http://www.badscience.net/2008/06/all-time-classic-creationist-pwnage/
All time classic creationist pwnage
June 24th, 2008 by Ben Goldacre in bad science |
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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