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Conservapedia talk:Lenski dialog (view source)
Revision as of 20:15, June 20, 2008
, 20:15, June 20, 2008→General Reply
(this discussion is limited to those who accept the logical premise repeated above: "it's unscientific for others to repeat as true an unverified claim based on concealed data." Sermons, rants and illogical postings can be made elsewhere. Thanks.--[[User:Aschlafly|Aschlafly]] 16:14, 20 June 2008 (EDT))
(this discussion is limited to those who accept the logical premise repeated above: "it's unscientific for others to repeat as true an unverified claim based on concealed data." Sermons, rants and illogical postings can be made elsewhere. Thanks.--[[User:Aschlafly|Aschlafly]] 16:14, 20 June 2008 (EDT))
::: Thank you. Let us look at claim number 1, that a strain of E. coli evolved the ability to utilize citrate. This is from page 2 of the paper (and onto page 3):
:::: After 33,127 generations, one population, designated Ara-3, displayed significantly elevated turbidity that continued to rise for several days (Fig. 1). A number of Cit+ clones were isolated from the population and checked for phenotypic markers characteristic of the ancestral E. coli strain used to start the LTEE: all were Ara-, T5-sensitive, and T6-resistant, as expected (2). DNA sequencing also showed that Cit+ clones have the same mutations in the pykF and nadR genes as do clones from earlier generations of the Ara-3 population, and each of these mutations distinguishes this population from all of the others (30). Therefore, the Cit+ variant arose within the LTEE and is not a contaminant. The evolved Cit+ variant grows to high density in DM0 (a citrate-only medium), produces vigorous colonies on minimal citrate (MC) agar plates, and causes a positive color change on Simmon’s citrate agar, all of which indicate that it can use citrate as a sole carbon source. In DM25, Cit+ cells undergo a period of rapid growth on glucose that is followed by slower growth on citrate (Fig. 2). Also, growth on citrate is inhibited by the citrate analog 5-fluorocitrate (data not shown), as was observed for the one previously reported Cit+ mutant of E. coli (42, 43).
::: So, there was a population that could utilize citrate. The claims made are (1) it was not a contaminate (the data asserted is that it had the markers of the earlier populations), (2) it had mutations found in earlier strains from the same evolving populations. (3) It grows in a glucose-free environment and can use citrate as a carbon source. (4) It continues to grow on citrate/glucose medium after the glucose is exhausted (while other E. coli stops growing).
::: Data explicitly supplied (figure 1) shows the ability of strains after the mutation to grow on citrate only (glucose free) medium. I assert this is direct (not derived) data since (I believe) the optical density is directly measured and that is what is shown in figure 1. Further data (figure 2) compares a strain with the mutation and one without and shows the with strain continues to grow after the glucose is exhausted while the without strain stops growing. Again, this is OD data directly reported. (I could of course be mistaken and OD data is in fact derived from other data, like excess radiation exposure, in which case someone please correct me.)
::: The derived data is that the mutated strain has markers from the ancestral source and has specific mutations from more recent ancestors (that is, there are presumably DNA and other analyses which show these things which are not shown). He also reports on growth on other specific media (minimal citrate (MC) agar plates and Simmon’s citrate agar) where we are told only that on the first, the growth is vigorous, and on the second produces a color change. Finally (in what seems to be a parenthetical comment) growth in inhibited by the "citrate analog 5-fluorocitrate", but that data is not shown, and it is noted that was reported by the other known E. coli variant that can utilize citrate. (I interpret this as simply reporting that the variant they found is likely the same or very similar to the variant previously reported. That is interesting but not, it seems to me, relevant to the result of the paper, so the lack of supplied data does not seem significant to me.)
::: So, what could you ask for? The OD reports from saved samples shown in figure 1 seem unambiguous as to the ability of the strain, after 33000 to utilize citrate, and so, except as qualified next, the basic claim seems to me to be verified. I cannot imagine what additional data with respect to OD you could ask for unless you are claiming that they mistranscribed the data (in which case, I repeat, resolve it how? Look at Lab books?)
::: So here is the qualification: could it be a contamination? They explain how they reject the contamination hypothesis. You could say that was very important to your confidence and so you would like to see the specific test results for the markers and mutations. That is certainly a specific question and one that could be answered, although with some (perhaps significant) expenditure of time and money.
::: As to the growth on other media (minimal citrate (MC) agar plates and Simmon’s citrate agar) the paper simply describes the growth as vigorous and the color changing. But these reports seem unambiguous in that they could be in error only if the investigators were misrepresenting their findings. Here again, what would you like to see? Lab books? Because this could only be false through fraud, the lab books would presumably in that case also be fraudulent.
::: So it seems to me that all one could ask for is the dna/marker data that verifies that the cit+ samples are not contaminates. Perhaps, if you were willing to pay for the tests, one could ask for ancestral, close to mutation, and post mutation samples on which to repeat the tests.
::: Let us leave fraud aside. So then the question is, did they make (honest) mistakes? It frankly seems unlikely to me because the tests seem straightforward: the ability to utilize citrate seems very easy to test unambiguously (smear some on a citrate/no glucose base and see what happens). The differences between growing vigorously and hardly are surely great enough that one could not mistake one for the other. The contamination tests, while much more complicated, also seem standard. DNA sequencing is a well-established technique. There are looking for specific loci ("DNA sequencing also showed that Cit+ clones have the same mutations in the pykF and nadR genes as do clones from earlier generations of the Ara-3 population"). I am not sure how the markers mentioned are identified but I again think this is a standard test.
::: So, to repeat my conclusion: the only thing I feel is worth asking about (all this is about result 1, there was a mutation which allowed utilization of citrate) is the contamination question. There they presumably have data which confirms there statements but I am not sure whether it is reasonably to ask them for it absent some specific concern. (Here an experienced microbiogist would be helpful, if I have the field right: is their description of how they determined that the strain was not contaminated reasonable and the tests they did straightforward and unambiguous, or is there room for reasonable doubt? Answering that is beyond my knowledge. I would be pleased to hear from such an expert.)
::: As to claim 2, I understand it less well, but could discuss it in more detail but I feel I have gone on long enough discussing claim 1. I would be pleased to read differing analyses of claim 1, particularly with regard to where the authors might reasonably be incorrect, absent fraud. divaricatum 13:09 June 20, 2008 (PDT)
==Note re. article==
==Note re. article==
As an aside, I' wonder if someone couldn't place some information at the head of the article here? At present, the article simply starts into a "first letter" to "a Prof. Lenski". The article should have a little setup to introduce readers to what on Earth it's all about. There is no reference in the article to the rest of the debate, basically. Just an FYI. [[User:StatsFan|StatsFan]] 13:17, 20 June 2008 (EDT)
As an aside, I' wonder if someone couldn't place some information at the head of the article here? At present, the article simply starts into a "first letter" to "a Prof. Lenski". The article should have a little setup to introduce readers to what on Earth it's all about. There is no reference in the article to the rest of the debate, basically. Just an FYI. [[User:StatsFan|StatsFan]] 13:17, 20 June 2008 (EDT)