Talk:Letter to PNAS

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It's an excellent draft, DinsdaleP. I made a few minor revisions above. After others improve this, then I'll plan on sending it to PNAS later this week. —The preceding unsigned comment was added by Aschlafly (talk)
I like it. I'll sign my name to it when the time comes.--DamianJohn 09:35, 22 July 2008 (EDT)

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Thanks for the feedback - When applying changes, please keep in mind that the "Text" section in the final version needs to be 250 words or less. If there are important points to add that would exceed this limit, they could be added to the main Flaws in Richard Lenski Study article instead since PNAS is being asked to respond to the full list there, and not just the summary. --DinsdaleP 09:47, 22 July 2008 (EDT)


I think if i would have presented some draft of that quality to my supervisor i think i would not have reached the door of his office alive and in one piece. It starts with the fact that the correct citation of the article is missing. Please use the appropriate form, inclucing journal number and page. Please have a look at other PNAS Letters. Restate the central issue you criticise in the first sentence, then explicitely describe what your claim about the same issue is and state using what method you come to your conclusion. Keep a neutral tone. Don't make requests. It is obvious that the original author should respond (please look at PNAS for examples of responses, which are published at the same location). Plese fill in your numbers and precise arguments at the points where i left the dots in the following suggestion (Please note that nothing of this is my opinion, i just tried to rephrase your opinions in a way that they have the chance to be exposed to a broader view - i skipped tyhe details, because i will not rephrase your arguments, just the structure):
Recently ...... inferred from their experiments (1) that ...... . We analyzed the statistical analysis in terms of ..... and conclude that several variables do not scale as .... . Using hypothesis tests under such circumstances is, in our opinion, ...... , and we do not understand how the authors of the original publication ..... their results.
The replay experiments yield an ..... scaling with .... . We do not find a consistent value of ..... between the experiments. Furthermore the statistical deviation due to ...... in each sample set does not allow to infer ..... with a sufficient precision. This lack of scaling makes, in our opionion a constant or random source of contamination a likely explanation for a random observation of the ...... dependence of the mutation rate claimed in the paper. The following calculation supports this hypothesis: ....... .
Furthermore we point out that Fig. ... contains a serious disagreement with .....: while the data would suggest ..... from gen. ..... the figure suggests .....
We find the material cited in the original article (2)...(n) about the same long-time experiment not to describe the following procedures and experimental constants in a way accessible to us: Handling of ..., contamination rates of ...., and ..... We would kindly ask the authors to clarify these issues. --Stitch75 12:48, 22 July 2008 (EDT)
No offense taken. I have no experience in these types of submissions, and would appreciate it if you could restructure the submission improve the quality while adhering to the 250-word limit. As I suggested above, it makes the most sense to incorporate these revisions into the main page for this article, where length is not an issue. --DinsdaleP 12:52, 22 July 2008 (EDT)
I realized that you have obviously not much experience in it; getting the right tone for a scientific publication is hard and i had to try it quite some times on conferences and i still dont get it right sometimes - and from what you said seem to be a student. Sadly, it is against my conviction to rephrase the original arguments in the right way because it would make me an co-author of argumentations i strongly object. In case you did not realize it, helping here to get the structure right doesn't mean i agree - actually the two reasons i would like to see it published is because then the (wrong) idea that scientific journals are not accepting criticism could be obviously be put aside and because i would like to see the needed scientific rigorousity applied to the arguments presented here, because this would put this discussion onto a scientific basis. Quite frankly - i am a liberal by the standards of this site. But i believe the discussion must be carried out with all respect to define the borders of science. The more effective the discussion is carried out, the better the outcome will be. I am willing to listen, as i have proven here, even when beeing treated by people like Mr. Schlafly as if I would be one of his students, while evaluating his qualification in natural sciences quickly shows that i more likely could supervise him in the issues he discusses here (which is something he has proven all along). Regarding that, i am close to giving up, but nevertheless i have seen that a lot of conservatives actually are willing to lead this discussion in a scientific way, which is something, which fulfills me with hope. I recommend you not to fight a fight in where you don't understand the arguments. Don't pick up arguments from others. If you can not fill in the missing words, numbers and arguments in my text, i cant help you. I see what Mr. Schlafly believes, however i do not know how to get the calculation right to support his hypothesis (random or contant mutation rate) - and, this is most likely not because of a lack of statistical knowledge. The only way i would see is to use the rudest form of descriptive statistics and agreggate the data in a very specific way, while ignoring the structure of the experiment - and ignoring the fact that the authors pointed out the problem they see and adressed them. So i can only give oy a few hints (maybe i can form a short contibution to conservapedia; i am just thinking about the title):
If you claim something is wrong, put your opposing claim in a positive formulation, with a supporting calculation, in contrast . Even if the calculation is simple, this is very important to provide it. E.g. we estimate a rate of x+-y per z for dataset N, in which we aggregated generations a,b,c,d, etc .... In the end, you should either prove a mathematical mistake (which was not done) or shoe you hypothesis is more likely.
Don't be rude. You are not the referee and you are not member of a commitee to examine scientific misbehaviour. Dont act like one (and even referees have a friendlier tone usually). Dont act like an personal enemy either. Don't ask for retraction of the article. It is up to the author to make the conclusion respond or retract. This happens more often than you may think as a response to an critisism (actually it's fun to read the "reply section" of scientific journals - sometimes you find things like: "yes, the commenter was right we copied the paper and retract it"). And you are never requesting, but you are kindly asking. Everybody understands that "kindly asking" does not mean "kindly asking" in this context.
Always give full and specific citations which back your claims. Give it in the form required by the specific journal. General citations like "materials on his website" will make your text bein trown out in the editorial screening (because you can not expect that somebody read trough all information to find something backing you claim - this is your job). See for specific styles [http://en.citizendium.org/wiki/Citation_style]. Ypu may even reference a page/paragraph/eq/figure number to point the reader to what you mean (for papers longer than 4 pages i usually do that).
Run a style checker over your text to eliminate common style mishaps.
Most important: go to your university library. Take the time to just read a few PNAS Letters and replys, and the original articles (Try to finde some with an easy understandable subject). Understanding how these are written and how authors usually reply will help you to get your one right. You are writing against somebody who has twenty years of experience in a field of publishing in natural sciences. You seem to have little experience and Andrew Schlafly, honestly, neither. This game is an uphill battle and unfair game anyway. Make sure you maximize your chances by understanding the rules of the game.
Focus on a single you are sure about. It is better to present one claim well that two claims badly.
Good luck. You will need it. --Stitch75 14:22, 22 July 2008 (EDT)
"Stitch75", you seem to think that the truth depends on whether PNAS accepts it. It doesn't. Lenski's paper is badly flawed regardless of whether he admits it, PNAS admits it, or you admit it. That's the beauty of the truth: it doesn't require admission by anyone. I'm fine with Lenski and PNAS refusing to admit the flaws in their paper. After all, if they really cared about quality then I doubt they would have published their flawed paper after merely 14 days or less of peer review.--Aschlafly 15:38, 22 July 2008 (EDT)

I tend to agree with you Andy. I say we get this thing sent to PNAS and see what happens. If they refuse to answer it then we know what that means, and if they thumb their noses at you that's fine too. However I have a little more faith than you in the system and I hold out hope that they'll respond to our queries. Anyway lets get this thing sent. --DamianJohn 15:50, 22 July 2008 (EDT)

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I'd like to thank Stitch75, because he took the time to explain his points constructively, and I learned something from them. (I'm actually an IT Specialist in my 40's, not a full-time student, but learning is a never-ending process and I appreciated the lesson). I consider myself bound by the same ethical constraints on editing that he mentioned, because these objections to Lenski's work are Mr. Schlafly's, not my own. I tend to believe that the Lenski experiment was properly executed, but I'm a strong believer in the scientific process, and Mr. Schlafly's objections deserve a fair hearing whether one believes in them or not. My contribution is to help in the process of getting these objections to the proper forum, namely PNAS, and leaving the response up to them. --DinsdaleP 16:20, 22 July 2008 (EDT)

Stich has given you brilliant advice, and you throw it away. He has told you that your letter will not get published, and it will have nothing to do with it's content. And when it doesn't get published you will claim it as a victory. If you take his advice and continue to take it, you will make it so no one can simply claim your letter wasn't accepted because it didn't match the criteria set out for letters to PNAS. Now if you have a well written and correctly laid out letter, and then it isn't published, at least you have a leg to stand on.

As a lawyer I would have expected you to understand that certain documents need to be written in set styles, and obey certain rules. Have you published anything (this isn't meant to be derogatory, it's a geniune request), I am positive you must have done so. When you did your citations would have had to be correctly arranged, and many other rules obeyed. Law suits are written up in a set style, and no one would dream of simply scribbling a note and saying check out this website, and expect to be taken seriously. So why do you expect a scientific journal to accept whatever you send them? Follow the procedures, then you have a right to complain if nothing happens. Raggs 10:12, 25 July 2008 (EDT)

Stitch75's advice has already been disregarded, and it seems as though you have arrived at your final word choice for the letter. I think that the letter in its current state is fatally flawed and would not warrant publication by PNAS or any other reputable scientific journal. I say this not because I think that the objections raised in the letter are misguided, but because they are presented as assertions without rationale or supporting evidence. For what it's worth, I'll address the five points individually and offer suggestions to improve them:

Your insulting tone (any other "reputable" journal) discredits yourself, but I'll respond this one time to you below.--Aschlafly 22:22, 27 July 2008 (EDT)
1)Drop the complaint about Fig 3. The paper's hypothesis does not depend upon the jump in mutation rate happening at 31,000 generations; it's merely a graphical representation of the difference between the contingent hypothesis and the rare mutation hypothesis. Nobody has objected that the y-axis of the graph lacks numerical values, have they? Also, since this figure represents the hypothesis formed before the data was obtained, where should the jump have gone? It's location is arbitrary until the data is collected. The abstract and the results section state that the data supports a potentiating event at the 20,000th generation. Since the paper does state the p-value of the third replay, it's inaccurate to say that the paper fails to admit anything.
No scientific paper should present a graphical depiction of a falsehood, without indicating that it is false. Figure 3 suggests that the potentiating mutation occurred at the 31,000th, despite the data proving otherwise. If the authors won't correct that error, then they're unlikely to correct any other error also.--Aschlafly 22:22, 27 July 2008 (EDT)
It is not a falsehood; it is a hypothesis. The hypothesis must be formed before data is collected. They hypothesis was that a potentiating mutation occurred that increased the rate of mutation to Cit+. Prior to running the experiment, it is impossible to know when (or even whether) that potentiating mutation occurred. Given that, it is not an 'error' to show the jump at the 31,000th generation, or the 15,000th, or the 10,000th - any point picked for the figure is abitrary. The hypothesis was not that a potentiating mutation took place at the 31,000th generation. For Lenski to put the graph jump at the 20,000th generation would imply that he got the data and then altered the original hypothesis to make it a perfect fit with the results - and that would be an ethical breach. The data collected suggest that the hypothesis was correct in that a potentiating mutation took place - and they further suggest that this mutation took place at about the 20k generation point. This does not disprove fig 3; it refines it. Again, you may as well object that fig 3 doesn't provide numerical values on the y-axis.--Brossa 10:39, 28 July 2008 (EDT)
2)This point is where I think your best argument lies, but it should be restated along the lines of: the null hypothesis suggests a fixed mutation rate rather than historical contingency. However, the largest replay experiment did not demonstrate the expected increase in Cit+ mutations, and was consistent with the null hypothesis with a p-value of 0.0823 by the Monte Carlo test method.
Your reply to the second point is unresponsive to the flaw. You seem to completely misunderstand it, or hope others do. Any fixed "mutation rate" should scale with sample size, yet the data prove otherwise.--Aschlafly 22:22, 27 July 2008 (EDT)
Previous comment removed by Kallium 09:01, 30 July 2008 (EDT)
The paper plainly states, "The third replay experiment was similar in design to the second, but on a larger scale." So I don't know why you imply that the experiments were significantly different. Yet the results from the second and third experiments do NOT scale with sample size, thereby disproving any plausible type of fixed mutation rate.--Aschlafly 23:22, 29 July 2008 (EDT)
Sorry- I reread the supporting materials and methods and you are correct about the experimental conditions. Perhaps I was confusing with the first; I don't know. In any case I have retracted the comment.
Nonetheless, claiming that the lack of expected scaling disproves the entire paper is still an unsupported methodological leap. The point is that based on the good P-values, the Cit+ clones arose later than expected in all three replays (independent of one another) based on the mathematical model of the null hypothesis. Thus it was apparently not a single, fortuitous and completely random event. I explain that under #3 below as it is better suited to that section.Kallium 09:01, 30 July 2008 (EDT)
The third replay experiment was similar in design but clearly, not the same in some aspects. As I noted previously, their plating densities were higher in the third experiment. That was an change in the experimental conditions. Blount et al. noted that the results produced a smaller number of mutants than expected -- assuming the conditions really were comparable -- but apparently, the conditions were not effectively the same.--Argon 20:52, 31 July 2008 (EDT)
You write, "but apparently, the conditions were not effectively the same." That's known as circular reasoning. You can't accept that the mutations do not scale, and so you insist that somehow the conditions "apparently" must have been significantly different. Under your approach, you'd insist there must have been a significant difference in the experiments no matter what the evidence is or what the paper says (it says they were similar).--Aschlafly 20:57, 31 July 2008 (EDT)
At a basic level Argon’s argument is not circular. Any appearance of circularity arises from ambiguous wording in the last clause in his statement.
We have three propositions:
1. If the conditions were the same the same then the results would be the same (“if C then R”)
2. The results were not the same (“R”)
3. The conditions were the same (“C”)
These three premises are inconsistent. That being so, you can set any two of three as the premises and negate the third as the conclusion. The second proposition is not an issue: all are agreed that the results were not the same (did not scale). So the question is do we accept the first proposition and reject the third or do we accept the third and reject the first? That is to say do we argue:
First argument:
C
Not-R
Conclusion: Not-if C then R
Or do we argue:
Second argument
If C then R
Not R
Conclusion: Not-C
Neither argument is circular (does not have its conclusion as part of its premises). The choice between them may be arbitrary but what we have is a lack of corroboration of the disputed premises (“If C then R” and “C”).
Except that we do have alternative corroboration for the conclusion of the second argument and the negation of a premise in the first argument: “Not-C” is specifically stated in the paper, necessitating rejection of the first argument.
If you reject the first argument on the basis of the second argument then it would be circular (you conclude “Not-C”, thus you reject the first argument, thus you adopt the second, thus you conclude “Not-C”, which is where you started from). Whether Argon has done that depends on what “apparently” refers to. If it refers to the paper saying it was not the same then it isn’t circular. The argument is
the paper says “Not-C”,
thus you reject the first argument,
thus you adopt the second,
thus you conclude “Not-C”
“Not-C” does not support “the paper says “Not-C”” and the circularity is broken.--Toffeeman 09:07, 1 August 2008 (EDT)
In the third experiment, additional clones were used. The authors write: "Clones were chosen to maximize the diversity of colony morphologies from each sample, in case only certain types could produce Cit+ mutants." This is different from the selection of clones in the first and second experiments. Also in contrast to the second experiment which grew cells in DM500 media, they used DM1000 and DM2000 media to grow the cells in the third replay. Cells were plated at higher densities in the third replay experiment.
As the authors comment, when they designed the third replay conditions, they assumed that their changes would not cause significant differences. Still, there clearly were differences in the results and there were some differences in the conditions. Note that if, as Andy initially suggested, the initial cultures were contaminated with Cit+ cells, one might expect that contamination to scale as well between the second and third experiments.
In any case, the authors clearly noted the anomaly, admitted that they're not sure why it happened and cited the statistics from the third replay experiment in their paper (The results still trended with the previous experiments). It's up for readers to decide whether their conclusions are reasonable, based on the data the authors have presented. Most likely, future experiments, particularly with whole genome sequencing of the isolated clones, will confirm or deny the paper's conclusions. That's pretty much how science works at the cutting edge. Another method would be for you to find a microbiology lab to request the clones and try reproducing the experiment.--Argon 12:14, 1 August 2008 (EDT)
Argon, making basic errors of logic and statistics and ignoring flaws even after they are pointed out is not "pretty much how science works at the cutting edge," as you put it. It's clear that nothing will persuade you to question this paper. Your herculean efforts to claim that the third and second experiments were so different as to explain their failure to scale is disproved by common sense, logic, and the paper's own statement that these experiments were similar. At this point I suggest that you open your mind for your sake. But you have free will to do as you like, including even insisting that 2+2=5.--Aschlafly 12:35, 1 August 2008 (ED
Andy, it's no skin off my teeth if future results disconfirm the current hypothesis. I never publicly called Lenski out or asserted that his conduct was unbecoming when I hadn't read the paper fully. I was never 'rebuked' publicly by Lenski. I don't have papers or grants subject to review by Lenski or a relationship anyone in his lab. So no, I don't 'have a dog' in this debate.
Science is tentative at the cutting edge. I do not think for one moment that the paper is the "be all and end all" of all research on the subject or that every detail has been exhaustively investigated. I do question the paper, like all first papers in a research topic, but on the whole, I think the conclusions are *reasonably* supported. In my work with bacteria I have seen very different results from what I initially presumed were relatively insignificant changes. Later experiments suggested why the experiments were unexpectedly sensitive to those changes. For the Cit+ work from Lenski's lab, I'm pretty confident that later experiments out of Lenski's lab will either more solidly confirm or ultimately reject the conclusions of the Blount paper. The best data will come from sequencing work being planned now. But at least for now, I think theirs is a reasonable conclusion, given what they've encountered so far. YMMV.
Of course, imagine the better quality dialog you might have had if you'd waited until now to contact Lenski with specific questions based on a thorough reading of paper. In any case, as I mentioned previously (message now gone), if you're convinced of what you've written, by all means please fire off your letter --Argon 14:33, 1 August 2008 (EDT)
Argon, I find your comments to be incoherent. You've already been blocked once for your endless, uninformative talk, and if you post more rants rather than contributing to this encyclopedia then your account will be blocked permanently. Godspeed to you if you decide to leave.--Aschlafly 17:13, 1 August 2008 (EDT)
3)The claim that the use of Monte Carlo resampling test was an error is unsupported by argument or counterclaim. Why is the use of that test an error? Problematically, if the test itself is invalid, why are you willing to accept the p-value for the third replay? Furthermore, the Monte Carlo test was not the test used to combine the three experiments to arrive at the final p-value of p<0.0001 - that was a Z-transformation method. Perhaps your real objection lies with this technique rather than the Monte Carlo test.
Monte Carlo resampling will often result in small p values for rarely observed events, and it is error to use that technique to draw conclusions in such circumstances. By the way, I don't accept that approach for analyzing the Third Experiment. The data in the Third Experiment are entirely consistent with the null hypothesis.--Aschlafly 22:22, 27 July 2008 (EDT)
In your own words, "your reply... is unresponsive to the flaw." Would you care to reference that statement about Monte Carlo resampling? Why don't you accept that approach for analyzing the third experiment- would you care to explain that statement or keep repeating it? And what statistical calculations can you present to support how the data for the third experiment are consistent with the null hypothesis? You complain about others' flawed statistics yet your statistics are strangely absent.Kallium 23:06, 27 July 2008 (EDT)
If you can formalize your objection to the Monte Carlo resampling, then by all means do so and include it in the letter - with a reference, if possible. This is an honest suggestion, not sarcasm. Something along the lines of 'With one million resamplings without replacement, the Monte Carlo technique will potentially underestimate the p-value by x% if the probability of an event is below y; see Statistician et al, 1997'. If you're basing your acceptance of the null hypothesis on some other statistical technique that gives you some other p-value, then you should report the technique and the p-value. If you think that the Monte Carlo technique gives a lower bound to the p-value, such that it must be higher than 0.08, then say so.
Although the P-value for the third experiment was not equal to or less than the arbitrary 0.05, but was instead 0.0823, this is still not consistent with the null hypothesis. Consider the alternative perspective- if you're 91.77% confident in deviation from the null hypothesis (based on P=0.0823), then conversely you could say that you are 8.23% confident that the null hypothesis was verified. To have been consistent with the null hypothesis, the P-value for the third experiment would have been in the ballpark of P=0.95. Thus a P-value of 0.0823 is nowhere near supporting the alternative hypothesis.Kallium 09:01, 30 July 2008 (EDT)
The null hypothesis does not have to be proven; it is assumed to be true by default. The burden is on the experimenter to disprove the null hypothesis. The 0.05 point is a historical accident and is arbitrary, but hallowed by long use. There may be only an 8% chance that the null hypothesis is correct in the third replay, but that's enough. That doesn't detract from the fact that the combination of replay experiments was highly significant.
It is interesting to note that the results for the second and third replays were presented in such a way as to minimize the number of times that an individual cell mutated to Cit+; the data are presented as "independent Cit+ mutants". It is mentioned that in the third replay 7 of the 8 plates gave rise to multiple Cit+ colonies, which was attributed to a two-mutation process; one of which took place during the population growth phase and one that took place after the bacteria were plated. Had the results been reported as 'number of Cit+ colonies formed', the mutations would have 'appeared' to scale better. I'm not arguing that the data should have been presented that way - I think that the inter-replay scaling is a red herring. It would also have made it impossible to include the first replay, since in that setting it was impossible to state just how many times the Cit+ trait arose independently in those cultures - almost certainly just once per culture, but not provably. What matters is that the intra-replay pattern of Cit+ mutation was the same across 3 different experimental setups. --Brossa 19:05, 30 July 2008 (EDT)
4)It was not 'an error' to include later generations in the replay experiments, because those generations provide information that bears on the contingency hypothesis- they can indicate if the contingency 'window' closes. It would be a valid request that the authors provide an explicit description of the techniques used to exclude the presence of occult Cit+ cells from the samples used in the replay experiments. At some point you will have to accept or reject that it is possible to do so, routinely, using basic laboratory techniques. If you accept that it is possible, the only way to prove that the routine procedures failed is to repeat the experiment with more rigorous controls and show a different result. Otherwise your objection boils down to "because I said so". If you reject categorically that it is possible to screen all Cit+ cells out, then all of microbiology comes into question, because these are truly fundamental techniques used across thousands of labs for many, many years.
Your analysis here is absurd. Trace Cit+ cells inevitably existed after the 31,000th generation, and it's foolish to claim otherwise. It was error to include these generations in the data, and there was no valid reason to do so. The potentiating mutation, if any, would have occurred earlier! Indeed, it occurred before the 20,000th generation according to Lenski's own analysis.--Aschlafly 22:22, 27 July 2008 (EDT)
You completely missed the point of Brossa's comment and again only keep repeating yourself without elaborating. Do you have experience employing the bacteriological methods referred to?Kallium 23:06, 27 July 2008 (EDT)
The statement that trace cit+ cells inevitably existed after the 31,000th generation requires that there are no techniques to remove them from the mixed-population sample. As others have told you, these techniques do exist and are reliable. You can request that PNAS publish exactly what technique was used (most likely dilution and plating on an indicator medium). Your option then is either to attack the method (difficult, since the techniques have been around for a very long time) or the execution (which would require that you or someone else repeat the experiment with the same technique and obtain different results).
Or, taking a different tack - the paper states that it is impossible to exlude an origin for Cit+ that is earlier than the 31,000th generation. So how many generations prior to 31,000 should have been eliminated from the replay?--Brossa 10:39, 28 July 2008 (EDT)
5)This point is, in my opinion, the worst of the lot, mostly because it is meaningless - what does 'combined based on outcome rather than sample size' mean?- but also because it restates the claim in #3, that there was some problem with the technique used to combine the three experiments into a final p-value. If you object to the Z-transformation method, you should state why; if you object to the result, you should be able to say what you think the result should be - with a different p-number that you calculate yourself.
The hypothesis of a mutation rate is obviously dependent on sample size, yet the paper combined the results of experiments having vastly different sample sizes as though that did not matter. Point 5 illustrates that the self-contradiction of the statistical analysis in the paper.--Aschlafly 22:22, 27 July 2008 (EDT)
Again, show what you think is wrong by showing statistically what should have been done and what numerical results should have been obtained. Recall the bridge analogy, if you read it.Kallium 23:06, 27 July 2008 (EDT)
The combination of samples of different sizes is standard practice in the sciences - so you must be objecting to the particular technique used. If you object to the Z-method, state your reasons in the letter. If you have a preferred method, state it in the letter and defend it. Best of all, use your preferred method and present your results. By 'the hypothesis of a mutation rate', are you referring to the calculations of mutation rates? Because the data for those calculations were not obtained from the three replay experiments.--Brossa 10:39, 28 July 2008 (EDT)

I would hope that you would at least run this letter past a sympathetic scientist (someone from DI?) before you submit it, to confirm that these concerns are in a legitimate format.--Brossa 20:10, 27 July 2008 (EDT)

Oh how you cling to the views of others! Logic does not depend on what some think, or the perception of what some think. The readers of this page are smart enough to look at the logic and admit the truth. So are you. Rest assured that logic does not care that some reject it.--Aschlafly 22:22, 27 July 2008 (EDT)
Oh how you cling to your views! The problem with logic is that it only works with knowledge- almost all of the replies on this page have been trying to teach you something about microbiology and/or statistical analysis but you are convinced you understand it better than those who have many years of experience working with them, although you continue to misinterpret basic concepts covered in any undergraduate microbiology, genetics or statistics course. Where is the logic in ignoring the input of all those who have actual training and experience in the fields you are discussing? How is that having an "open mind"?Kallium 23:06, 27 July 2008 (EDT)
Oh, how I cling to the views of others! Yes, which is why I have an accountant and an attorney and a doctor and a statistician and an architect - I accept that other people have greater experience and knowledge in certain areas than I do. If I want to charge my lawyer with malpractice, it behooves me to check with another lawyer to see if my complaint has merit, or if I'm even articulating the complaint correctly before I show up in a courtroom.--Brossa 10:39, 28 July 2008 (EDT)
I wasn’t planning on making any more comments, but in perusing other articles on this site I found that part of the Atheism article reminded me of Brossa’s comment:
“Christian apologist JP Holding rightly states that Bible exegesis and Bible exposition is a multi-disciplinary pursuit, and often critics of the Bible have not done a fraction of the due diligence required to make an allegation regarding the Bible. Holding states the following:
““Having now been engaged in apologetics for eight years actively and more years than that on the side, I have long since come to a conclusion that I have shared with others, but will now present in a systematic form here for the first time. My conclusion is a warning that is appropriate for any new readers (hence I link this article from my front page) and will be familiar to veteran ones.
"I'll sum it up to begin: Whenever you run across any person who criticizes the Bible, claims findings of contradiction or error -- they do not deserve the benefit of the doubt. They have to earn it from you. Here's why.
"It doesn't take very long to realize that a thorough understanding of the Bible -- and this would actually apply to any complex work from any culture -- requires specialized knowledge, and a broad range of specialized knowledge in a variety of fields....
"Not even most scholars in the field can master every aspect -- what then of the non-specialist critic who puts together a website in his spare time titled 1001 Irrefutable Bible Contradictions? Do these persons deserves [sic] our attention? Should they be recognized as authorities? No, they deserve calculated contempt for their efforts. (By this, I do not mean emotional or behavioral contempt, but a calculated disregard for their work from an academic perspective.) They have not even come close to deserving our attention, and should feed only itching ears with similar tastes.””
Now let’s change the academic subject (I leave out the introductory paragraph of Holding’s quote):
“Whenever you run across any person who criticizes scientific reports, claims findings of contradiction or error -- they do not deserve the benefit of the doubt. They have to earn it from you. Here's why.
"It doesn't take very long to realize that a thorough understanding of microbiology and evolutionary biology-- and this would actually apply to any complex work from any field of science -- requires specialized knowledge, and a broad range of specialized knowledge in a variety of fields....
"Not even most scholars in the field can master every aspect -- what then of the non-specialist critic who puts together a website in his spare time titled 7 Irrefutable Richard Lenski Study Flaws? Do these persons deserve our attention? Should they be recognized as authorities? No, they deserve calculated contempt for their efforts. (By this, I do not mean emotional or behavioral contempt, but a calculated disregard for their work from an academic perspective.) They have not even come close to deserving our attention, and should feed only itching ears with similar tastes.”
I do not post this as satire or mockery, but as another serious attempt to provide perspective. Ironic that Holding’s quote is in an article on Conservapedia, which at the same time is rightly concerned about double standards.Kallium 22:38, 28 July 2008 (EDT)


Brossa has made several excellent points. I would add that there is a disconnect between your primary claim and the list. You should rethink your thesis statement or choose different "flaws" that fit it better, since your primary claim that the flaws "negate [the paper's] claim that E. Coli bacteria underwent an evolutionary beneficial mutation" does not follow from those listed. With your flaws, with the possible exception of #4 depending on interpretation (and even then, where did the undetected Cit+ cells come from?), you are arguing against historical contingency, not whether or not Cit+ cells evolved. In other words, the flaws you claim are questions of mechanism, i.e. the dynamics of how the Cit+ cells arose, but your thesis statement questions whether or not they arose at all from Cit- populations. So even if those flaws were true, they would not negate the "evolutionary beneficial mutation" as you say but rather just historical contingency as a path to it. Kallium 21:23, 27 July 2008 (EDT)
No, point #2 indicates that the paper's data disprove any plausible mutation rate, because the mutations did not scale with sample size. Point #2 thereby negates the claim of "an evolutionary beneficial mutation" as insisted by the paper.--Aschlafly 22:22, 27 July 2008 (EDT)
See my above post regarding scaling of mutation rate. As for disproving "any plausible mutation rate", are you referring just to Cit+ variants, or truly any mutation rate? If the former, where do you propose the Cit+ cells came from in the first place, and if the latter, see my above post about basic microbiology. Also, your letter claims that flaw #2 disproves a fixed mutation rate, not, as you just said, any mutation rate. So which are you claiming?Kallium 23:06, 27 July 2008 (EDT)

Contents

Is this correct?

"The following flaws in this PNAS paper negate its claim that E. Coli bacteria evolved through a beneficial mutation" Flaws in an argument would tend to put the conclusion in doubt rather than show it to be false. Is the assertion that Lenski has not proved his point or that the data and methodology prove his point is false? This sentence reads to me to be asserting the latter. --Toffeeman 12:36, 4 August 2008 (EDT)

As explained here, several of the flaws do disprove some of the paper's assertions. For example, the Third Experiment disproves the contingency hypothesis as depicted in Figure 3. Also, the failure of the mutations to scale demonstrates that there is not a fixed mutation central to the paper.--Aschlafly 12:53, 4 August 2008 (EDT)

==How about this

I'm not going to say I know much about the science but I made this suggestion a few days ago (in the article page). It is certainly a lot shorter, and I think a little more polite. What do you think Andy

Word Count

Is the 250 limit for the body text - the 'meat' of the letter? Or everything? RobCross 11:42, 25 July 2008 (EDT)

I believe it applies only to the Text portion. --DinsdaleP 11:44, 25 July 2008 (EDT)


Completion of the cc: list

I don't think it's appropriate to submit without specific names in the cc: list. If those were meant to be placeholders then they need to be filled in ASAP. Also, the inclusion of congressional representatives overseeing funding does nothing but add an implied threatening tone to the submission. If this is about questioning his science as reported in the PNAS, then let's keep it focused there - PNAS has nothing to do with the funding of his research and this detracts from the focus of this submission. For that reason, I'm also removing the "refusal to provide data" line from this text, because it's out of the scope for what should be discussed with PNAS. --DinsdaleP 11:44, 25 July 2008 (EDT)

I agree with what you have said. I think we should send out a separate letter to the congresspeople. There are two separate, though very related issues. The rigor of the experiment (this is what PNAS deals with) and the fact that such research is given funding (Congress and the watchdog groups have to do with this part). Lets address the first problem before we look at the second. -RoyS 17:05, 25 July 2008 (EDT)
If the letter should find a broader audience, I would find i terribly interesting what the scientific advisors of the presidential candidates have to say about this. --Stitch75 20:22, 29 July 2008 (EDT)

Link in Letter

Andy or any of the other sysops: I think it would be a very good idea if you locked the page which the letter refers too. This is necessary, because the last thing we want is to be embarrassed by liberal vandalism that does not reflect what Conservapedia is really about. -RoyS 16:57, 25 July 2008 (EDT)

That makes sense to me - good idea. --DinsdaleP 16:59, 25 July 2008 (EDT)
Thanks. Also, we should completely check all of the sources and make sure each is completely verified, because we don't want are argument to be made less credible by some silly mistakes. -RoyS 17:02, 25 July 2008 (EDT)

Availability of data

The comment about the availability of data should be removed. The PNAS guidelines for letters [1] state that letters must not include "accusations of misconduct". They have a separate procedure for issues regarding data and material availability. ("Contact pnas@nas.edu if you have difficulty obtaining materials").--YoungA 09:18, 26 July 2008 (EDT)

I thought about this, but PNAS can simply omit the sentence at the end upon publication. It seems unnecessary and inappropriate to break this letter into two separate ones just for one sentence.--Aschlafly 16:26, 27 July 2008 (EDT)
It seems more inappropriate to knowingly submit something to PNAS that is against their guidelines and then expecting them to edit the unacceptable comment out on their end. I'd suggest that the "PNAS Letters" submission will be taken more credibly if we respect their guidelines, and instead send the version with the "withholding data" accusation to the appropriate parties separately, and copy PNAS as a courtesy. My grandfather told me I'd never regret taking the high road, and 40-plus years later his advice has served me well. --DinsdaleP 10:08, 29 July 2008 (EDT)
I agree fully with DinsdaleP especially because i doubt that they may edit something out. i could imagine some copyright reasons will contradict that. --Stitch75 20:19, 29 July 2008 (EDT)

My sixpenn'orth

I think this reads very sharply and is a pretty punchy 250 words worth - I know it's difficult to express complicated ideas so concisely. A couple of very minor, nitpicky comments: should Lenski's article have its PNAS edition/page citation in brackets? And I'd thought the Editor of PNAS would not be a cc, but the principal recipient.

Congratulations to Andy and all who contributed to this. Bugler 15:58, 27 July 2008 (EDT)

Thanks for your suggestions, which I've incorporated and addressed. Godspeed to you, Bugler!--Aschlafly 16:25, 27 July 2008 (EDT)

Mailing

Has it been sent yet?--YoungA 11:32, 29 July 2008 (EDT)

Not yet. I had to tend to some other duties recently. Any more suggestions?--Aschlafly 21:08, 29 July 2008 (EDT)
This is a very interesting letter. I would love to see how Lenski wriggles out of these points. However, unless it is sent soon I fear the topicality of the original will be lost and it will be buried away somewhere. I hope it gets sent very soon. Regards, AckerLite 10:58, 1 August 2008 (EDT)

Affiliations

I think the affiliation line is inappropriate, since it should not contain a job description, but the organization under which the reasearcher carries out his research (as a matter of fact i cant figure out the legal structure of conservapedia). In this case it could be no affiliation or Mr. Schlaflys Employer. As far as i understand (see the conservapedia video), conservapedia was founded by Mr. Schlafly as an additional resource to his educational work. As far as i understand he carries out his function as a teacher of precollege students in relation to the Eagle forum university (please correct me if this is wrong), which would make this his affiliation.

I am correcting you because your comment about Eagle Forum and my teaching program for precollege students is baseless and wrong.--Aschlafly 21:08, 29 July 2008 (EDT)
Mr. Schlafly, just for interest and avoiding future misunderstandings: The course advertised on the webpage of the Eagle forum University (Eagle Forum University), led by you is then different from your "pre-college" teacher duties. Did i get it right? Or does eagle Forum University purely advertise for external courses? Anyway i think the discussions here have come to a dead point, so i think it would be good if you make up your mind to send the letter. --Stitch75 12:23, 3 August 2008 (EDT)
Many people volunteer and provide course material to Eagle Forum University, a free site that welcomes learners of all ages. It's amusing how some liberals pretend there is a "vast right-wing conspiracy," or something like it, every thing someone points out how wrong a liberal statement or action is.--Aschlafly 14:53, 3 August 2008 (EDT)
For one who often complains of insulting comments from others, that was an unnecessarily hostile response. The line "please correct me if this is wrong" was straightforwardly asking for clarification. The appropriate response would have --Stitch75 12:45, 30 July 2008 (EDT)been, "My function as a teacher is not carried out in association with the Eagle Forum, so listing that as my affiliation would be inaccurate." It didn't warrant such an accusatory tone. That's the second time you've had a reaction like that to the Eagle Forum even being mentioned. Please read before you judge.Kallium 22:54, 29 July 2008 (EDT)
The conspiracy theories by liberals about conservatives are tiresome, and the liberal denials when confronted with the baseless errors are even worse. Wikipedia is filled with such junk, claiming that anyone the liberals disagree with is a creationist, a John Birch Society member, or some cultist. When the errors are removed, they reappear again and again, without apology by the people who make the errors.--Aschlafly 23:17, 29 July 2008 (EDT)
He's only asking if you're affiliated with you mother's organization. It's a fair question, it seems to me, and not a very far leap of logic. Corry 23:57, 29 July 2008 (EDT)
Corry is correct- it was just a question. And there are five problems with Aschlafly's response, all baseless claims of his own: 1) Where is the conspiracy theory he refers to (affiliation and conspiracy are not synonymous)? 2) Where is the denial of his correction that he is not affiliated with [won't mention the name since three out of three times it has been even mentioned, there have been very hostile responses]? There- I acknowledge that there is no affiliation with said other organization. 3) How did the original affiliations comment or my posts indicate political leanings (I in fact do not fit Aschlafly's description of liberals)? 4)What exactly was the error? "As far as I understand it" followed by "please correct me if I'm wrong" are not hallmarks of "baseless claims". The post simply demonstrated and incorrect understanding and a desire to assess its accuracy, a very rational approach. 5) What do any of Aschlafly's disagreements with Wikipedia have to do with being asked about affiliations on this site?Kallium 09:01, 30 July 2008 (EDT)
Mr. Schlafly, you got my question wrong. I honestly don't know if you teach your class in some kind of bigger structure (and it is not stated here in conservapedia). And i also don't know what legal status conservapedia has (or how its funded). However, your job title should not appear in the affiliations line. If your work leading to this letter was carried out in any organization bigger than just yourself, this is the right thing to go into the affiliations line. If you (seems to be tha case) did this completely on your own behalf, i think i would skip the affiliation. --Stitch75 12:45, 30 July 2008 (EDT)

Stich75 has it correct. "Teacher of pre-college students" is not an affiliation but a job title. Is "www.conservapedia.com" the actual name of the affiliated organization or is it something like 'Conservapedia, Inc.'--Argon 21:02, 31 July 2008 (EDT)

I don't think the affiliation really adds or subtracts from the letter. It's more or less a formality, continuing to discuss it rather diverts attention from the main issue and we're seriously in danger of falling out over it. "Anyway i think the discussions here have come to a dead point, so i think it would be good if you make up your mind to send the letter." Agreed 100%, if the letter isn't "near enough" right now then it will never be.--Toffeeman 15:20, 3 August 2008 (EDT)
Agreed. Pull the trigger and see whose foot gets shot.--Argon 10:23, 4 August 2008 (EDT)

Progress

I think there should be a timeline for this, like when the letter was sent, was a confirmation received and if so when. Also When a publication date is scheduled - if they dare do it. AckerLite 14:36, 8 August 2008 (EDT)

I sent it earlier this week, and have received confirmation from both PNAS and its Editor-in-Chief, Randy Schackman. I've been told it will be reviewed. Now I've been asked to resubmit through its formal manuscript submission process, which I'm sorting through now.--Aschlafly 15:14, 8 August 2008 (EDT)
Minor correction: Schekman.--Argon 16:01, 8 August 2008 (EDT)
Update: I resubmitted the letter as a manuscript pursuant to PNAS's formal submission process, per its request.--Aschlafly 17:46, 9 August 2008 (EDT)

I dont know if this is the place to ask, but is there any progress with this letter ? I dont know what the publishing cycle is like for these journals , thanks Markr 18:35, 8 September 2008 (EDT)

I am very interested to see what happens with this however, in knowing the evolutionist mindset, I am guessing that it will be rejected. ClarkeD 18:41, 8 September 2008 (EDT)

Here is the status from PNAS:

"August 21, 2008 ...

Dear Mr. Schlafly,

Your Letter to the Editor was received in our office on August 20, 2008 and assigned manuscript tracking number 2008-07877. All co-authors have been notified of the receipt of this submission.

Your Letter will be forwarded to the Editorial Board for consideration. The Board may decide to accept, reject, or ask for revisions to your Letter. Additionally, the Board may solicit a response from the authors. Accepted Letters will be published online only.

You may check on the status of your manuscript at any time by clicking the link below and selecting the "Check Status" link: View the manuscript:"

Upon clicking the link on Sept. 8, 2008, it reveals:

Status:

Manuscript # 2008-07877
Current Revision # 0
Submission Date 2008-08-20
Current Stage Under Editorial Board Review
Title Statistical Considerations in the Presentation of the E. Coli Data
Manuscript Type Letter to the Editor
Special Features and Colloquia N/A
Classification Biological Sciences/Evolution
Corresponding Author Andrew Schlafly (Conservapedia)
Co-Author Andrew Schlafly (corr-auth)
Author Conflict of Interest

Stage Start Date
Under Editorial Board Review 2008-08-21
Quality Control Review Completed 2008-08-21
Quality Control Issue Identified 2008-08-11
Quality Control Review Started 2008-08-08
Author Approved Submission 2008-08-08
Waiting for Author Approval of Converted Files 2008-08-08
File Conversion Complete 2008-08-08
Waiting for File Conversion 2008-08-08
Manuscript Information Submitted 2008-08-08
Manuscript Files Submitted 2008-08-08
Preliminary Manuscript Information Submitted 2008-08-08 --Aschlafly 18:49, 8 September 2008 (EDT)

Thanks for the update! ClarkeD 18:54, 8 September 2008 (EDT)

thanks for the update Markr 21:17, 8 September 2008 (EDT)

Response is in: PNAS Response to Letter.--Aschlafly 21:43, 12 September 2008 (EDT)
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