Schlafly goes down in flames. Major pwnage alert

Anyone been following the spat between Conservpedia'a Andy Schlafly
and Richard Lenski.

http://scienceblogs.com/pharyngula/2008/06/hubris_gall_arroganceinanity.php

Lenski's: Awesome second reply - reproducing here as I might be proven
wrong but doubt Conservapedia have the guts to keep it on their site.

Richard Lenski wrote:
"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 New Scientist 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 New Scientist 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 1020 =
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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