in the biological domain.
This clearly states the importance of variation in evolutionary studies. As to the question of whether NS and GD should be seperated or both lumped together as NS, it makes absoloutely no difference, not one iota. Genetic drift is as much an example of heritable variation and differential retention as NS is, it is just not directed or biased if you prefer, the paper's authors say NS as they have decided to designate this as the top level term.
This still doesn't remove the importance of variation from the discussion of natural selection. Neither Genetic Drift nor Natural selection can operate on a homogenous population.
Syamsu writes:
It is not an unsupported assertion because it comes from your quote of talk.origins. It demonstrates the talk.origins interpretation of natural selection as teleological, because there they separate natural selection from genetic drift etc. In the paper natural selection is equated to evolution, and this empties natural selection of teleology. In talk.origins evolution consists of natural selection and neutral drift, so natural selection is separate from neutral drift. Therefore it is teleological in the way explained before.
It does not demonstrate that talk.origins interpretation is teleological, it demonstrates that naive theories of evolution in which NS unopposed would produce optimal solutions are teleological. Unless you can show that the generally accepted theory of evolution at TO is one where NS unopposed gives rise to optimal solutions then you are still just making statements with absoloutely no support.
'Darwinists' do not have a three step sampling program, you just sample the population and derive a picture of its genetics. You have to do this over several generations because NS/evolution is a trend over time. Nature does all the rest, the exact cause of the retention of the specific genetic traits in particular instances, such as increased longevity or fecundity, is irrelevant to the detection of trends within a population.
Any probabilistic formulation of evolution highlights how useless your individual organism focus is. You can't do stats on 1 organism anymore than you can have selection operating on a population with no variation.
You have yet to actually show the teleological thinking in anything other than an adaptationist formulation of evolution, I would appreciate an explicit and simplistic explanation of your line of reasoning. Please don't rely on reference to the papers we have been discussing as our interpretations of what they say seem to be at such odds with each other that it would do nothing but further confuse the issue.
I'm also not quite sure what your point is supposed to be with regards to teleology and atheism. Certainly the removal of teleological thinking is consistent with a strictly materialist point of view, but since that is the only point of view which has facillitated successful science it seems reasonable within the boundaries of science. Outwith the science people are free to believe whatever they like.
You seem to be both castigating evolutionary theory for being teleological and castigating science for trying to exclude teleological thinking as a way of sneaking atheism through by the back door. Either you think that teleology is an acceptable concept in science or you don't, which is it?
TTFN,
WK
This message has been edited by Wounded King, 06-03-2004 12:29 PM

This message is a reply to:
 Message 106 by Syamsu, posted 06-03-2004 11:34 AM Syamsu has replied

Replies to this message:
 Message 108 by Syamsu, posted 06-04-2004 8:09 AM Wounded King has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 109 of 276 (112744)
06-04-2004 9:48 AM
Reply to: Message 108 by Syamsu
06-04-2004 8:09 AM


You can't meaningfully sample a population of 1 anymore than you can select from a population of 1, you don't have to be just meaning something different to Wilkins you have to be using 'sample' as a word meaning deomthing totally different to what everyone in the world considers sample to mean, here is the dictionary.com entry for sample to help understanding.
Syamsu writes:
You are essentially arguing that things like comparison of same, should be in a different theory altogether, then comparison of variants, which is absurd, and leads to the erronuous conclusion of natural selection as a separate force, and all kinds of errors and deceptions. They should obviously all be part of the one theory.
No that isn't what I'm arguing, you can study the population genetics of a heterogeneous population if you wish, but it won't show you anything relating to natural selection, genetic drift or evolution until there is some heritable variation going on. Things which stay exactly the same from generation to generation are not evolving.
You have never shown to anyones satisfaction, other than perhaps your own, that comparisons are absurd this seems to be the baseless basis of your entire argument. Your stable populations are part of evolutionary theory in as much as they are periods of stasis between periods of evolution. However since I have never heard of any totally homogeneous populations of anything, certainly nothing with a population suitable for the species to continue, with the possible idealised exception of clonal populations of bacteria in the laboratory, it seems highly unlikely that a situation ever occurs, certainly not in nature, where populations with no variation continue to have no variation over several generations, even in the absence of any selective pressure random mutation and genetic drift would make a population deviate from homogeneity over several generations. In fact I would imagine the only situation in which it would be possible would be if the animal was under very high selective pressures to maintain its genome in exactly the same state in its entirety.
What people who assert the lack of purpose in nature tend to do, is to make purpose natural. They are the ones who tend to produce the pseudoscience, it is of no benefit to science as far as I can tell. Anyway the assertion of lack of purpose violates the ideal of objectivity obviously. If you say the planets going round the sun is without purpose, then that's just your subjective opinion. Of course these people would try to have a scientific definition of purpose, love, selfishness, God, soul, free will etc. so that they can scientifically say that there is no purpose there, but there is purpose elsewhere. Obviously this kind of practice leads to the ideal of objectivity becoming undermined in a confusion about the meaning of words.
Ah, gibberish. That absoloutely fails to make anything clear, although I would agree that you seem to be suffering some confusion as to the meaning of words. It certainly doesn't explain your claims about teleology being fundamental to modern evolutionary theory, nor does it answer my question as to whether you believe teleology has a place in science, a question for which a one word answer should be sufficient.
Why are you incapable of providing a simple explanation for any of your positions. I have asked you to break down a number of points for me and all I have had in reply has been obfustication and repetition.
TTFN,
WK
P.S. Are you prepared to concede that Newton's laws of mechanics are not universally applicable to all areas of science Yet? Or that teleology is not a concept whose appearance in science is unique to biology?

This message is a reply to:
 Message 108 by Syamsu, posted 06-04-2004 8:09 AM Syamsu has replied

Replies to this message:
 Message 110 by Syamsu, posted 06-04-2004 10:54 AM Wounded King has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 112 of 276 (112764)
06-04-2004 11:46 AM
Reply to: Message 110 by Syamsu
06-04-2004 10:54 AM


Syamsu writes:
It refers to the relationship of the organisms to the environmenet in terms of fitness for reproduction.
If you think that that is quite specific then there is no way we are ever going to have a meaningful discussion. In what way does it refer to the relationship of the organism to its environment in these terms? Give us your idiosyncatic defintion of sampling. A specific defintion, not a vague wibble.
I have already told you numerous times that biologists already describe individual organisms this way, yet you continuously ridicule the practice of describing this way (referring to homogenous populations not existing etc.)
Biologists very rarely describe singel organisms this way and conclude that that is meaningful in and of itself. What biologists do is look at a small sample of a population hardly ever a single individual, I defy you to show that the majority of research is focused on the study of specific individuals. They may then make general observations about an entire species based on these few observations, the point is that these are generalisations. In general all humans are born with two legs, but there are a number of specific cases where they aren't. For someone who is bemoaning the lack of precision in natural selection you seem all to happy to embrace a generalisation about an organism as the be all and end all of knowledge about all members of the population that individual belongs to.
One of the reason why this has been the case is because until very recently we didn't have the technology neccessary to detect a lot of the variations in populations. Even if an organism is morphologically identical to another it may have a significantly different set of physiological parameters, it may have many proteins with differing and significant amino acid sequences effecting metabolic rates. It is reasonable to make generalisations about classes from a sample of a population, it is mistaken to make them from one instance, this is one of the reasons that science relies on replication to such a great extent.
Please offer an example of 'those things that go to prove that your position is quite absurd'. And then show where I ever stipulate that all biology must bow down to variation, we are talking about evolution and natural selection, end of story, both of these things have an absoloute requirement for variation, if you can show me even a hypothetical situation in which either evolution or NS can occur in the absence of any variation I will be astounded.
I would like to ask a moderator to reject your post on account of avoidance of argumentation offered several times before. I think that is the only way this discussion can progress to a conclusion, with an impartial moderator arbritating points like that.
Please by my guest, bring a moderator in if you feel you must. I sincerely doubt that you will find one impartial enough to review this thread and agree with your conclusion that I am the one avoiding making substantive responses to points. Please let me know when you have got a Mod on the case, I've always wanted to be a controversial figure of mystery.
The theory I posit is right and meaningful as a fundamental theory, and that's as far as I need to go as far as I can tell.
Fair enough, unfortunately all you have provided is a fundamental theory of population dynamics which involves looking at animals as and noting if they breed or not. You can use it to keep an accurate record of a popultions numbers if you look at all the animals in the population, individually of course, and then collate but not compare the data. Unfotunately your theory is useless in the context of evolutionary theory, but please fell free to try and show any way there can be evolution, rather than stasis, in a population with no variation and how your theory could explain or detect it.
In regards to your strawman about variation, I could then equally posit the strawman that natural selection is only applicable if every organism is varying in every respect.
Except that you haven't shown my argument to be a strawman, simply stated that it is so. Your strawman is patently false as you can obviously select between variants on 1 single area of variation, you have yet to show how you can meaningfully select on the basis of no variation.
t's unfortunate that you apparently don't understand why saying something like "the planets going round the sun is purposeless" is not a scientific statement. I don't think there is much wrong with my explanation, the issues are quite complex and paradoxical of themselves. Dawkins and Haeckel can assert blind purposelessness of evolution, and then Dawkins can turn around and say that the purpose of organisms is reproduction.....
I never said that that statement was scientific, but thank you for putting words in my mouth. You have yet to provide a one word answer (Hint: the word should be yes or no) as to whether teleology has a place in science, in your opinion. I have no problems with Richard Dawkins being wrong, I'm not married to the chap. Richard Dawkins is as fallible as the next person, unless perhaps the next person is you, in which case I would give Dawkins the benefit of the doubt.
TTFN,
WK
P.S. Any response to the P.S. in my last post?

This message is a reply to:
 Message 110 by Syamsu, posted 06-04-2004 10:54 AM Syamsu has replied

Replies to this message:
 Message 113 by Syamsu, posted 06-04-2004 12:58 PM Wounded King has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 118 of 276 (113276)
06-07-2004 9:55 AM
Reply to: Message 113 by Syamsu
06-04-2004 12:58 PM


Syamsu writes:
Are you denying that at the basis of natural selection, genetic drift etc. are individual observations like these?
Arguably the entire point of population genetics is to obviate the need for individual observations such as these, they may consitute the basis of trends in the population but knowledge of these specific instnace is not neccessary to observe those trends. All of these events are automatically factored in when we look at the genetic constitution of the population over several generations. The specific cause of death/ reproduction for 1 individual is irrelevant. Handily nature itself has taken care of integrating all the relationships between individual organisms and all aspects of their environment including all other organisms in that environment.
If you think for a second that it is feasible to account for every single environmental factor, or even just those contributing to a specific instance of death, affecting 1 individual let alone a population, then you are sadly mistaken, would that we had such omniscience.
Of course fitness is to do with reproduction, its all about reproductive success!! But in a homogeneous population differences in reproduction will have no evolutionary significance. You can argue that by looking at an individuals reproductive success, but only in comparison to other members of the population, you can rank its 'fitness' if you define fitness solely as being the number of offspring. You can't measure an individuals fitness in an evolutionary sense however without looking at the ability of a certain trait to spread through the population.
Perhaps you would be interested in the work of Lloyd Demetrius on producing a analogous framework for evolution to thermodynamics. He has a theory he terms directionality theory, which is nothing to do with teleology, it is directional in as much as it proposes that evolution is under certain specific parameters a uni-directional process leading to an increase in what he terms 'evolutionary entropy' which is a measure of the indeterminacy of the age of the mother of a randomly chosen individual.
A review of this idea published in PNAS is freely available online here.
Let me know what you think of this theory.
TTFN,
WK

This message is a reply to:
 Message 113 by Syamsu, posted 06-04-2004 12:58 PM Syamsu has replied

Replies to this message:
 Message 119 by Syamsu, posted 06-07-2004 11:32 AM Wounded King has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 120 of 276 (113310)
06-07-2004 12:29 PM
Reply to: Message 119 by Syamsu
06-07-2004 11:32 AM


Dear Syamsu,
The interest of doctors might be on the individual but I would deny that the focus of biologists is, most emphatically. As I pointed out, you may need to study a number of individuals to draw general conclusion but the study of any specific instance is not the purpose of biology, except in as much as it increases our knowledge of variation within the general population. Medicine which hstarted out as a great discipline of generalisation from basic anatomy on down/up and is only now really focussing on the benefits of understanding the variations between people in crafting individual treatments, having previously only seen the variation in things such as hereditary syndromes and congenital defects.
You are merely being obtuse with your comments on a case where the population as a whole is decreasing. The fact that the population as a whole is decreasing does not mean that there is not still differential fitness amongst varying sub populations, it does not exclude the possibility of extinction at all. In the most extreme case where a sampler blithely ignored the numbers of the population and only measured the proportions of the variants then there could be a scenario where the frequencies of all the traits suddenly go to zero since the entire population has vanished, but it is absurd to propose this is how pop. gen. studies are intended to work. If you are trying to sample organisms for a pop. gen. study then the total population is obviously going to be an important factor to ensure you have a large enough sample to be representative of the population. Evolutionary biology is not carried out in a vacuum, it is intinsically linked to all the other many and varied branches of biology. Scientists studying the pop. gen. of a population are also likely to be studying its population dynamics.
Trait A was photosynthesis for instance, only identified as variants with green coloring by those seeking to abstract in terms of populationshare. So how have you helped anything by ignoring how photosynthesis works in individuals?
This is sheer nonsense. You seem to believe that NS/ population genetics must be able to explain everything in glorious isolation with no reference to any other field of biology. You need not understand how photosynthesis works to see that organisms with the 'green' trait are outcompeting non-green organisms, you might need to work out what was going on in photosynthesis to begin to explain exactly why that trait was leading to an increase in fitness, and if you saw that the trait only conferred a benefit in populations with access to sunlight that might set you on the right track. If you were truly looking at the genetics, in terms of the actual DNA sequence, then you might be able to isolate the specific locus/ loci of the trait and begin to dissect out the photosynthetic process genetically. It is facile to do this sort of thing with our current knowledge, the benefit of NS/ pop. Gen. is that it can help you identify interesting traits (either beneficial or detrimental) in the first place and you can then go on to find out exactly what those traits are and how they confer that benefit, ideally at least.
This isn't how photosynthesis was discovered historically but it wouldn't be theoretically impossible. If you had the neccessary molecular biology and genetics knowledge, but lacked the microscope as a tool, you could probably determine much of the genetics and biochemistry of photosynthesis but you probably couldn't deduce the structure of the chloroplast although you might be able to deduce its existence if you knowledge of other areas was advanced enough. Of course whether you could ever reach that sort of depth of knowledge without having ever discovered the microscope is another question entirely.
What is 'real' fitness?
The only thing I can say about the article is that it seems to be very far away from anything that would be in a basic textbook about either evolution or natural selection. I doesn't seem to me the authors are positing some fundamental theory of natural selection or evolution.
I can understand you wanting to see arguments at a basic textbook level, in fact I highly reccommend that you start reading some textbooks dealing with evolution at some point, it really would help.
If you don't see the relevance of this paper to the one you reference in the OP then I don't see what you saw in that first paper. The first paper proposed that statistical methods such as those used in thermodynamics were the appropriate analogies for the volutionary process. The paper I referenced show a specific appraoch where a statistical method analogous to that used to model uni-directional phenomenon in thermodynamics was used to model a uni-directional phenomenon in evolution, strenghtening the proposal that probabilistic thermodynamics, and not deterministic newtonian mechanics, is the right way to go to look for classical physical phenomena analogous to those we see in evolution.
TTFN,
WK
P.S. Do you still intend to contact the MODs?
P.P.S. Any feelings on the questions in my previous P.S.s?

This message is a reply to:
 Message 119 by Syamsu, posted 06-07-2004 11:32 AM Syamsu has replied

Replies to this message:
 Message 123 by Syamsu, posted 06-07-2004 2:09 PM Wounded King has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 124 of 276 (113341)
06-07-2004 3:20 PM
Reply to: Message 123 by Syamsu
06-07-2004 2:09 PM


Dear Syamsu,
Thank you for showing that you also fail to understand Dawkin's Selfish gene theory. One of the main points of which is that there is no dichotomy between 'selfish' genes and altruistic behaviour at the organismal level.
Thank you for finally addressing the issue of teleology in science. It was aristotle that formalised teleologies place in science and science is, with a few retrograde steps, moving steadily away from teleological theories.
I'll try and find you a suitable study tomorrow, I'm at home now so I only have access to abstracts not the full text of papers.
TTFN,
WK

This message is a reply to:
 Message 123 by Syamsu, posted 06-07-2004 2:09 PM Syamsu has replied

Replies to this message:
 Message 125 by Syamsu, posted 06-08-2004 6:11 AM Wounded King has replied
 Message 126 by Wounded King, posted 06-08-2004 6:26 AM Wounded King has not replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 126 of 276 (113539)
06-08-2004 6:26 AM
Reply to: Message 124 by Wounded King
06-07-2004 3:20 PM


Dear Syamsu,
A couple of papers relevant to the topic we were discussing. The first is a review of population genetic studies in 4 different endangered species and the second a study of bearded vultures.

A role for molecular genetics in biological conservation.
S J O'Brien
Proc Natl Acad Sci U S A. 1994 June 21; 91 (13): 5748—5755
The recognition of recent accelerated depletion of species as a consequence of human industrial development has spawned a wide interest in identifying threats to endangered species. In addition to ecological and demographic perils, it has become clear that small populations that narrowly survive demographic contraction may undergo close inbreeding, genetic drift, and loss of overall genomic variation due to allelic loss or reduction to homozygosity. I review here the consequences of such genetic depletion revealed by applying molecular population genetic analysis to four endangered mammals: African cheetah, lion, Florida panther, and humpback whale. The accumulated genetic results, combined with physiological, ecological, and ethological data, provide a multifaceted perspective of the process of species diminution. An emerging role of population genetics, phylogenetics, and phylogeography as indicators of a population's natural history and its future prognosis provides valuable data of use in the development of conservation management plans for endangered species.

Phylogeography, genetic structure and diversity in the endangered bearded vulture (Gypaetus barbatus, L) as revealed by mitochondrial DNA.
Godoy JA, Negro JJ, Hiraldo F, Donazar JA.
Mol Ecol. 2004 Feb;13(2):371-90.
Bearded vulture populations in the Western Palearctic have experienced a severe decline during the last two centuries that has led to the near extinction of the species in Europe. In this study we analyse the sequence variation at the mitochondrial control region throughout the species range to infer its recent evolutionary history and to evaluate the current genetic status of the species. This study became possible through the extensive use of museum specimens to study populations now extinct. Phylogenetic analysis revealed the existence of two divergent mitochondrial lineages, lineage A occurring mainly in Western European populations and lineage B in African, Eastern European and Central Asian populations. The relative frequencies of haplotypes belonging to each lineage in the different populations show a steep East-West clinal distribution with maximal mixture of the two lineages in the Alps and Greece populations. A genealogical signature for population growth was found for lineage B, but not for lineage A; futhermore the Clade B haplotypes in western populations and clade A haplo-types in eastern populations are recently derived, as revealed by their peripheral location in median-joining haplotype networks. This phylogeographical pattern suggests allopatric differentiation of the two lineages in separate Mediterranean and African or Asian glacial refugia, followed by range expansion from the latter leading to two secondary contact suture zones in Central Europe and North Africa. High levels of among-population differentiation were observed, although these were not correlated with geographical distance. Due to the marked genetic structure, extinction of Central European populations in the last century re-sulted in the loss of a major portion of the genetic diversity of the species. We also found direct evidence for the effect of drift altering the genetic composition of the remnant Pyrenean population after the demographic bottleneck of the last century. Our results argue for the management of the species as a single population, given the apparent ecological exchangeability of extant stocks, and support the ongoing reintroduction of mixed ancestry birds in the Alps and planned reintroductions in Southern Spain.
The second paper requires a subscription to see the full text but the abstract is detailed enought to show its relevance to our discussion.
TTFN,
WK

This message is a reply to:
 Message 124 by Wounded King, posted 06-07-2004 3:20 PM Wounded King has not replied

Replies to this message:
 Message 127 by Syamsu, posted 06-08-2004 9:58 AM Wounded King has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 128 of 276 (113578)
06-08-2004 10:27 AM
Reply to: Message 127 by Syamsu
06-08-2004 9:58 AM


Dear Syamsu,
Have you read the paper or only the abstract?
TTFN,
WK

This message is a reply to:
 Message 127 by Syamsu, posted 06-08-2004 9:58 AM Syamsu has not replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 129 of 276 (113582)
06-08-2004 10:57 AM
Reply to: Message 125 by Syamsu
06-08-2004 6:11 AM


Dear Syamsu,
Why not actually appeal to a moderator/ admin if you think I am flaunting the forum rules? They are contactable, e-mail the relevant mod or start a thread in a suitable forum. At the moment you seem to feel that bleating and passing my rebuttals off as complicated fudge and avoiding your points will be seen as a reasoned argument. Why not instead address my points or formulate your questions in a clear way which actually makes sense. Ideally these should actually be in the form of a question as well.
If you specify anything that you consider 'complicated fudge' I will endeavour to simplify it. I have often asked you to do the same thing with your own posts with a generally lamentable lack of success, akthough there have been a few instances of clarity breaking through in some of the threads we have discussed on.
I certainly don't appeal to my own authority, I believe you are being confused by what we term 'evidence' which is when there is actually something seperate from your own claims which supports those claims. I am not saying my argument is better than yours because of my authority. I am saying it is better because I have consistently presented evidence from the scientific literature to support my claims while the best you have managed is to repeatedly cannibalise a philosophy paper to cherry pick quotes you believe support your theories, and then repeated the same things over and over again.
If you object to my suggestions that you are unfamiliar or prone to misinterpretation of some basic areas of science then all you have to do is show that my claims that you lack understanding are false by addressing the specific issues on those areas which I raised, such as the place of Newtonian mechanics in science, and demonstrating the depth of your grasp.
TTFN,
WK

This message is a reply to:
 Message 125 by Syamsu, posted 06-08-2004 6:11 AM Syamsu has replied

Replies to this message:
 Message 130 by Syamsu, posted 06-08-2004 10:53 PM Wounded King has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 131 of 276 (113766)
06-09-2004 4:17 AM
Reply to: Message 130 by Syamsu
06-08-2004 10:53 PM


Dear Syamsu,
I'm quite sure that if I had argued that genetic drift and natural selection should be part of one theory, without referencing some paper, that you would have denied that there was any kind of prejudice in excluding genetic drift from natural selection. You would have referenced all the papers talking about genetic drift, so to suggest that there is no prejudice against genetic drift by excluding it from the logic of natural selection, just as you now suggest that there is no prejudice against extinction of all variants for the same reason, by referencing some paper mentioning extinction.
You haven't said whether you have read either paper, from what you say it sounds like you haven't. Both of the papers make a very explicit case for the importance of genetic variation in the study of extinction. Please, just because you aren't capable of supporting your arguments with evidence don't dismiss mine as irrelevant with a wave of your hand.
If you can't actually read the bearded vulture paper due to a lack of access then why not focus on the PNAS review which you certainly can get access to.
I have indeed shown that genetic drift is not excluded from the study of population genetics, in what way does this not rebut the suggestion in your paper. The fact that you have one highly speculative theoretical paper, albeit one that makes some interesting points, In no way makes the case you seem to think it does.
And also why don't you argue the same thing with Dawkins. How can Dawkins hypothesize selfishness and altruism in the beginning of the book, but not mention mutual benefit, and mutual destruction as part of the hypothesis? Is this a stupid simple error Dawkins is making, or am I being stupidly simplistic to assume that these rules in organizing knowledge would apply to actual science? Can't you see how prejudicial it is to lift out a couple of relationships, and ignore the others in the hypothesis?
No where you are being stupid is in commenting on a book which you appear not to have read beyond the beginning of the book. Dawkin's does deal with mutualism/ reciprocal altruism. There is a considerable body of literature about evolutionarily stable strategies and game theory which show how mutualistic relatonships evolve.
You can seperate trends due to selection from those due to drift in a study of a populations genetics, this doesn't mean that they operate in a way analogous to Newtonian forces.
Is it equally prejudicial to try and work out the motion of planets without factoring in the gravitational effects of Alpha Centauri? All you are showing is that you fail to grasp the way science is done at all, let alone in evolutionary biology.
The environment does not 'have' to select between one variant and another, it is quite possible to have variation which does not lead to a variation in fitness. Since you only determine a variation in fitness over successive generations there is no reason variants cannot have equal fitness.
are you saying that the environment selects between variant options to reproduce (as you quite emphatically said before in this thread)
Could you reference this? I have certainly never said it excludes the possibility of extinction, a population going extinct can still have one variant reproducing more than the others. As I pointed out this is only a problem if you insist on looking at the frequency of variation as a percentage or some such abstracted measure, you can just as well look at the raw data in terms of numbers and get the additive benefit of being able to measure the populations dynamics, it all rather depends on how you are doing your measurements/ experiment.
Population genetics does not exclude any of the relationships you have put forward. I do agree that whether an organism reproduces or not, is the filter through which selection operates but this is exactly the same as the environment selecting 'between variant options to reproduce'. The selection is done by the totality of the organisms environment, the other organisms in the same environment are under the same selecvtive pressures therefore the environment is selecting and that selection is reflected in the genetic contsitution of subseqeunt genrations which is determined by the reproductive success of specific variants in the previous genration. The environment 'selects' in the same way that a hill 'selects' the path a ball rolling down it will take.
TTFN,
WK

This message is a reply to:
 Message 130 by Syamsu, posted 06-08-2004 10:53 PM Syamsu has replied

Replies to this message:
 Message 132 by Syamsu, posted 06-09-2004 6:45 AM Wounded King has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 133 of 276 (113811)
06-09-2004 8:12 AM
Reply to: Message 132 by Syamsu
06-09-2004 6:45 AM


The fact that definitions contain different words does not neccessarily mean that they are not self evidently the same, whether they are 'exactly the same' seems like a point of semantics the way you present it.
The fact that reproduction is the filter through which selection acts does not mean that this has to be acting on all traits all the time. A population in which both variants are enjoying equal reproductive success and the gene frequencies are stable is not one where natural selection is in evidence, but it is something which is modelled by population genetics. It is also not evolution.
As I pointed out the population genetics are based on real numbers taking from the population those numbers will, unless some very poor experimental design was in evidence, reflect the numbers of the actual population.
I will admit that if absoloutely no organism in a population has any offspring then looking at population share breaks down but only because there is no population which will be self evident to those looking at the population genetics, you could then say that the population share of all the genotypes in the population was 0 but it is easier just to say the population is extinct.
Within that population one variant can be selected for over another and the population level still decrease. You can still look at it solely in terms of population share if you wish by simply looking at the population at a further remove. Local instances of extinction may occur after all but there are wider populations of which that is only a subset. Within that wider subset one specific population with its own profile of genetics and variation is rendered extinct. If you wish I could direct you to a number of papers which deal with local extinction and re-invasion of particualr environments, but you seem to have nothing but contempt for actual scientific research which relates to the questions we are trying to discuss.
I wasn't talking about both not getting selected, I assumed that your -/+ notation refered to population levels due to reproductive success, perhaps if you made the assumptions behind your notation more explicit things would be easier. The relationship between organism in terms of their roles as one anothers environment is a fairly complex concept with a lot of factors involved, you seem to be approaching it as something trivially easy to model.
Please just one straight answer, have you read either of the papers?
TTFN,
WK

This message is a reply to:
 Message 132 by Syamsu, posted 06-09-2004 6:45 AM Syamsu has replied

Replies to this message:
 Message 134 by Syamsu, posted 06-10-2004 1:41 AM Wounded King has replied

  
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