Talk:Conservapedia challenge

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A challenge! Very well, Sir, I accept!

I am not a rich man and would be unable to handle all the data accumulated over twenty years. Neither do I think it acceptable to enjoin a publically funded organization to spend the large sums required to send such a large amount of data without a defined public benefit.


Let us, then, agree a hypothesis that can be tested by ' 'some' ', of Prof. Lenski's unpublished data. I will then procure from said Professor either: 1) That very data, which I will then deliver to you, or 2) An admission from the Professor that he does not have that data

If I succeed you will: 1) procure me one pint of Fuller's "London Pride" at the Nicholson's pub in the Strand, London, and display a picture of me drinking it on the front page of Conservapedia. 2) Publish a statement on the front page of Conservapedia stating that you accept Professor Lenski's honesty and professionalism.

I await: 1) Your hypothesis 2) The data that would test it 3) Your "prize" should I fail

Regards Tony Lloyd (User:TonyLloyd

Your "offer" is fascinating but also self-contradictory. On the one hand you imply that there are voluminous data ("spend the large sums required to send such a large amount of data"), but on the other hand you suggest that Lenski may not have any such data! You also seem to misunderstand or ignore the purpose and benefits of public scrutiny, as the data are not merely for me ("your hypothesis" and "data that would test it") but for all the public who paid for the data.--Aschlafly 13:18, 3 July 2008 (EDT)
As I have asked elsewhere Mr Schlafly I really do think you need to clarify nature of the data requested and who would examine it, and explain if you accept the data are represented by the organisms (and if you think the data are not represented by the organisms explain why not.)--British_cons (talk) 13:28, 3 July 2008 (EDT)


At least one blogger has already claimed to have won the challenge: No Latitude. He cites and links to the following data: http://myxo.css.msu.edu/lenski/pdf/2008,%20PNAS,%20Blount%20et%20al.pdf http://www.pnas.org/content/103/24/9107.full.pdf+html http://myxo.css.msu.edu/lenski/pdf/2004,%20Plant%20Breeding%20Reviews,%20Lenski.pdf http://myxo.css.msu.edu/lenski/pdf/2003,%20JME,%20Lenski%20et%20al.pdf http://myxo.css.msu.edu/lenski/pdf/2003,%20PNAS,%20Cooper%20et%20al.pdf

Of these, the last is particularly data-rich.

The missing data are very specific. The above citation list is a common tactic of distraction: try to obscure by burying the reader with volumes of meaningless or less meaningful info. Most of the dates on those cites are years ago, predating when key data could have even occurred.--Aschlafly 14:05, 3 July 2008 (EDT)
Most of the dates on those cites are years ago But not ALL of them, right? What about those citations which do not predate what you are looking for? Also, the Lenski dialogue now exists on several talk pages besides this one, some of them archived. I'm a busy person and do not have time to go hunting around through dozens if not hundreds of posts. Would it be too much of an imposition to ask you to state here, in a concise manner, what data exactly that would satisfy your request? - I say this in part because many of your interlocutors are trying to make YOU look unreasonable by making it appear as though you want Lenski to ship you on old mustard jar full of e coli (yes, I'm exaggerating)...I think it would do this discussion some good to refocus it on a short list of exactly what it is you're looking for...AliceBG 14:19, 3 July 2008 (EDT)
The oldest paper there is from generation 20,000.JPohl 14:20, 3 July 2008 (EDT)
Most of the dates on those cites are years ago Well, yes. The experiment has been running for two decades, has it not? Of course most of the related data is going to be years old.--Jimbb2004 22:45, 4 July 2008 (EDT)

There is no contradiction in "obtaining or admission of non-existence". If a piece of data is essential for a conclusion and yet does not exist then that non-existence provides bad faith on the part of the person reaching (and publishing) the conclusion.

I do understand about 'public scrutiny'. However this undefined 'public scrutiny' is vacuous testing 'in potentia'. I am suggesting actual public scrutiny. I am suggesting formulation of a hypothesis and a test which that hypothesis may fail. If it escapes refutation it will become corroborated. If it fails then we must accept that failure.

Cheers

Tony (on a windows mobile device and unable to "sign")

The value in public scrutiny is to allow many to review the data. Your insistence on a single "hypothesis" is contrary to the very benefit of public review. Also, it's obvious to me that Lenski will not allow public scrutiny of the publicly funded data, and thus proposing a hypothesis would be a fool's errand.--Aschlafly 16:01, 3 July 2008 (EDT)

Has the PNAS been contacted regarding this matter? --Jareddr 16:04, 3 July 2008 (EDT)

You're welcome to do so. PNAS does not make it easy to contact it, and accountability is far from clear at that publication. If you can post an appropriate contact here, then I'd be happy to follow up with it about its stated policy and what the procedure is for ensuring compliance with it.--Aschlafly 16:12, 3 July 2008 (EDT)
pnas@nas.edu • phone: 1-202-334-2679 • fax: 1-202-334-2739 —The preceding unsigned comment was added by MarieB (talk)
To elaborate on the contact info, "Authors must make Unique Materials (e.g., cloned DNAs; antibodies; bacterial, animal, or plant cells; viruses; and computer programs) promptly available on request by qualified researchers for their own use. Failure to comply will preclude future publication in the journal. It is reasonable for authors to charge a modest amount to cover the cost of preparing and shipping the requested material. Contact pnas@nas.edu if you have difficulty obtaining materials." Here would be another good spot. [1]--Jareddr 16:32, 3 July 2008 (EDT)
Thanks MarieB, I just called the number for PNAS that you provided. The PNAS staffer said that I should first contact the author to request the data, which I have done, and if that is unsuccessful, as it has been, then the next step is to contact PNAS at the above email address.
Jareddr's description of PNAS policy is incomplete. In fact, PNAS has adopted "UPSIDE", which is the Uniform Principle for Sharing Integral Data and Materials Expeditiously. That standard establishes that the "author's obligation is ... to release data and materials to enable others to verify or replicate published findings," and that the "upside" is that this "keeps science honest." Moreover, PNAS expressly rejects "a requirement that the material be used for research purposes." [2]--Aschlafly 16:56, 3 July 2008 (EDT)
Yeah but they really aren't saying that any tom, dick or harry should have access. They say:
"PNAS does not endorse this restriction because we believe that it would limit the sharing of materials with industry. Requiring a company to not make commercial use of scientific results seems wrong in principle and hardly enforceable. The overriding principle is that once something is published it should be freely shared by everyone."
So they want the information to be freely shared with "industry". MAnderson 17:34, 3 July 2008 (EDT)
The statement says "once something is published it should be freely shared by everyone." Do you really think a clarification is necessary about what "by everyone" means?--Aschlafly 18:59, 3 July 2008 (EDT)
Your the lawyer, everything needs to be clear. It says "by everyone" not "for everyone". Considering the preceding sentences it clearly means that everyone should have to share with some people or groups, not every person or group. MAnderson 20:28, 3 July 2008 (EDT)
Andy in his letter Lenski did make it clear how his data would share by everyone. So long as everyone has a freezer capable of -80 degree temperatures, a contract of disposal of medical watse, the labratory to study the bacteria and are willing to sign the nessary paper work, then you can have it. This is because he is not going to go around handing out bacteria to people because it is not safe.
All the papers listed above have the data you need. You seem to forget this was not one publication but many going back several years. The data for the early parts of the experiment are in the earlier papers, you just need to read them. The big problem of this saga is you don't know what data you actually want. DanielB 19:17, 3 July 2008 (EDT)
The missing data are identified in Richard Lenski. We do not permit the repetition of falsehoods here, and unless you can fill in those boxes then you will not be allowed to continue to state here that these identified data have been produced.--Aschlafly 19:46, 3 July 2008 (EDT)


Recall that I filled in one of those 'boxes' previously. It was removed with the description: "removed least important point, which was obscuring more important ones". Here was that entry:
Under "Study Omissions"
Owing to the low concentration of glucose in DM25 medium...
DATA ON SPECIFIC CONCENTRATIONS USED?
A Lenski defender says: From the first page of the paper in question (Blount, Z. D., C. Z. Borland, and R. E. Lenski. 2008. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. PNAS, USA 105:7899-7906):
"To address the repeatability of evolutionary trajectories and outcomes, the long-term evolution experiment (LTEE) with Escherichia coli was started in 1988 with the founding of 12 populations from the same clone (2). These populations were initially identical except for a neutral marker that distinguished six lines from six others. They have since been propagated by daily 1:100 serial transfer in DM25, a minimal medium containing 25 mg/liter glucose as the limiting resource (2, 22)."--Argon 11:42, 30 June 2008 (EDT)
WHERE IS THE DATA MEASURING OR CONFIRMING THE 25 MG/LITER GLUCOSE? DID THAT CONCENTRATION EVER CHANGE?
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.
--Argon 10:19, 5 July 2008 (EDT)

Contents

What missing data?

In order that this Conservapedia Challenge be run on a fair and comprehensible basis could someone provide a clear satatement of exactly what data is missing? --DenningMR 18:07, 3 July 2008 (EDT)

I havent really been following this so much so am unsure what data is missing (I'll look around this site though and find out) however I am interested in the outcome. Not being a US citizen I have little legal recourse as I am sure is wasn't my tax dollars footing the bill! JJacob 19:42, 3 July 2008 (EDT)

The missing data are identified in Richard Lenski.--Aschlafly 19:46, 3 July 2008 (EDT)
Yes, I saw that but how much of that missing data is provided in the five links posted above? --DenningMR 19:51, 3 July 2008 (EDT)
You can let us know, DenningMR. Citing a pile of meaningless links on the internet is the oldest trick in the book.--Aschlafly 22:01, 3 July 2008 (EDT)
That rather indicates to me that you are not even sure whether there is any data missing at all. --DenningMR 22:08, 3 July 2008 (EDT)

Thanks for the link, and yes, I see what you mean about this data. I will leave it to the legal/science team however as its outside my realm of knowledge. I am interested though. JJacob 19:55, 3 July 2008 (EDT)

Just comment/ask the Editor, or the corresponding affilliation.

1) First look at cited publications. Publishing data does not necessarily mean that he sends you the datafiles.

2) If you doubt a scientific publications content on a scientific basis, just write a comment in an appropriate form (title, abstract, length depending on the journal). Send it to the address of the editor of the original article. He will screen it for form, content, and style (if you dont write it in a more calm mood that you write your rants here, it will not be accepted). A comment is a standard way of forcing somebody to reply, because the editor will ask the authors to respond and both, comment and reponse are published together. Be specific (you arent). A request like: "In Fig.x the error bars are missing and we believe these are necessary" has much more chances of beeing followd than "which data? where how certain?". Make in the following paragraph explicitly clear what you problem is. e.g.: The region (x) inf Fig.(y) is not displayed in a resolution high enough to exclude (z). Make it clear that you are not the only one who believes that this is necessary by citing other works, where the author do capture a certain point in higher resolution. Don ask for unreasonable things (which would essentially require screening a colletion of 10000 Photos taken over twenty years....).

3) If you suspect scientific misbehaviour (like: falsifying data, faking results etc), report it to the responsible person in the research organization the other person works for. For such things you can loose your job and your phd title. Refrain from blaming the referees for not hunting scientific misbehaviour. The function of a referee is NOT to search for scientific misbehaviuor, but to check the conciseness, consitency and completeness of the things presented in the paper. (if somebody really fakes data it will be impossible withpout spending a long time in the lab, some people really fake data in a very tricky way)

If you suspect both, do both. Howver if you have nothing more than your scientifically worthless comments about articles, which are, as far as i read and understood them, written to the highest scientific standards (i have seldom read a more clear and concise paper than Lenskis one), spare your readers from your whining. Sadly the highly statistically nature of the experiment makes it in principle difficult to reproduce (which in the past hast tempted more scientists into faking data, look for "Schön Affair"). But the befault in scientific publications is to believe that the author did at least not fake data, so i trust the authors in this point fully because all of them seem to have a clean scientific record.


Legal Note: Lenski does not own all that data. His university owns the material. The way it works is, you file an MTA with the university for whatever it is you want, and you are generally expected to bear the standard costs of providing it to you. This is accepted practice in science. If you want the data, do this, and then if they turn you down you could perhaps sue Michigan State for some kind of discrimination. To go outside these procedures is to request special treatment.

I didn't get much out of your comment, as you seem to ignore or misunderstand the value of public scrutiny of data. There is no requirement of suspecting misbehavior or fraud, obviously, in order to acknowledge that public access to publicly funded research has substantial benefits. All it takes is a recognition that no researcher is perfect and flawless.
Your point about the university is interesting, but unsupported. It may be that the State of Michigan or Michigan State University has a requirement of disclosure. Information about that is welcome.--Aschlafly 10:02, 5 July 2008 (EDT)

Freedom of Information act

The challenge on the front page refers to Lenski’s Federally funded research. Conservapedia’s article about about Federally funded research says:

  • “As part of the Fiscal Year (FY) 1999 Omnibus Appropriations Act (P.L. 105-277), Congress included a provision introduced by Senator Richard Shelby (R-AL) that for the first time allows the public to obtain federally funded research data collected through grants and agreements with universities and other nonprofit organizations.”

If this work was federally funded, and if the legislation says what Conservapedia says it says, then a competent lawyer should have no problem in formatting the questions into a FOI request. Have I won the challenge?Tolerance 09:39, 5 July 2008 (EDT)

No, that doesn't work because unfortunately the Shelby Amendment has been construed not to enforce FOIA in the manner you suggest.--Aschlafly 09:56, 5 July 2008 (EDT)
Shame. But what, in that case, is the point about the work being "Federally Funded"? If you are saying that FOIA does not (for some reason) cover the work then why mention that its Federally Funded and then say that FOIA doesn't cover it? I dont understand. Is it a way of saying the law should be expanded? Tolerance 10:35, 5 July 2008 (EDT)
I see you have not yet answered on this. Probably because I did not make my question clear. (It may be be because my medicines.) My question is: Why would you make a challenge: - ""Who will be first to figure out a legal means for obtaining public disclosure of Lenski's underlying federally funded data?"" - If you already know that the freedom of information act gives no authority or means to ask for this federally funded data. It seems a strange thing to do.Tolerance 14:17, 5 July 2008 (EDT)
Obviously FOIA is not the only legal means for obtaining information.--Aschlafly 16:34, 5 July 2008 (EDT)

Quick quiz: What form would the data for the Ara marker take? How is it tested?

One bit of data that is said to be missing is how the markers for the strains were tested. I have starter question for those who would like to see the data (and those people only, not those who've already demonstrated an understanding of microbiology): How is the Ara marker tested and what data would one write in one's notebook if one performed such tests? Would one describe a number, a sequence of bases, colors, taste, smell, optical density or isoelectric point? What instruments would be used to measure the results? How was it performed in Lenksi's lab?

What about T5 sensitivity testing?

And what things could go wrong in an experiment to test the Ara marker? What controls would you run to test for errors?--Argon 10:00, 5 July 2008 (EDT)

When you demonstrate a recognition of the benefits of public scrutiny of data, Argon, there might be more interest in your postings. Put another way, do you really think Lenski is perfect and there can be no flaws in his analysis of data?--Aschlafly 16:33, 5 July 2008 (EDT)
If it were me, I would first make sure I'd read not just the primary paper but a solid survey of the related and referenced papers to collect as much information as possible about the techniques used. If I still didn't understand, I might pull out a microbiology textbook or find a microbiologist to discuss the work, and then I'd ponder some more. I might even ask the first author to explain some of details. Only after all that, if something clearly did not appear to be supported by the data would I consider error or fraud. Then, the next step for me would be to try to reproduce the experiment. If that failed, I would contact the journal editors and the authors, report my results and work to see the source of the discrepancy. In my opinion, Andy, your order of approach has been almost the exact opposite of what most scientist would do.
As for demanding the data for 'public scrutiny', there are benefits and there are costs. Can anyone at any time waltz into any lab and demand copies of any researcher's data, especially when there is not hint of fraud or error and the requesting party shows no ability to understand the results and has not even read the literature pertaining to the work? After all, I demonstrated that some of the information you demanded was already present in the paper -- On the paper's very first page. Others (including myself) have provided links to additional papers that describe their key procedures but it would appear you haven't read them. Is that *really* the optimal use of a taxpayer funded researcher's time? Andy, if there is suspicion of fraud there are procedures in place that can lead to the examination of lab notebooks. Have you investigated how to report your suspicions to the correct organizations? Yes or no?
On the other hand, if a researcher supposes a simple error in the results, the most common and time-tested method for verification is to reproduce the work in another lab. That is the gold standard for scientific experiments. As I've mentioned previously, work like marker verification would be simple and quick. Furthermore, it's clear from the 'replay experiments' that culturing of the pre-Cit+ strains can produce Cit+ mutants. So even that can be verified in labs with relatively little expense (just daily subculturing for a few weeks). Andy, have you contacted any microbiologist to discuss the paper or test the strains that Lenksi is making available?
Andy, throughout all this 'debate', you've frequently demanded that others show you the data or give you proof about their claims. The reason why I asked about how the Ara markers are tested is for you to show that you've read and understood the key papers. In my opinion, until you demonstrate a recognition of the benefits of understanding the papers and the techniques behind them, most observers would find it hard to believe the you could assess whether there are flaws in the paper. I remain surprised with what appears to me as disconcerting lack of interest in how the actual experiments were performed and what they mean. At this point it's clear to many, including some long-time editors here, that the demand for 'public scrutiny' does not offset the costs to taxpayers for collating and sending you the data.
I'll grant that what I write might not be interesting to you, but others probably find it relevant.--Argon 10:44, 6 July 2008 (EDT)

Plans for the data?

Let's assume Lenski hands over everything outlined tomorrow. Mr. Schafly, what are your plans for analyzing the data? Who has the freezers and other equipment? If you don't have anyone with that equipment, how do you plan to analyze it? If you expect Lenski to hand over live bacteria, you need to show proof that you're able to contain it properly. As others have stated, you're the lawyer; if you get the documents and bacteria samples, but you don't have the storage capability, do you plan to be liable if these E. coli bacteria infect someone and cause them harm because of this "challenge"'s unpreparedness? - LafinJack 10:48, 5 July 2008 (EDT)

"LafinJack", please try to understand and acknowledge the benefits of public scrutiny, and also recognize the apparent existence of "data" as referenced in the article (not merely bacteria).--Aschlafly 11:05, 5 July 2008 (EDT)
Mr Schlafly, I have previously tried to find out if you accept if the data are mainly in the organisms. Mr Lenski makes this point quite strongly in his letter. Do you accept that the main substantiating data are held within the organisms? And if you feel that this is not the case - why not?--British_cons (talk) 14:32, 5 July 2008 (EDT)
I too would be greatly interested to see the reply. Can't most of the experimental results and all of the key conclusions of the replay experiments be evaluated with the strains in hand?--Argon 14:43, 5 July 2008 (EDT)
I've been clear about the request for "data", a term that does not ordinarily include organisms. I recall that Lenski himself in the paper claims that he analyzed "data", and one of his co-authors did not. The table in the entry here on Lenski illustrates with great specificity what the undisclosed data are. No, it is not necessary to perform experiments and generate new data in order to review existing data for a published paper.--Aschlafly 16:30, 5 July 2008 (EDT)
First, Mr. Schlafly (if you like, my real name is Scott), I specifically said "the documents and bacteria samples", yet you act as if I am only talking about the bacteria. Second, even if you had those documents you'd be stuck with another problem: you are essentially charging Mr. Lenski with either misinterpreting or making up the results in his research. Assuming you had every single document (be it paper or electronic or whatever) on your desk this very moment, what would cause you to suddenly believe them with those missing parts now included? If I'm interpreting your challenge correctly, you wish to come to your own conclusions about the E. coli study. How are you going to do that with documents that you clearly distrust? You would need to examine the bacteria generations themselves, not just the documents you think are incorrect, to come to an independent opinion. Mr. Lenski seems more than willing to comply with your data request, but I haven't seen something similar from you showing that you're capable of storing and examining the bacteria samples safely. When do you hope to have the facilities online or loaned out? - LafinJack 20:27, 5 July 2008 (EDT)
Addressing the table on Lenski- it would be worthwhile to state what the minimum requirements are for you to declare that the data is fully disclosed. For example, when you ask for data on daily turbidity observations, do you require a facsimile of every observation for all twelve cell lines for every daily transfer since 1988? A summary of only those observations which are 'unusual', according to some predetermined criteria? With or without facsimiles of those particular observations? With or without summaries and/or facsimiles of the tests performed to establish the cause of the unusual turbidity? When you ask for 'data' on contamination, do you wish for a summary of every contamination event for all twelve cell lines over since 1988, or just the Ara-3 line? Are facsimiles required? When you ask for 'higher resolution data underlying the figure', is it acceptable to present the same data in a table form rather than a figure, or are facsimiles of the recorded observations needed? Each 'Question' can be narrowed down significantly. The legitimacy of the challenge can be enhanced by fixing the goalposts at the outset.
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