Talk:Richard Lenski

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Formatting

I borrowed a template from another wiki which might make the data section a bit easier to comprehend. I will include it here pending approval of senior sysops. Marge 12:03, 28 June 2008 (EDT)

Looks great. Please install in the entry as desired.--Aschlafly 12:55, 28 June 2008 (EDT)

Okay, I've moved it. I've also cut it from this page for economy's sake. Marge 13:07, 28 June 2008 (EDT)
Actually it makes the article look amaturish. For starters you have written in capitals and you have not explained why the missing data is significant which is the point of the side-by-side template to do a full rebuttle. DanielB 19:44, 28 June 2008 (EDT)
I agree. A discussion specifying what one expects from the 'missing' data and what usefulness such information would likely shed is necessary.--Argon 12:57, 30 June 2008 (EDT)
I agree that it is necessary to establish exactly what is being asked for in the terse comments on the right hand side, sadly such a discussion could get the majority of the contributors banned for the 90/10 rule. I myself have not contributed much to this question recently as a result of this rule. Could the powers that be explicitly suspend this rule on this issue so that the question may be freely discussed? --British_cons (talk) 13:12, 30 June 2008 (EDT)

Listing fields

I'm not a parodist, though I did make a mistake on what a CV is.

Suggestion: Disagreements with E Coli paper should go to a new section?

Shouldn't this be a brief bio of Lenski, and a link to the controversy over the paper, including the discussions and the emails, be part of that page instead of here? It looks pretty bad putting it on the main page. 18:11, 30 June 2008 (EDT) On the other hand, after doing some research, I don't think it's standard for faculty to put degree fields in a list of their degrees.

I googled "MSU biology", then went over the "Faculty List A-G". Here is what I found:

No list of degrees: 2 List with fields: 3 List without fields: 12

Finally, Oberlin is a liberal college, and they do focus mostly on liberal arts. Drochld 14:26, 29 June 2008 (EDT)

Template / formatting

Out of interest, I help to administer a private wiki where I work, and think this template is quite nice. Might I ask where you found it, and what (if any) associated copyright restrictions there are on it? Henry8th 15:49, 29 June 2008 (EDT)

Really, "Henry8th"??? That's an amazing coincidence you describe: you just happen to administer a "private wiki" at "work". Before wasting people's time with your silliness, how about convincing us a bit more of the earnestness of comment, as in providing the wiki version number, the type of your employer and the location of your "work". I'm sure the wiki developers who freely donate their efforts for use by all would be thrilled to learn of your profitable use.--Aschlafly 16:33, 29 June 2008 (EDT)
We run Mediawiki 1.6.7 (yes, I know we're incredibly out of date, but we can't upgrade to a newer one as that would require PHP5, whereas we need that server running PHP4 to support other older software). I make it a habit not to disclose too much personal information on the internet, I'm afraid, but I'm a PhD student at a UK university and I help to administer a wiki run by my research group. By "private" I mean "accessible only to people within my research group"; we find that a wiki is an efficient way for us to edit documents collaboratively. Henry8th 16:47, 29 June 2008 (EDT)
The copyright policy here says "Conservapedia grants a non-exclusive license to you to use any of the content (other than images) on this site with or without attribution".JPohl 11:53, 30 June 2008 (EDT)
However, since it was admitted above that the template is not CP's creation, it should first be established whether or not the template was used in a correct way (and if any attributions are needed) before others borrow it from here. ZTak 12:06, 30 June 2008 (EDT)
I would ask the same question as ZTak above. Firstly, from a legal point of view I would want to be absolutely sure that any code I might upload to a server at my university was properly licensed (we have regular software audits, of course). Secondly, from an ethical point of view I would like to make sure that I can properly credit the original author of the template. As someone whose work involves writing computer programs, I certainly wouldn't appreciate it if someone took software I'd written and didn't attribute authorship correctly. Henry8th 14:36, 30 June 2008 (EDT)

Fact checking could use some work on the omissions section

I strongly encourage editors to confirm that the topics on this entry's 'omissions' section page really refer to "data not provided" and do not reflect the lack of understanding of the research. At a bare minimum it is necessary to completely read the actual article. 'Skimming' it quickly is not fair to the goals of this wiki or Lenksi's lab. To at least be diligent, I recommend that the authors of the "omissions" section go to Lenksi's lab web page here (https://www.msu.edu/~lenski/), and peruse (read, not skim) the many papers related to the Long-Term Evolution project that are referenced in the current paper.--Argon 11:57, 30 June 2008 (EDT)

I do not understand why my last edit was reversed

It seems to be common practice (and therefore not "odd") to not list what fields faculty majored in, and Oberlin is very liberal. Drochld 12:34, 30 June 2008 (EDT)

I'm not certain what 'liberal' has to do with anything and "odd" has pejorative overtones. Rather than worry about 'oddness' why not investigate the degrees? In his graduate program Lenski studied insects and evolution and around 1983, worked with Bruce Levin, moving into the study of microbial evolution.--Argon 12:51, 30 June 2008 (EDT)

This man is nothing but a farce

Why must we, the children of God, even acknowledge this liberal atheist (as if there is any other form of an atheist) on our glorious site? We are only feeding his overinflated ego by doing so. --Dexter111344 12:52, 30 June 2008 (EDT)

A problem with: "Lenski is best known for his claim to have observed evolution of E. coli in a long-term laboratory study,"

This recent study is but one of many papers by Lenksi et al regarding the evolution of bacterial populations in continuous culture. He is best known professionally for his in vitro experiments studying the population dynamics of genetic adaptations in bacteria and other studies in microbial evolution.--Argon 13:14, 30 June 2008 (EDT)

don't clutter this entry with meaningless edits????

The topic of the page is 'Richard Lenski'. I added additional bibliographic information about Lenski's professional awards and they are reversed as "meaningless edits"? And the 'odd' comment remains despite the fact that it's common to leave the subjects of the degrees out of web pages?--Argon 13:43, 30 June 2008 (EDT)

Yes, various links to things such as data as well. I thought data was central to the question at hand? Why not link to it (such as it is)? And a mention of his work with virtual organisms seems relevant - especially as it's mentioned again at the end.--British_cons (talk) 13:47, 30 June 2008 (EDT)

And now I'm a "Lenski supporter"? Anyone who actually read the paper and referenced the pertinent section of the article that clearly specified the glucose concentration used is a supporter? I think that addition of 'Lenksi supporter' is needlessly inflammatory. Furthermore, with regard to the question: WHERE IS THE DATA MEASURING OR CONFIRMING THE 25 MG/LITER GLUCOSE? DID THAT CONCENTRATION EVER CHANGE?", I also wrote: "A weighed amount of glucose is mixed into the medium. The paper states that the concentration listed was used in the media throughout the continuous subculturing experiment." and that got removed. Resubmitted.--Argon 18:14, 30 June 2008 (EDT)

shouldn't we move the E Coli paper discussion to a separate page?

It looks really cheezy to have this right on Lenski's biography, very unprofessional. Just have a link and move all that discussion to something like Lenski_E_Coli_controversy, don't erase a thing. Cathy 18:11, 30 June 2008 (EDT)

Wrong format for a debate

Ignoring all the other issues with this "article", the side-by-side table is really not made for a discussion. Maybe move that part to a debate page? It's quite silly to see an encyclopedia article doing a question-and-answer session with anonymous participants. --KevinM 18:18, 30 June 2008 (EDT)

Agreed. It's silly to post the page without doing the basic research. Better to corral the innuendos into debate pages.--Argon 18:20, 30 June 2008 (EDT)
Also, we have yet to discovere the proper attribution for the side-by-side table, and as such it should be taken down or it might constitute a violation of copyright. ZTak 18:25, 30 June 2008 (EDT)
Given that Marge said she took the template from elsewhere, it would presumably be straightforward for her to tell us where she found it. Given that information I'd happily aid the project by checking out this other wiki's copyright policy before reporting back here. Henry8th 18:45, 30 June 2008 (EDT)
My issue is mostly about using a left/right table when the left side is basically just the intro section while the right side is suddenly filled with a weird pseudo-debate that goes back and forth. It would be better to do it like this:
==Visual Inspection==
===Lenski's Paper===
(quote)
===Discussion===
(back and forth; not as debate, but in more encyclopedic "A claims B, to which C points out D." style)

==Study Omissions==
(quote)
And so on. It would make the article more readable. And it would have the added benefit of NOT USING SO MANY ALL-CAPS SENTENCES, BECAUSE DESPITE WHAT SOME SITES SAY, CAPSLOCK IS NOT THE CRUISE CONTROL FOR COOL. --KevinM 19:12, 30 June 2008 (EDT)
Furthermore, it would help review the status of claims rather than deleting them outright: Here's a most recent example: (removed least important point, which was obscuring more important ones)" Aschlafly. Revision as of 19:34, 30 June 2008
I think it is an important point in two senses: 1) If the level of glucose was not growth limiting then Cit+ mutants might not have been discovered. It is an important feature of the experiment in this instance. 2) It's clear that the glucose concentration was indeed disclosed. How about creating a section titled "Data someone repeatedly claimed was undisclosed but was actually found by looking" and move the deleted test there?--Argon 20:24, 30 June 2008 (EDT)


Atheist Lobbying Organization

Should this remain in the article, given that it was inserted by an identified (and subsequently banned) parodist? --Benp 20:52, 30 June 2008 (EDT)

Anything wrong with the cites for it? By the way, not every block is proper. If in error, and I don't know if this one was, the block is reversed.--Aschlafly 20:57, 30 June 2008 (EDT)


There's nothing wrong with the cites, per se; they just don't quite cover the assertion. The cited sources do a good job of establishing that the PNAS is largely atheistic (something which is pretty well-known anyway.) They don't really cover any "lobbying" activities, though. --Benp 21:04, 30 June 2008 (EDT)
OK, based on what you said, how about taking out the "lobbying" reference only? As to the rest, it's informative: most people don't know how atheistic the PNAS is.--Aschlafly 21:05, 30 June 2008 (EDT)
Will do. --Benp 21:06, 30 June 2008 (EDT)

Maybe need to add another section

It would probably be better to split the biographic information from the discussion of the letters exchanged with A. Schlafly. Perhaps a section titled: "Interactions with Andrew Schlafly" (or "site owner") would better hold that aspect.--Argon 21:05, 30 June 2008 (EDT)

e-mail

For public interest, could we at CP view the e-mail regarding the template here? If the claim in the e-mail has merit and further measures are pursued, it does not seem fair that the whole site should be punished for one man's refusal to remove the template. Perhaps we could see the e-mail and discuss whether or not the claim is valid. ZTak 22:04, 30 June 2008 (EDT)

Professor?

Is Lenski an actual professor? I know there are plenty of people who exaggerate their status ad pretend they're something they're not. I wouldn't be surprised at all if he's one of them, given what we know of him so far. Have we seen his credentials? TonyT 08:26, 1 July 2008 (EDT)

TonyT I was about to give you a serious response, but then I realized that you have to be joking so thanks for making me laugh. Rellik 15:30, 2 July 2008 (EDT)
He has been blocked as a parodist already, so don't bother responding. I'm thinking of removing this nonesense. HenryS 15:37, 2 July 2008 (EDT)
So has 'Rellik'. Isn't it sad to see two trolls having a conversation? Bugler 16:35, 2 July 2008 (EDT)

Digital Organisms

Lenski is famous for two things. His work with his work E. coli and his work with digital organisms. The work with digital organisms is the work referred to in a somewhat unclear way at the bottom of the page. I have twice tried to mention this other important aspect of his work and twice been reverted. This time the edit was called "Liberal Claptrap"!! One would have thought that, in an article about Richard Lenski, mention of what he actually does would be important and not "Liberal Claptrap".--British_cons (talk) 09:13, 1 July 2008 (EDT)

If I get no response, presumably I can assume it was reverted in error and I can put it back in?--British_cons (talk) 11:47, 1 July 2008 (EDT)
What did he do with E. coli, and what is a "digital organism"? --Ed Poor Talk 15:39, 2 July 2008 (EDT)
Ed, I think British is talking about the twenty or so years Lenski has been experimenting with and growing up 12 E. coli cell lines. This last bit with the citrate mutation is one entry among twenty years. -- Aaronp
Richard Lenski is a well known scientist. He is well-known for his 20-year project on E. coli. (I must say that I don't know how to respond to Mr Poor's question, "What did he do with E. coli" as the entire Lenski debate has been about his work with E. coli.) He is also well known for his work with Digital organisms. The final part of the existing article sort of talks about this in a rather confusing manner. Given that he is well-known for both these two things and that the article is about him, I had thought it would be a good idea to mention them both.--British_cons (talk) 08:23, 3 July 2008 (EDT)

Release data to other evolutionists?

The paper says that only two people analyzed the data: Lenski and a grad student whom I presume acts under his direction and control.--Aschlafly 15:59, 2 July 2008 (EDT)

He says in his email that he will release the E. coli samples to a competent scientist who asks for them. How is that no agreeing to release the data to other evolutionists? -- Aaronp

Lenski does say that in his email. He didn't say that he wouldn't release the data to a competent scientist that held creationist views. Really at this point a competent scientist with creationist credentials needs to step forward. MAnderson 16:13, 2 July 2008 (EDT)
Can we be more clear about "data" and "samples"? The point is whether anyone but his cronies has tried to replicate his results, or even to check whether his data and methods are sound. Peer review is not enough; that just means his article is worth publication; it doesn't mean he has discovered something which now automatically goes into the standard biology textbooks. --Ed Poor Talk 16:17, 2 July 2008 (EDT)

Peer review = check to see if his methods are sound. You may also note that the experiment took a while, and was published last month. It would be implausible for anyone to have tried to replicate the findings at this point. Murray 18:09, 2 July 2008 (EDT)

I took a quick look and could not find any promise by Lenski that he would release his data (which the paper says he analyzed) to anyone. Can you quote where you think Lenski promises to release his "data"? As to releasing samples to a "competent" scientist, Lenski places so many conditions on that it is doubtful to me that he would view any potential critic as "competent". Regardless, it's clear to me that Lenski will not submit to public scrutiny of the data that the paper says he analyzed.--Aschlafly 16:19, 2 July 2008 (EDT)
Well lets take what you've said as a given Ed. The data and samples are still available to a competent scientist. I am going to contact this Bohlin guy from Probe Ministries to see if he is interested or can find someone who is. I'll report back. MAnderson 16:23, 2 July 2008 (EDT)
You're embarking on a fool's errand, MAnderson. It's clear to me that Lenski won't release his data to anyone independent. I'm not even sure Lenski has any meaningful data to support his claims.--Aschlafly 16:27, 2 July 2008 (EDT)
Good to see that someone is actually trying, after a week or so of no action. Andy, with how many biologists have you discussed this paper's methodology?--Argon 19:35, 2 July 2008 (EDT)
Looks like someone likes this fool's errand of trying to persuade Lenski to turn over his federally funded data. But don't hold your breath, Argon.--Aschlafly 20:55, 2 July 2008 (EDT)
Think positive! Have you had any luck finding a microbiologist or similarly qualified researcher with whom you can discuss this paper as it is or the rest of Lenski's work? How about Doug Axe, with the DI's Biology Institute?--Argon 21:47, 2 July 2008 (EDT)
Note that the strains are the ultimate standard for reproducing the work. It would take less than a week for competent microbiologist to confirm that the strains have the markers specified. Sequencing of the specified regions could also be performed in about a week. In other words, all this could be accomplished in about half of the time this 'debate' has gone on. Running the strains through the replay experiments is also easy and would confirm the results. One can express an opinion about whether Lenski would share the strains as he says (a condition to which he is bound under the journal's rules), but that is pure speculation until someone actually makes the attempt.--Argon 19:49, 2 July 2008 (EDT)
Argon, I did ask Lenski to turn over the data, and so can you. He refused, and I'm confident he'll continue to say "no" to any independent scrutiny of his claims.--Aschlafly 20:55, 2 July 2008 (EDT)
That misses the point. If you don't trust his report in the paper why would you trust the data he sends you? The *strains* are the key to the paper. They either are or aren't as he says they are. You can't fudge a strain that is supposed to have been grown in continuous culture with an established lineage. Reproducibility of the methods with the materials is what verifies this work. (Actually, so does the whole genome sequencing which is planned in the next stage of the research). The strains *are* available and the requirements Lenski set for sending them are standard for the field. There are thousands of labs that could meet the criteria.
As I mentioned earlier: Verification of the strain markers could be accomplished in a week. Add another week for sequencing. I'd suggest either finding a sympathetic researcher to give you some help or wait until the whole genome sequencing gets reported later.--Argon 21:32, 2 July 2008 (EDT)


Maybe so, in any case I sent this email to Dr. Bohlin, a qualified biologist and creationist.
Dear Mr. Bohlin,
Some people at conservapedia.com are concerned that a paper published by Richard Lenski describing a beneficial mutation occurring in E.coli may deserve closer scrutiny. Mr. Lenski has said that he is willing to release his data and samples of the E. coli to a competent scientist for further research and review. You seem to have the proper credentials to make this request. Are you interested or are you aware of other scientist that are at your level and share your personal beliefs that might be interested? I think that everyone at conservapedia would appreciate your input.
Sincerely,
Mike Anderson
Conservapedia contributor
MAnderson 16:32, 2 July 2008 (EDT)
Can't hurt to try, and your efforts deserve praise, MAnderson. I hope for a sensible result from your inquiry, but unfortunately do not expect it.--Aschlafly 17:16, 2 July 2008 (EDT)
Mike, aside from the question of whether you persuade Dr. Bohlin to request and analyze the raw data or strains, perhaps you might ask if he finds any irregularities with methods described.--Argon 19:31, 2 July 2008 (EDT)

Andy Schlafly, please send a letter to Lenski asking him if he is an atheist

Andy Schlafly, please send a letter to Lenski asking him if he is an atheist. Conservative 17:34, 2 July 2008 (EDT)

Why? MAnderson 17:40, 2 July 2008 (EDT)
Have you read his writing on a discussion about science and religon and on science, church and state. --Rutm 17:52, 2 July 2008 (EDT)
I meant why is it relevant to his scientific work? MAnderson 17:55, 2 July 2008 (EDT)
Lenski says that with better words than I can in the second pdf I linked above. --Rutm 20:23, 2 July 2008 (EDT)
Clearly, he's not a 'Dawkins-ite'.--Argon 21:35, 2 July 2008 (EDT)

An Interesting Lenski Quote

From the first of the two papers Rutm linked:

I think the same facts of evolution--with the perpetual struggle for existence and genetic rewards for selfishness--could just as easily be used to support a religion that both Dr. Hefner and I would find repugnant.

Is it me, or is Dr. Lenski admitting that evolution can be used to support some extremely nasty philosophies? --Benp 21:30, 2 July 2008 (EDT)

I believe he's saying one could *attempt* to use it justify practically anything. But more likely, one would probably be committing something akin to a naturalistic fallacy in so doing.--Argon 21:42, 2 July 2008 (EDT)


Statistical Significance

The 2 instances in the little table that imply that statistical significance or lack thereof should be reported look a bit silly. The first phrase refers to the statement by Blount et al. that "A number of Cit+ clones were isolated..." on p7900. Asking how many is all well and good. But it appears the researchers decided how many to isolate, and it is nonsensical to ask about significance. The second phrase refers to the end of the sentence: "all were Ara-, T5-sensitive, and T6-resistant, as expected." It is potentially a bit more relevant here, but still doesn't make a lot of sense to simply ask generally about statistical significance - compared to what? Calculating significance is a way of testing the probability of sampling error, if that helps. Murray 11:01, 3 July 2008 (EDT)