Conservapedia gets schooled by biologist

http://www.twcenter.net/forums/showthread.php?t=176850

Richard Lenski is a biologist who recently found evidence for the
emergence of new traits among E.coli bacteria, in a fascinating
experiment which he has described in a paper in PNAS (best lay
coverage here). His results look a bit like evolution. You will note
that his paper includes the original data.
Andrew Schlafly is a startlingly predictable right wing christian
activist who runs Conservapedia. I highly recommend a look around
there if you’ve not already had the pleasure, because even the people
who run Conservapedia find it hard to tell whether the edits are being
made by god-fearing americans or naughty satirists.

Schlafly read Lenski. He got angry. He demanded the original data. It
was pointed out to him that the original data was in the paper. He
demanded the original data again. With menaces.
The following exchange is mirrored humbly and verbatim in case of
disappearance. It represents pwnage on a scale most of us can only
dream of.

First letter

June 13, 2008
Dear Professor Lenski,
Skepticism has been expressed on Conservapedia about your claims, and
the significance of your claims, that E. Coli bacteria had an
evolutionary beneficial mutation in your study. Specifically, we
wonder about the data supporting your claim that one of your colonies
of E. Coli developed the ability to absorb citrate, something not
found in wild E. Coli, at around 31,500 generations. In addition,
there is skepticism that 3 new and useful proteins appeared in the
colony around generation 20,000. A recent article about your claims
appears in New Scientist here:
http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html
Submission guidelines for the Proceedings of the National Academy of
Science state that "(viii) Materials and Data Availability. To allow
others to replicate and build on work published in PNAS, authors must
make materials, data, and associated protocols available to readers.
Authors must disclose upon submission of the manuscript any
restrictions on the availability of materials or information." Also,
your work was apparently funded by taxpayers, providing further reason
for making the data publicly available.
Please post the data supporting your remarkable claims so that we can
review it, and note where in the data you find justification for your
conclusions.
I will post your reply, or lack of reply, on www.conservapedia.com .
Thank you.
Andy Schlafly, B.S.E., J.D. Conservapedia

First Reply

Dear Mr. Schlafly:
I suggest you might want to read our paper itself, which is available
for download at most university libraries and is also posted as
publication #180 on my website. Here’s a brief summary that addresses
your three points.
1) "… your claims, that E. Coli bacteria had an evolutionary
beneficial mutation in your study." We (my group and scientific
collaborators) have already published several papers that document
beneficial mutations in our long-term experiment. These papers provide
exact details on the identity of the mutations, as well as genetic
constructions where we have produced genotypes that differ by single
mutations, then compete them, demonstrating that the mutations confer
an advantage under the environmental conditions of the experiment. See
papers # 122, 140, 155, 166, and 178 referenced on my website. In the
latest paper, you will see that we make no claim to having identified
the genetic basis of the mutations observed in this study. However, we
have found a number of mutant clones that have heritable differences
in behavior (growth on citrate), and which confer a clear advantage in
the environment where they evolved, which contains citrate. Our future
work will seek to identify the responsible mutations.
2. "Specifically, we wonder about the data supporting your claim that
one of your colonies of E. Coli developed the ability to absorb
citrate, something not found in wild E. Coli, at around 31,500
generations." You will find all the relevant methods and data
supporting this claim in our paper. We also establish in our paper,
through various phenotypic and genetic markers, that the Cit+ mutant
was indeed a descendant of the original strain used in our
experiments.
3. "In addition, there is skepticism that 3 new and useful proteins
appeared in the colony around generation 20,000." We make no such
claim anywhere in our paper, nor do I think it is correct. Proteins do
not "appear out of the blue", in any case. We do show that what we
call a "potentiated" genotype had evolved by generation 20,000 that
had a greater propensity to produce Cit+ mutants. We also show that
the dynamics of appearance of Cit+ mutants in the potentiated
genotypes are highly suggestive of the requirement for two additional
mutations to yield the resulting Cit+ trait. Moreover, we found that
Cit+ mutants, when they first appeared, were often rather weak at
using citrate. At least the main Cit+ line that we studied underwent
an additional mutation (or mutations) that refined that ability and
led to a large improvement in growth on citrate. All these issues and
the supporting methods and data are covered in our paper.
Sincerely,
Richard Lenski

Second letter

Dear Prof. Lenski,
This is my second request for your data underlying your recent paper,
"Historical contingency and the evolution of a key innovation in an
experimental population of Escherichia coli," published in PNAS (June
10, 2008) and reported in New Scientist ("Bacteria make major
evolutionary shift in lab," June 9, 2008).
http://myxo.css.msu.edu/lenski/pdf/2008,%20PNAS,%20Blount%20et%20al.pdf
http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html
Your work was taxpayer-funded, and PNAS represents that its authors
will make underlying data available. I’d like to review the data
myself and ensure availability for others, including experts and my
students. Others have expressed interest in access to the data in
addition to myself, and your website seems well-suited for public
release of these data.
If the data are voluminous, then I particularly request access to the
data that was made available to the peer reviewers of your paper, and
to the data relating to the period during which the bacterial colony
supposedly developed Cit+. As before, I’m requesting the organized
data themselves, not the graphs and summaries set forth in the paper
and referenced in your first reply to me. Note that several times your
paper expressly states, "data not shown."
Given that this is my second request for the data, a clear answer is
requested as to whether you will make the key underlying data
available for independent review. Your response, or lack thereof, will
be posted due to the public interest in this issue. Thank you.
Andy Schlafly, B.S.E., J.D.
www.conservapedia.com
cc: PNAS, New Scientist publications

Second reply

Dear Mr. Schlafly:
I tried to be polite, civil and respectful in my reply to your first
email, despite its rude tone and uninformed content. Given the
continued rudeness of your second email, and the willfully ignorant
and slanderous content on your website, my second response will be
less polite. I expect you to post my response in its entirety; if not,
I will make sure that is made publicly available through other
channels.
I offer this lengthy reply because I am an educator as well as a
scientist. It is my sincere hope that some readers might learn
something from this exchange, even if you do not.
First, it seems that reading might not be your strongest suit given
your initial letter, which showed that you had not read our paper, and
given subsequent conversations with your followers, in which you wrote
that you still had not bothered to read our paper. You wrote: “I did
skim Lenski’s paper …” If you have not even read the original paper,
how do you have any basis of understanding from which to question,
much less criticize, the data that are presented therein?
Second, your capacity to misinterpret and/or misrepresent facts is
plain in the third request in your first letter, where you said: “In
addition, there is skepticism that 3 new and useful proteins appeared
in the colony around generation 20,000.” That statement was followed
by a link to a news article from NewScientist that briefly reported on
our work. I assumed you had simply misunderstood that article, because
there is not even a mention of proteins anywhere in the news article.
As I replied, “We make no such claim anywhere in our paper, nor do I
think it is correct. Proteins do not ‘appear out of the blue’, in any
case.” So where did your confused assertion come from? It appears to
have come from one of your earlier discussions, in which an acoltye
(Able806, who to his credit at least seems to have attempted to read
our paper) wrote:
“I think it might be best to clarify some of Richard’s work. He
started his E.Coli project in 1988 and has been running the project
for 20 years now; his protocols are available to the general public.
The New Scientist article is not very technical but the paper at PNAS
is. The change was based on one of his colonies developing the ability
to absorb citrate, something not found in wild E.Coli. This occurred
around 31,500 generations and is based on the development of 3
proteins in the E.Coli genome. What his future work will be is to look
at what caused the development of these 3 proteins around generation
20,000 of that particular colony. …” As further evidence of your
inability to keep even a few simple facts straight, you later wrote
the following: “It [my reply] did clarify that his claims are not as
strong as some evolutionists have insisted.” But no competent
biologist would, after reading our paper with any care, insist (or
even suggest) that “3 new and useful proteins appeared in the colony
around generation 20,000” or any similar nonsense. It is only in your
letter, and in your acolyte’s confused interpretation of our paper,
that I have ever seen such a claim. Am I or the reporter for
NewScientist somehow responsible for the confusion that reflects your
own laziness and apparent inability to distinguish between a
scientific paper, a news article, and a confused summary posted by an
acolyte on your own website?
Third, it is apparent to me, and many others who have followed this
exchange and your on-line discussions of how to proceed, that you are
not acting in good faith in requests for data. From the posted
discussion on your web site, it is obvious that you lack any expertise
in the relevant fields. Several of your acolytes have pointed this out
to you, and that your motives are unclear or questionable at best, but
you and your cronies dismissed their concerns as rants and even
expelled some of them from posting on your website. [Ed.: citation
omitted due to spam filter] Several also pointed out that I had very
quickly and straightforwardly responded that the methods and data
supporting the evolution of the citrate-utilization capacity are
already provided in our paper. One poster in your discussions, Aaronp,
wrote:
“I read Lenski’s paper, and as a trained microbiologist, I thought
that it was both thorough and well done. His claims are backed by good
data, namely that which was presented in the figures. I went through
each of the figures after Aschlafly said that they were uninformative.
Actually, they are basic figures that show the population explosion of
the bacterial cultures after the Cit+ mutation occurred. These figures
show that the cultures increased in size and mass at a given
timepoint, being able to do so because they had evolved a mechanism to
utilize a new nutrient, without the assistance of helper plasmids. …
Lenksi’s paper, while not the most definite I’ve seen, is still a very
well-researched paper that supports its claims nicely.” (As far as I
saw, Aaronp is the only poster who asserted any expertise in
microbiology.) As further evidence of the absence of good-faith
discussion about our research, in the discussion thread that began
even before you sent your first email to me, I counted the words
“fraud” or “fraudulent” being used more than 10 times, including one
acolyte, TonyT, who says bluntly that I am “clearly a fraudulent
hack.” In the discussion thread that also includes comments after my
first reply, the number of times those same words are used has
increased to 20, with the word “hoax” also now entering the
discussion. A few posters wisely counseled against such slander but
that did not deter you. I must say, it is surprising that someone with
a law degree would make, and allow on his website, so many nasty
comments that implicitly and even explicitly impugn my integrity, and
by extension that of my collaborators, without any grounds whatsoever
and reflecting only your dogmatic adherence to certain beliefs.
Finally, let me now turn to our data. As I said before, the relevant
methods and data about the evolution of the citrate-using bacteria are
in our paper. In three places in our paper, we did say “data not
shown”, which is common in scientific papers owing to limitations in
page length, especially for secondary or minor points. None of the
places where we made such references concern the existence of the
citrate-using bacteria; they concern only certain secondary properties
of those bacteria. We will gladly post those additional data on my
website.
It is my impression that you seem to think we have only paper and
electronic records of having seen some unusual E. coli. If we made
serious errors or misrepresentations, you would surely like to find
them in those records. If we did not, then – as some of your acolytes
have suggested – you might assert that our records are themselves
untrustworthy because, well, because you said so, I guess. But perhaps
because you did not bother even to read our paper, or perhaps because
you aren’t very bright, you seem not to understand that we have the
actual, living bacteria that exhibit the properties reported in our
paper, including both the ancestral strain used to start this long-
term experiment and its evolved citrate-using descendants. In other
words, it’s not that we claim to have glimpsed “a unicorn in the
garden” – we have a whole population of them living in my lab!
[ http://en.wikipedia.org/wiki/The_Unicorn_in_the_Garden] And lest you
accuse me further of fraud, I do not literally mean that we have
unicorns in the lab. Rather, I am making a literary allusion. [
http://en.wikipedia.org/wiki/Allusion]
One of your acolytes, Dr. Richard Paley, actually grasped this point.
He does not appear to understand the practice and limitations of
science, but at least he realizes that we have the bacteria, and that
they provide “the real data that we [that’s you and your gang] need”.
Here’s what this Dr. Paley had to say:
“I think there’s a great deal of misunderstanding here from the
critics of Mr. Schlafly and obfuscation on the part of Prof. Lenski
and his supporters. The real data that we need are not in the paper.
Rather they are in the bacteria used in the experiments themselves.
Prof. Lenski claims that these bacteria ‘evolved’ novel traits and
that these were preceded by the evolution of ‘potentiated genotypes’,
from which the traits could be ‘reevolved’ using preserved colonies
from those generations. But how are we to know if these traits weren’t
‘potentiated’ by the Creator when He designed the bacteria thousands
of years ago, such that they would eventually reveal themselves when
the time was right? The only way this can be settled is if we have
access to the genetic sequences of the bacteria colonies so that we
can apply CSI techniques and determine if these ‘potentiated
genotypes’ originated through blind chance or intelligence. But with
the physical specimens in the hands of Darwinists, who claim they will
get around to the sequencing at some unspecifed future time, how can
we trust that this data will be forthcoming and forthright? Thus,
Prof. Lenski et al. should supply Conservapedia, as stewards, with
samples of the preserved E. coli colonies so that the data can be
accessible to unbiased researchers outside of the hegemony of the
Darwinian academia, even if it won’t be put to immediate examination
by Mr. Schlafly. This is simply about keeping tax-payer-funded
scientists honest.” So, will we share the bacteria? Of course we will,
with competent scientists. Now, if I was really mean, I might only
share the ancestral strain, and let the scientists undertake the 20
years of our experiment. Or if I was only a little bit mean, maybe I’d
also send the potentiated bacteria, and let the recipients then repeat
the several years of incredibly pain-staking work that my superb
doctoral student, Zachary Blount, performed to test some 40 trillion
(40,000,000,000,000) cells, which generated 19 additional citrate-
using mutants. But I’m a nice guy, at least when treated with some
common courtesy, so if a competent scientist asks for them, I would
even send a sample of the evolved E. coli that now grows vigorously on
citrate. A competent microbiologist, perhaps requiring the assistance
of a competent molecular geneticist, would readily confirm the
following properties reported in our paper: (i) The ancestral strain
does not grow in DM0 (zero glucose, but containing citrate), the
recipe for which can be found on my web site, except leaving the
glucose out of the standard recipe as stated in our paper. (ii) The
evolved citrate-using strain, by contrast, grows well in that exact
same medium. (iii) To confirm that the evolved strain is not some
contaminating species but is, in fact, derived from the ancestral
strain in our study, one could check a number of traits and genes that
identify the ancestor as E. coli, and the evolved strains as a
descendant thereof, as reported in our paper. (iv) One could also
sequence the pykF and nadR genes in the ancestor and evolved citrate-
using strains. One would find that the evolved bacteria have mutations
in each of these genes. These mutations precisely match those that we
reported in our previous work, and they identify the evolved citrate-
using mutants as having evolved in the population designated Ara-3 of
the long-term evolution experiment, as opposed to any of the other 11
populations in that experiment. And one could go on and on from there
to confirm the findings in our paper, and perhaps obtain additional
data of the sort that we are currently pursuing.
Before I could send anyone any bacterial strains, in order to comply
with good scientific practices I would require evidence of the
requesting scientist’s credentials including: (i) affiliation with an
appropriate unit in some university or research center with
appropriate facilities for storing (-80ºC freezer), handling
(incubators, etc.), and disposing of bacteria (autoclave); and (ii)
some evidence, such as peer-reviewed publications, that indicate that
the receiving scientist knows how to work with bacteria, so that I and
my university can be sure we are sending biological materials to
someone that knows how to handle them. By the way, our strains are not
derived from one of the pathogenic varieties of E. coli that are a
frequent cause of food-borne illnesses. However, even non-pathogenic
strains may cause problems for those who are immune-compromised or
otherwise more vulnerable to infection. Also, my university requires
that a Material Transfer Agreement be executed before we can ship any
strains. That agreement would not constrain a receiving scientist from
publishing his or her results. However, if an incompetent or
fraudulent hack (note that I make no reference to any person, as this
is strictly a hypothetical scenario, one that I doubt would occur)
were to make false or misleading claims about our strains, then I’m
confident that some highly qualified scientists would join the fray,
examine the strains, and sort out who was right and who was wrong.
That’s the way science works.
I would also generally ask what the requesting scientist intends to do
with our strains. Why? It helps me to gauge the requester’s expertise.
I might be able to point out useful references, for example. Moreover,
as I’ve said, we are continuing our work with these strains, on
multiple fronts, as explained in considerable detail in the Discussion
section of our paper. I would not be happy to see our work “scooped”
by another team – especially for the sake of the outstanding students
and postdocs in my group who are hard at work on these fronts.
However, that request to allow us to proceed, without risk of being
scooped on work in which we have made a substantial investment of time
and effort, would be just that: a request. In other words, we would
respect PNAS policy to share those strains with any competent
scientist who complied with my university’s requirements for the MTA
and any other relevant legal restrictions. If any such request
requires substantial time or resources (we have thousands of samples
from this and many other experiments), then of course I would expect
the recipient to bear those costs.
So there you have it. I know that I’ve been a bit less polite in this
response than in my previous one, but I’m still behaving far more
politely than you deserve given your rude, willfully ignorant, and
slanderous behavior. And I’ve spent far more time responding than you
deserve. However, as I said at the outset, I take education seriously,
and I know some of your acolytes still have the ability and desire to
think, as do many others who will read this exchange.
Sincerely,
Richard Lenski
P.S. Did you know that your own bowels harbor something like a billion
(1,000,000,000) E. coli at this very moment? So remember to wash your
hands after going to the toilet, as I hope your mother taught you.
Simple calculations imply that there are something like 10^20 =
100,000,000,000,000,000,000 E. coli alive on our planet at any moment.
Even if they divide just once per day, and given a typical mutation
rate of 10^-9 or 10^-10 per base-pair per generation, then pretty much
every possible double mutation would occur every day or so. That’s a
lot of opportunity for evolution.
P.P.S. I hope that some readers might get a chuckle out of this story.
The same Sunday (15 June 2008) that you and some of your acolytes were
posting and promoting scurrilous attacks on me and our research
(wasn’t that a bit disrespectful of the Sabbath?), I was in a church
attending a wedding. And do you know what Old Testament lesson was
read? It was Genesis 1:27-28, in which God created Man and Woman. It’s
a very simple and lovely story, and I did not ask any questions, storm
out, or demand the evidence that it happened as written at a time when
science did not yet exist. I was there in the realm of spirituality
and mutual respect, not confusing a house of religion for a science
class or laboratory. And it was a beautiful wedding, too.
P.P.P.S. You may be unable to understand, or unwilling to accept, that
evolution occurs. And yet, life evolves! [ http://en.wikipedia.org/wiki/E_pur_si_muove]
From the content on your website, it is clear that you, like many
others, view God as the Creator of the Universe. I respect that view.
I find it baffling, however, that someone can worship God as the all-
mighty Creator while, at the same time, denying even the possibility
(not to mention the overwhelming evidence) that God’s Creation
involved evolution. It is as though a person thinks that God must have
the same limitations when it comes to creation as a person who is
unable to understand, or even attempt to understand, the world in
which we live. Isn’t that view insulting to God?
P.P.P.P.S. I noticed that you say that one of your favorite articles
on your website is the one on “Deceit.” That article begins as
follows: “Deceit is the deliberate distortion or denial of the truth
with an intent to trick or fool another. Christianity and Judaism
teach that deceit is wrong. For example, the Old Testament says, ‘Thou
shalt not bear false witness against thy neighbor.’” You really should
think more carefully about what that commandment means before you go
around bearing false witness against others.

.

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