Thursday, July 03, 2008

Conservapedia: Demanding the wrong data

Conservapedia, led by Mr. Schlafly, has gone on an internet-Crusade against Richard Lenski. The latter published a paper that describes, in the best sense, evolution observed in the laboratory independent of similar but isolated populations. This did not sit well for the inane demands of Schlafly.

Cue to a page demanding that people figure out how to get the data from the experiment.

The data wanted?

Visual inspection
Evolution of Cit Function in Population Ara-3. The LTEE populations are transferred daily into fresh medium, and the turbidity of each is checked visually at that time. ...
Data on these observations?

What data is Schlafly looking for? He doesn't clarify. Is he looking for the level of turbidity each transfer, every day for over twenty years, all over twelve populations? The data is not only unnecessary, it doesn't make sense to demand it.

Turbidity can differ on new cultures by minimal levels of opaqueness without changing the quality of the culture itself. Cultures are sterilized before they are used.

Is Schlafly looking for how the experiment's monitors measured the turbidity? A meter to measure turbidity? Holding it up to the light?

...the cultures are only slightly turbid when transferred. Occasional contaminants that grow on citrate have been seen over the 20 years of this experiment.
Data? When and how many?

Again, what is he looking for? Which days were turbidity levels observed to be higher? Lower? Or is he looking for what days contaminants were found on cultures? He needs to clarify.

Of course, asking for information on contaminants is ridiculous to try to find some way to prove that Lenski's experiment is due to contaminants, based on the next request...

These contaminated cultures reach much higher turbidity owing to the high concentration of citrate in the medium, which allows the contaminants to reach high density. (When contamination occurs, the affected population is restarted from the latest frozen sample.)
Data for when that occurred, and how often?

The information regarding contamination restarts most likely are available, but do not need to be included in the paper for the very reason listed in the parentheses. When contaminants are found, that population is discarded and a fresh culture is begun from the last frozen sample. This means that when contaminants were found with the bacteria, the bacteria culture was removed from the experiment. Its results are no longer included in the experiment.

Demanding this information, again, is useless for anything more than getting extra, unimportant data. It will not change the outcome of Lenski's paper or conclusions.

A Richard Lenski defender says, "If interested in a thorough review, contact the group directly, with a legitimate request for data. Otherwise, the disclaimer is a more than adequate description of the sample handling process."
In fact, two requests were made directly to Lenski for data, without success. His second response was rude and insulting.

Schlafly fails to mention that Lenski linked (and I followed suit in a previous posting) to the papers with the information on the populations from when the first possible mutations giving rise to the ability for the E. coli bacteria to metabolize citrate came, to his final paper (paper 180) before Conservapedia took offense.

So far, the "extra" data Schlafly wants, as far as I can tell from the Conservapedia page on Lenski, is not only immaterial, but likely never recorded because, through thousands of other experiments over the history of science, they are irrelevant. Demanding irrelevant and immaterial data, then saying the lack of it makes the experiment suspect, is not only dishonest, but shows levels of disrespect and ignorance of science.

The Numbers Please?
After 33,127 generations, one population, designated Ara-3, displayed significantly elevated turbidity that continued to rise for several days (Fig. 1).
Higher resolution data underlying figure not provided despite request.

What would higher resolution data do for Schlafly? Show that instead of a very smooth upward climb, there was one day where turbidity did not get as opaque as the day before?

The graph, Figure 1, shows Optical Density (OD) at 420nm from three restarted populations began from the CIT+ mutated population had slightly differing densities early, but their differences were far narrower days later. Requesting far more detailed graphs will not change the results that the graph shows. It's impossible to figure out what information Schlafly feels he can extract from more resolution, other than trying to find the exact densities rather than a good estimate.

More missing Numbers
A number...
Data? How many? Statistically significant?

Schlafly cannot read, or chose not to try.

"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)."

[Note: Corrected reference linkage, error made by blog author, not experiment's author]

The (2) refers to reference 2, which is:
"Lenski RE, Rose MR, Simpson SC, Tadler SC (1991) Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. Am Nat 138:1315–1341."

Referring to Figure 2, on the following page of the paper. What does the figure state?

"Fig. 2. Growth of Cit- (blue triangles) and Cit+ (red diamonds) cells in DM25 medium. Each trajectory shows the average OD for eight replicate mixtures of three clones, all from generation 33,000 of population Ara-3."

Was there another number Schlafly was looking for?

We're Professional Scientists
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
Data? How many? Statistically significant?

Follows the one before. If Schlafly wants a definitive answer beyond what's in the paper, he should ask a definitive question, rather than "How many?" How many what? How many Cit clones were isolated? How many markers were checked?

Schlafly seems highly concerned with data, but not very concerned with making himself clear.

Missing Characteristics
...were Ara, T5-sensitive, and T6-resistant, as expected (2)
Data about these and other characteristics?

Schlafly did not read to page 7 of the paper, apparently. Else he would have found this:

"The Long-term Evolution Experiment. The LTEE is described in detail elsewhere (2, 22). Briefly, two ancestral clones of E. coli B were each used to found six populations. The ancestors differ by a single mutation that allows one of them to use arabinose (Ara+). Ara- and Ara+ cells make red and white colonies, respectively, on tetrazolium–arabinose (TA) plates, but the mutation is neutral in the environment of the LTEE (2). The twelve populations have been propagated for almost 20 years by daily serial dilution in DM25, a minimal salts medium that has 139[uM] glucose and 1,700[uM] citrate (2). Given 1:100 dilution and regrowth, the populations achieve ~6.64 generations per day, and they have evolved for over 40,000 generations in this experiment to date. Every 500 generations, population samples are frozen at -80°C with glycerol added as a cryoprotectant."

What other characteristics would he like? He should state each specifically.

A Richard Lenski defender says, "Interested parties should consult the literature on these topics. It is not within the scope of this paper to address the significance of these markers."
What is missing from disclosure are the data that the markers were actually observed in a reliable and conclusive manner in this study.

Schlafly here seems to be accusing Lenski and his lab of dishonesty for no other reason that he does not like the results of the experiment. If Schlafly has any reason to believe the data is manipulated or faulty, beyond that he doesn't like the results, he should make clear why he believes this, and what data specifically he would want. Making an accusation that the observations were not reliable or conclusive without any indications why is not sufficient.

DNA sequencing also showed...

What is Schlafly requesting? How the DNA was sequenced? What the sequences were? The former can be done in numerous, scientifically supported ways, and arrive at the same results. The data could end up in millions of pieces of information for a single generation. What would Schlafly want?

A Richard Lenski defender says, "The inclusion of this data would be considerably more extensive than appropriate for the inclusion in this paper."
No one asked for the data to be printed in the paper. What is missing is disclosure of the data on the website, or upon public request.

Exactly what information Schlafly wants is still unclear. Does he want every sequencing done during the experiment? Only the Cit+ retesting? What? What he's asking could easily reach one trillion pieces of information; is he willing to pour through them all to ensure the experiments results were thorough?

More missing data
...that Cit clones have the same mutations in the pykF and nadR genes as do clones from earlier generations of the Ara-3 population, ...
Data about these and other characteristics?

What information would Schlafly want here? The same mutations are the same mutations. Does he want the specific base pairs and how they differed? Does he want the proteins produced? Does he want how they matched the mutations? The characteristics are already listed in the paper, as stated above. The data, again, is unclear what Schlafly wants.

...and each of these mutations distinguishes this population from all the others (30).
Data distinguishing "This population from all the others"?

Perhaps the fact that they are Cit+?

Fast Tracked
Therefore, the Cit variant arose within the LTEE and is not a contaminant.
The astoundingly short 14-day PEER REVIEW period, measured from the day the paper was sent out for review to the day of formal contribution by Lenski after acceptance, raises questions as to whether there was any meaningful peer review of this at all.

The peer-review was done to ensure that procedures and methodologies were proper. This is typical of peer-review and does not reflect poorly on the results. If another institution capable of handling E. coli properly and wishing to inspect the results of the experiment are able to request the samples from Lenski's lab. After the publication, the only people who have complaints about the results are people who don't like the results, not people who question the experiment's integrity.

As with before, I've not only provided 100% legal ways to get this data, but I've pointed out where data Schlafly himself has overlooked is available.

I'm still awaiting the award of completing the first ever Conservapedia Challenge.


At 7:18 AM, Blogger RepubAnon said...

So much missing data - the complete family tree of each person who made each batch of the growth media, and what they'd eaten every day of their entire lives up to that point (might affect their lab technique...) (/snark) Seriously, the Conservapedia objections seem to be that a 20-year long study's raw data wasn't published in its entirety. That's a whole bunch of lab notebooks.

At 1:36 PM, Blogger Blake Stacey said...

All well and good. . . except that the site's name should really be spelled Conservapædia, with an æ (æ) or at least an ae.


At 8:29 PM, Blogger moioci said...

I think what Schlafly's getting at is the notion that the citrate utilization somehow arose from a contaminant, by gene transfer or some such means. But he can't come out and say it, because once it's stated as an hypothesis, it will be subject to refutation, so he hides behind "I'm a LAWYER, dammit!"

At 10:37 AM, Blogger Argon said...

Go to the history pages about Lenski's 'omissions'. Find this section removed:

Under "Study Omissions"
Owing to the low concentration of glucose in DM25 medium...


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)."--[[User:Argon|Argon]] 11:42, 30 June 2008 (EDT)


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.

At 10:37 AM, Blogger Argon said...

This comment has been removed by the author.


Post a Comment

<< Home