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Conservapedia talk:Lenski dialog (view source)
Revision as of 00:11, June 28, 2008
, 00:11, June 28, 2008→Reply to comments in archive
::::::: But your opposite approach above, which essentially suggests there are no data that can be released, doesn't withstand scrutiny either. Figure 1 is plainly a low-resolution representation of underlying data that must exist. The greater resolution should be released. Similarly, there should be data underlying the essential assertion that a particular sample was not contaminated, while others had been. For example, the paper asserts that "[a] number of Cit clones were isolated." How many were isolated? If those data exist, then it should be released along with the other data. If those data do not exist, then that is even more telling.--[[User:Aschlafly|Aschlafly]] 11:34, 27 June 2008 (EDT)
::::::: But your opposite approach above, which essentially suggests there are no data that can be released, doesn't withstand scrutiny either. Figure 1 is plainly a low-resolution representation of underlying data that must exist. The greater resolution should be released. Similarly, there should be data underlying the essential assertion that a particular sample was not contaminated, while others had been. For example, the paper asserts that "[a] number of Cit clones were isolated." How many were isolated? If those data exist, then it should be released along with the other data. If those data do not exist, then that is even more telling.--[[User:Aschlafly|Aschlafly]] 11:34, 27 June 2008 (EDT)
:::::Regarding the questions highlighted by [[User:Aschlafly|Aschlafly]] to which [[User:Princetonian|Princetonian]] also responded: Many of the techniques questioned are standard procedures that a trained microbiologist would understand. Let's take this apart by question:
:::::'''''...the turbidity of each is checked visually at that time. [DATA ON THESE OBSERVATIONS?]'''''
:::::This is qualitative observation. Every microbiologist does this when they pull their cultures out of the incubator. The evaluation an experimenter asks: Can you see through the test tube or not? Is the culture denser or lighter than the last time you looked? The reported observations are the data.
:::::'''''...Owing to the low concentration of glucose in DM25 medium [DATA?]'''''
:::::A reference to the description of the media is provided in the paper and is included on Lenksi's web pages. I linked to that page recently in another comment. It is general knowledge among microbiologists that nutrient limited cultures will reach a peak density that depends on the concentration of the limiting nutrient.
:::::'''''...Occasional contaminants that grow on citrate have been seen over the 20 years of this experiment. [DATA?]'''''
:::::Observation. Either they saw contaminated cultures or not.
:::::'''''...(When contamination occurs, the affected population is restarted from the latest frozen sample.) [DATA FOR WHEN THAT OCCURRED?]'''''
:::::Not relevant for the results. It's just their way of saying how they restarted the experiment whenever they suspected a contamination. It does not alter the experimental outcome.
:::::'''''...one population, designated Ara-3, displayed significantly elevated turbidity that continued to rise for several days (Fig. 1).[HIGHER RESOLUTION DATA UNDERLYING FIGURE?]'''''
:::::Higher resolution is not really necessary. The graph provides a ''qualitative'' visualization that starkly reveals that the cultures underwent a change that allowed them to grow to a significantly higher density than previously. They report in the text the actual generation were the change occurred and that seems to line up with the transition in the figure (take out a ruler, if necessary). Their subsequent experiments bracketed the strains from points before, during and after the obvious population transition.
:::::'''''...clones were isolated from the population and checked for phenotypic markers characteristic of the ancestral E. coli strain used to start the LTEE: all [DATA?] were Ara, T5-sensitive, and T6-resistant, as expected (2) [DATA ABOUT THESE AND OTHER CHARACTERISTICS'''''
:::::Derived from observation. The phenotypic markers are described elsewhere and the means of testing them are well known by professional microbiologists. The origin of the strain and its markers can be determined by following the references provided. The strain is also referenced on Lenski's pages here: https://myxo.css.msu.edu/ecoli/strainsource.html Other information about how they tested markers can also be found starting from here (provided by Lenski): https://myxo.css.msu.edu/ecoli/
:::::'''''...DNA seqencing also showed [DATA?] that Cit clones have the same mutations in the pykF and nadR genes as do clones from earlier generations'''''
:::::Report of observation. They sequenced the specified genes and found no difference in base-by-base comparisons. There is no need in this paper to print all sequences side by side as they're the same. The words, "no difference" transmits the same information in less space as showing all the identical sequences side-by-side with the original, previously released sequence. See also the next lines.
:::::'''''...each of these mutations distinguishes this population from all [DATA?] of the others (30).'''''
:::::See reference (30) from Lenksi's paper. It describes how the genes in those populations were originally sequenced. The ancestral sequences were uploaded into GeneBank, a publically accessible sequence repository, and the identifying mutations were presented in the supplemental table published on the PNAS web site along with the original paper.
:::::'''''...Therefore, the Cit variant arose within the LTEE and is not a contaminant [THIS CONCLUSION NEEDS TO BE CHECKED BY INDEPENDENT REVIEW OF THE ACTUAL DATA, WHICH I DOUBT OCCURRED IN THE BRIEF PEER REVIEW OF THIS PAPER]'''''
:::::The authors reported the actual data in a manner that is readily understood and accepted by microbiologists. The data and analysis is not terribly complex or confusing for someone familiar with the field (and quite a few who aren't expert microbiologists). Andy, I've seen little requested that isn't standard practice & generally understood among microbiologists or not already available if one follows the references provided in the paper.
:::::Just a word about reading the professional, scientific literature: Scientific papers are by the nature of their medium, mostly brief, to the point and highly condensed. Rather than repeat all the background information that others in the field may already know and encouraged to limit the length by journals with page limits, authors provide references to other papers. They also use terms that are well-defined within their profession to shorten the text further. One wouldn't expect a layman with no experience in biology to easily digest the paper. To point is not to obfuscate but to simmer the paper down to essentials that others in the field can readily understand. With some effort to become familiar with the underlying & established techniques & science, determined, non-experts can eventually pick up this information. I'd respectfully suggest to anyone *seriously* interested in the paper but not comfortable with the technical details, that they may want to find a knowledgeable biologist willing to explain. At least they should read the entire paper and the additional papers referenced within. Consider asking DI's research institute or Behe for help with understanding the techniques behind the work.--[[User:Argon|Argon]] 20:11, 27 June 2008 (EDT)
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