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Author
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Topic: Article in Commentary critiques eye evolution
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Argon
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Member # 276
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posted 12. June 2003 12:32
Pim writes:
quote:
I find it fascinating that Warren seems to be critiquing a paper which he has not seen or read. Warren's assertions and accusations seem to lack in reality and familiarity it seems to me.
This disconnect recurs frequently and is well documented.
Perhaps a prerequisite for posting in the Literature Review forum should be to actually read the paper.
[ 12. June 2003, 13:04: Message edited by: Argon ]
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warren_bergerson
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posted 12. June 2003 15:18
It appears from the materials presented here that Nilsson does use the expression ‘Computer modelling of eye evolution’ to refer to ‘Disney/Darwin type artistic representations of possible phenotype transformations’. IMO, it is materially misleading to refer to ‘phenotype transformations’ as ‘computer modeling of evolution’.
Apparently, as suggested by both the Nilsson and Pelger work and the Lenski study, peer review standards allow the publications that suggest or hint at the ability to model or simulate ‘the evolution of the eye’ or ‘the evolution of complexity’ when in fact the so called models or simulations would not meet rigorous scientific standards. Pulling a rabbit out of a hat is not ‘creating a rabbit’. Simulating a change in the size of a wing or beak is not the same as simulating the evolution of a wing or beak. Artificial mathematical transformations are not ‘demonstrations of the biological evolution of complexity’.
There is, it appears, a substantial difference of opinion as to what constitutes ‘misleading presentations’ and what constitutes ‘legitimate scientific demonstrations’.
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RBH
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Member # 380
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posted 12. June 2003 16:35
Warren claims quote:
It appears from the materials presented here that Nilsson does use the expression 'Computer modelling of eye evolution' to refer to 'Disney/Darwin type artistic representations of possible phenotype transformations'. IMO, it is materially misleading to refer to 'phenotype transformations' as 'computer modeling of evolution'.
And how "materially misleading" is it for warren to claim that an expression appeared in a paper that he has clearly not read? I have just reread Nilsson & Pelger's (1994) paper one more time. Nowhere do I find the expression "computer modeling of eye evolution," say nothing of seeing it refer to "Disney/Darwin type artistic representation of possible phenotype transformations."
The only occurrence of the expression "computer modeling of eye evolution" in this thread is in Pim's (10. June 2003 01:56 ) reference to this site on which Nilsson briefly describes the work that he and his colleagues are doing to follow up on the research reported in the Nilsson & Pelger paper. In that work, as I read it, they are actually testing evolutionary models that warren asserts do not exist: quote:
We now continue this line of research by computer simulations of eye evolution. These simulations are made to accurately mimic a realistic genetic control, and involves selection from populations of partially mutated offspring. The project has three principal aims: 1, to understand the conditions and criteria that select the fundamental optical types of eye (compound and simple etc) during early eye evolution; 2, to better understand the fine tuning of eyes to special visual requirements and habitat conditions; 3, to provide an insight into the mechanisms of genetic control required for evolution in general and eyes in particular.
warren further wrote quote:
There is, it appears, a substantial difference of opinion as to what constitutes 'misleading presentations' and what constitutes 'legitimate scientific demonstrations'.
One might also note that there is a substantial difference between criticism based on ignorance and informed criticism based on the knowledge of material that is enabled by actually reading it.
I note with interest (but no surprise) that warren still has provided no support for his false assertion about my interpretation of the paper.
RBH
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warren_bergerson
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posted 12. June 2003 19:46
RBH, like Shakespeare’s friend ‘may protest too much’, but there is at least strong circumstantial evidence that Berlinski’s complaint is valid. Nilsson and Pelger, and those siting their studies as evidence, do seem to be attempting to suggest that the old, old, Darwinian gradual change demonstrations can be passed off as some type of ‘simulation of evolutionary processes’.
As with even the most blatant misleading practices by those in power, there will always be ‘we would never do that’ and ‘you aren’t qualified to make such a claim" argumets. A fair number of individuals will look at Berlinski’s argument and note he is only stating the obvious, standard operating procedures in biology today. Others will respond as have most of the posters in this thread. Almost no one will change their opinions based on any ‘evidence’ or ‘arguments’ presented.
IMO, the only interesting questions raised are "Are there objective criteria and procedures which could be used to evaluate Berlinski’s claim?" and "Are there standards and procedures which would prevent the type of abuses Berlinski suggests may have occurred?". While we may debate whether the abuses occurred in this instance, there is no doubt that misleading research and misleading interpretations of research are not uncommon events.
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RBH
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posted 12. June 2003 21:04
Warren asks quote:
"Are there objective criteria and procedures which could be used to evaluate Berlinski's claim?"
I'll give you one novel approach: Read the Nilsson and Pelger paper. That will allow direct evaluation of Berlinski's claims about its contents.
I note (with less interest and still no surprise) that warren has still not addressed support for his false claim about my interpretation of the Nilsson and Pelger paper.
RBH
[ 12. June 2003, 21:08: Message edited by: RBH ]
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Pim van Meurs
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Member # 541
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posted 12. June 2003 22:14
Warren:
Your claims are close to insulting since they suggest without much supporting evidence or even an attempt on your part to read the relevant papers that scientists and especially those involved in evolutionary biology may be guilty of fraud and misleading statements.
quote:
While we may debate whether the abuses occurred in this instance, there is no doubt that misleading research and misleading interpretations of research are not uncommon events.
Truely amazing that Warren accuses others of misleading interpretations but fails to read the relevant research which he claims as examples.
I agree with RBH that so far (also not my surprise) Warren has failed to support these claims.
Certainly Warren's unfamiliarity with the research he criticizes should be an indication of the strength or weakness of his arguments.
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Rex Kerr
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Member # 632
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posted 13. June 2003 05:41
It's a little dangerous to assume a Gaussian distribution about a mean, select heavily for one tail, and then assume that the distribution is still Gaussian about the selected value. Unless I'm misunderstanding yersinia's summary, it looks like that's what N&P did.
A more realistic pessimistic estimate might provide time for allelic diversity to build up after successive rounds of selection. Domesticated species provide one way to estimate how long that might take (e.g. domesticated cats show a wide range of phenotypes despite having gone through a domestication bottleneck within 10k years or so). It would be interesting to see how inclusion of this factor would affect evolution times. They might have to be a bit less pessimistic (more realistic) in some of their other estimates to get an instructive result.
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warren_bergerson
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Member # 262
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posted 13. June 2003 08:13
It is probably a waste of time, but let me formally restate my position.
First, Michael presented a summary, based on Berlinski’s article, of a complex argument whose conclusion can be stated as "Nilsson, Pelger, and/or some of the individuals using their study are materially and knowingly misinterpreting the study and its implications". My comments stated that "Based on 1) the information presented in the discussion here, 2)information generally available, and 3)using objective evaluation criteria, the argument and conclusion presented by Michael based on Berlinski’s article at least appear to be valid( and will be recognized as valid by a fair number of observers).
The materially misleading ‘interpretations’ of Nilsson, Pelger, study can be stated as
1. The Nilsson and Pelger study provides scientifically significant evidence regarding the process by which the eye evolved. The suggestion has been made by Nilsson and others that the study is the basis for "Computer modeling of eye evolution".
2. The Nilsson and Pelger study provides scientifically significant analysis of the speed or rate of eye evolution.
The first interpretation is materially and knowingly misleading, 1) because it is not a new type of demonstration but simply a rehash of the Darwin’s gradual change demonstrations (the type of physical transformation that cartoonists like Disney have often demonstrated) and 2) because given the current state of knowledge, no computer models or simulations exist of complex evolutionary changes. To my knowledge, neither Darwin nor most scientists until very recent times, would have ‘interpreted’ gradual change demonstrations as models of the evolutionary processes.
The second interpretation is materially and knowingly misleading because it suggests or implies a scientific estimate of the rate at which the did or could have involved. Again, the knowledge needed to perform such scientific analysis does not exist. As described, the study simply calculates speeds based on arbitrary and non-validated assumptions.
I repeat, there appears to be a wide range of opinion and practice as to what constitutes acceptable and unacceptable interpretations of research articles. If , IMO, you impose reasonably rigorous scientific standards, then at least some of the interpretations and uses of the Nilsson and Pelger study have been materially and knowingly misleading. IMO, this rather obvious conclusion can be reached based on the information available.
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Michael Francisco
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Member # 769
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posted 13. June 2003 11:12
As to the 'you need to read the article' argument: I have read Berlinski's article, the Nilsson and Pelger paper, and most all of the responses posted on the internet (graciously linked by Pim).
As my second post made it clear, I think that parts of Berlinski's article are not entirely convincing given a close reading of the N&P article. (Particularly relating to all the 'missing calculations' which are apparently in the cited literature that he failed to look up).
However, I do believe that the article has been substantially misrepresented by those supporting evolutionary pathways to the complex system of the eye. The article does just what it says to do...(most agree to this), but what does the article not do?
My largest complaint with the article is that it models one aspect of eye evolution, admits important aspects of eye development that are left out, and then makes bold claims about timeframes for eye evolution. It seems that using the N&P article to provide a timeframe "300,000 years" estimate of eye evolution is quite misleading.
The misleading nature of the article's use also includes the somewhat stale 'model' vs 'simulation' debate. As I previously stated, these words can be nearly synonymous, but to many readers, and in the context used by Dawkins specifically, calling the work a computer simulation of eye evolution, or a computer model of eye evolution for that matter, seems to imply the article proves more than it does.
Hence my conclusion that Berlinski’s article is useful for nothing less than calling attention to a widely used scientific article that proves less than is claimed of it.
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Pim van Meurs
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Member # 541
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posted 13. June 2003 12:19
Warren about Berlinski argues that Berlinski claimed that:
"Nilsson, Pelger, and/or some of the individuals using their study are materially and knowingly misinterpreting the study and its implications"
What worries me is that without having read the relevant paper(s) and without much reservation Warren seems to accept his 'interpretation' of Michael's conclusions and extends it to other biological research without much effort to provide any supporting evidence for his claims.
Thus it is fascinating when Warren objects to the study based on 'As described, the study simply calculates speeds based on arbitrary and non-validated assumptions."
And yet that approach seems to describe many of Warren's 'assertions' about Darwinism.
Thus when Warren claims:
quote:
I repeat, there appears to be a wide range of opinion and practice as to what constitutes acceptable and unacceptable interpretations of research articles. If , IMO, you impose reasonably rigorous scientific standards, then at least some of the interpretations and uses of the Nilsson and Pelger study have been materially and knowingly misleading.
I would certainly agree that claims by those who have not spent the time and effort to actually read the paper may have been erroneous. Of course to claim that this was knowingly misleading is something that only those individuals can resolve. Certainly in a scientific discussion it seems to be an acceptable presumption that those who criticize a certain position have taken the time and effort to familiarize themselves with the relevant issues.
So far however Warren's arguments have been imho sloppy, insulting, illogical and unsupported.
Examples of such can be found in Warren's postings including
quote:
A fair number of individuals will look at Berlinski’s argument and note he is only stating the obvious, standard operating procedures in biology today.
and
quote:
While we may debate whether the abuses occurred in this instance, there is no doubt that misleading research and misleading interpretations of research are not uncommon events.
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warren_bergerson
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posted 13. June 2003 15:35
Quote: Hence my conclusion that Berlinski’s article is useful for nothing less than calling attention to a widely used scientific article that proves less than is claimed of it.
Pim, it appears, is concerned not with misleading literature and misleading uses of literature, but with the possibility that it might be possible for outsiders to recognize abuses in scientific research without going through an in-depth review and analysis.
As a starting point, it is important to note that misleading research and misleading uses of research is not a phenomena limited to evolutionary biology. Second, it appears that there are many similarities among the misleading practices used in different areas. Third, in many, even most instances, there are relatively simple techniques for recognizing a deceptive practice.
Berlinski and Michael Francisco point out that the Nilsson and Pelger article ‘proves less than is claimed of it’. It is not particularly difficult to confirm that this conclusion is valid, since what is claimed or implied to be present in the article is not known to exist anywhere else in the literature, and the individuals making the claims regarding the article have failed to provide confirming evidence supporting the claims. IMO, there are quite a number of individuals outside the biological sciences capable of recognizing the type of misleading claim being discussed here based on the information presented in the discussion.
The fact that there exists a wide range of opinions on what constitutes a deceptive practice and on how widespread these deceptive practices are in the areas of genetics and evolutionary biology. A statement of an obvious fact does not require supporting evidence. It seems somewhat misleading to interpret such observations as insulting .
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Rex Kerr
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posted 13. June 2003 18:07
The statement of an obvious fact absolutely requires supporting evidence, as what is obvious to one person may not be obvious to another, and some extremely "obvious" things are, in fact, wrong.
Added in edit: I suppose I should provide evidence.
Your obvious facts about deceptive practices in genetics and evolution are not obvious to me.
And it is obvious that when you look out at the world, you see what's out there in a continuous stream. (Except, nonobviously, your blind spot; various optical illusions; prediction of motion; during saccades, etc. etc. etc..)
[ 13. June 2003, 18:10: Message edited by: Rex Kerr ]
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Pim van Meurs
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posted 14. June 2003 13:02
Warren ponders:
Pim, it appears, is concerned not with misleading literature and misleading uses of literature, but with the possibility that it might be possible for outsiders to recognize abuses in scientific research without going through an in-depth review and analysis.
Warren is using what I consider to be misleading terms here since I have never stated that I am not concerned with misleading uses of literature. In fact I opposed quite strongly Warren's conclusions about the above mentioned papers without Warren having had an opportunity to actually read said papers. Such approaches to 'scientific inquiry' can easily lead to misleading and/or erroneous conclusions. Hence my suggestion that Warren supports his assertions based on the actual papers.
Warren continues to make claims he (may I say as usual?) fails to support with any evidence. An obvious fact he claims? If it were that obvious surely Warren would not have such trouble making a convincing case?
As Rex points out so clearly "Your obvious facts about deceptive practices in genetics and evolution are not obvious to me."
Warren's continued claims about deceptive practices in science remain insulting when they are unsupported by any relevant evidence.
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RBH
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Member # 380
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posted 14. June 2003 19:43
Warren made another significant mis-statement it might be worth correcting. He wrote quote:
The materially misleading 'interpretations' of Nilsson, Pelger, study can be stated as
1. The Nilsson and Pelger study provides scientifically significant evidence regarding the process by which the eye evolved. The suggestion has been made by Nilsson and others that the study is the basis for "Computer modeling of eye evolution".
...
The first interpretation is materially and knowingly misleading, 1) because it is not a new type of demonstration but simply a rehash of the Darwin?s gradual change demonstrations (the type of physical transformation that cartoonists like Disney have often demonstrated) and 2) because given the current state of knowledge, no computer models or simulations exist of complex evolutionary changes. To my knowledge, neither Darwin nor most scientists until very recent times, would have 'interpreted' gradual change demonstrations as models of the evolutionary processes.
Nilsson & Pelger provided evidence (not a conjecture or unsupported hypothesis) that there is an incremental morphological pathway from a flat patch of light-sensitive cells to a focused lens eye similar to a invertebrate eye. Where warren writes 'Disney," he might want to substitute D'Arcy Thompson, whose "On Growth and Form" is closer in spirit (and to some degree, in substance) to the Nilsson and Pelger work than is Disney. That presupposes, of course, that warren has heard of D'Arcy Thompson. Given his universal claims about the state of biological knowledge, surely warren must know D'Arcy Thompson's work.
The argument with respect to the eye by anti-evolutionists has been similar in part to that about IC structures in general, that there is no smooth incremental pathway to a developed eye and that therefore it could not have evolved by regular old Darwinian processes. What Nilsson and Pelger showed was not that the eye evolved (and they didn't claim to have shown that), but that there really is a smooth pathway to it.
Warren's use of "knowingly misleading" is, like Berlinski's hysteria, a red herring, drawing attention away from what was actually shown in Nilsson and Pelger's work that is so threatening to the IDist argument, namely, that there is a smooth path.
warren further wrote that it is materially misleading that quote:
2. The Nilsson and Pelger study provides scientifically significant analysis of the speed or rate of eye evolution.
...
The second interpretation is materially and knowingly misleading because it suggests or implies a scientific estimate of the rate at which the did or could have involved (sic). Again, the knowledge needed to perform such scientific analysis does not exist. As described, the study simply calculates speeds based on arbitrary and non-validated assumptions.
"The knowledge needed to perform such scientific analysis does not exist"? This from a non-scientist, a man who less than a year ago did not know how to access PubMed, and who even now apparently hasn't read the original Nilsson & Pelger paper? How on earth would he know whether "the knowledge necessary" exists or not? In actual fact, biologists and paleontologists have been routinely estimating rates of morphological evolution for some time and it is regularly measured in a number of contexts to gauge rates of evolutionary change. The unit of measurement of morphological evolution is the "darwin." I refer warren (or at least those readers who actually read the literature) to Google search, PubMed search, or PNAS search and read some of the results of the search. Nilsson and Pelger supplied references (which Berlinski failed to consider) to support what warren apparently claims are "arbitrary and non-validated assumptions," unless warren is referring to something other than the Berlinski misreadings. Once again, how would warren know that? Perhaps as a start warren should list the "arbitrary and non-validated assumptions" to which he refers, with specific reference to page numbers and text in the Nilsson and Pelger paper, so we know what's at issue in his view.
Finally, I note again (still with no surprise at all) that warren has not yet either supported or retracted his false claim about my interpretation of the Nilsson and Pelger paper.
RBH
[ 14. June 2003, 19:51: Message edited by: RBH ]
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warren_bergerson
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posted 15. June 2003 07:42
Frances/Pim, is back to his rather boring strategy of 1)not addressing any of the arguments being presented and 2)demanding anyone who doesn’t agree with his unsupported beliefs must provide evidence.
Rex- The issue of deceptive practices involves is the interaction between standards, practices, and enforcement. If the standards used to judge are consistent with standards operation practices and there is no enforcement/penalty for deceptive practices then, from the perspective of the standards used there are no deceptive practices. However, the same practices that are judged acceptable from one set of standards, may be classed as deceptive when viewed from another set of standards and using another set of enforcement rules.
As I have stated previously, I believe scientific standards should be dynamic best practices standards. As I have also stated, I believe these standards require, explicit formulation of models and theories, precise definitions of terms, variables and concepts, and one-test-falsifies testability. Studies of the type produced by Nilsson and Pelger are being interpreted as supporting some evolutionary theory, when, IMO, no theory meeting the required standards exists.
RBH- Quote: Nilsson & Pelger provided evidence (not a conjecture or unsupported hypothesis) that there is an incremental morphological pathway from a flat patch of light-sensitive cells to a focused lens eye similar to a invertebrate eye.
As far as I know, there is no serious scientific debate/interest on/in the question of ‘whether’ the eye evolved. There is no scientific debate/interest on/in the existence of an incremental morphological pathway for eye evolution. The questions of current interest in science are "By what processes did the eye evolve?" and "How fast did the eye evolve?"
It appears that Nilsson and Pelger may have provided a more detailed description of the eye evolution morphological pathway than previously existed. An improved or more detailed description of the pathway is undoubtedly of some scientific interest at least to specialists.
The study or the interpretations and uses of the study become ‘potentially misleading’ when it is suggested that the morphological pathway described provides ‘evidence’ relating to the speed of eye evolution or it is suggest the described pathway provides evidence relating to the processes of eye evolution.
Quote: The argument with respect to the eye by anti-evolutionists has been similar in part to that about IC structures in general, that there is no smooth incremental pathway to a developed eye and that therefore it could not have evolved by regular old Darwinian processes.
It will be noted that smooth morphological pathways exist by logical necessity. Cartoonist can and do create and demonstrate smooth transformations from one form to another (such as a transformation from animal to machine). Smooth morphological pathways by themselves tell us very little about evolutionary processes or speeds.
We know from selective breeding experiments that it is possible to generate some gradual morphological changes. This does not mean ‘any gradual morphological change can be induced’. The fact that 1)incremental change can be induced, and 2) some types of evolutionary change appear to involve incremental change, does not even support the conclusion that gradual incremental change is produced or caused by old Darwinian processes.
Quote: In actual fact, biologists and paleontologists have been routinely estimating rates of morphological evolution for some time and it is regularly measured in a number of contexts to gauge rates of evolutionary change.
Biologists can measure or estimate rates of some types of morphological change. They also know perfectly well that you can not simple extrapolate rates from on type of change to another, and that there are limits to how far you can extrapolate observed rates. The knowledge does not exist to predict the complex changes associated with eye evolution. The Nilsson and Pelger study provided only speculative calculations based on arbitrary assumptions, because that is all that is achievable with current knowledge.
Quote: Finally, I note again (still with no surprise at all) that warren has not yet either supported or retracted his false claim about my interpretation of the Nilsson and Pelger paper.
By all appearances, you continue to argue in support of the interpretations which are being labeled misleading.
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