Lenski gives Conservapædia a lesson

Posted 24 June 2008 by PZ Myers

Once again, Richard Lenski has replied to the goons and fools at Conservapædia, and boy, does he ever outclass them. For a quick outline of the saga, read this summary at A Candid World; basically, Andy Schlafly has been demanding every bit of data from Richard Lenski's work on the evolution of E. coli, despite the fact that Schlafly doesn't have the background to understand it and doesn't have any plan for what he would do with it if he got it. Lenski has been polite and helpful in his replies; his first response is a model for how to explain difficult science to a bullying ideologue. Now his second response is available, and while he has clearly lost some patience and is unequivocal in denouncing their bad faith efforts to discredit good science, he still gives an awfully good and instructional discussion.

I've put the whole thing below the fold, in case you'd rather not click through to that wretched hive of pretentious villainy at Conservapædia.

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.

140 Comments

Unsympathetic reader · 24 June 2008

What was the link Lenski provide that the idiots censored?

Winawer · 24 June 2008

@1: From the conversation on the conservapedia talk page, it appears to have been to a page on Rational Wiki. I can only speculate, though, since they only refer to it as "RW" and "the cesspit of the internet". I also have no idea what *specific* page is referenced.

Robin · 24 June 2008

Well said, Dr. Lenski! Bravo!

iml8 · 24 June 2008

An articulate response by a person whose reasonableness was being
strained.

I do have to laugh that the infamous "Dr. Richard Paley" was at work
in this business, and "Dr. Paley" was being his usual sly self:
"OK, guys, you insist on being shown the money, go get the bacteria
and see what you can do with them."

White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

raven · 24 June 2008

Lenski used a sledge hammer on a cockroach.

Conservapedia is misnamed anyway. The real name is Lieapedia.

Mike O'Risal · 24 June 2008

It often occurs to me that a lot of the Creationist wackaloons think that scientists work like they do in movies about mad scientists. As if material is just sent out to whomever we happen to like best, as if our work isn't subject to independent review. Frankly, it sounds a lot more like the way religious figures work than it does like the way scientists collaborate and communicate, examine and critique, in the real world.

What Schlafly is requesting is tantamount to being allowed into a laboratory while work is in progress so that he can stand around, kibbitz, make notes about things he doesn't understand and demand answers to whatever question pops into his mind. Like any bully, he'll soon throw a tantrum when he doesn't get his way.

DavidK · 24 June 2008

"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.”"

These creationists wouldn't have the foggiest idea what to do with the stuff. And despite what their bible says, bearing false witness seems to be their forte.

raven · 24 June 2008

Lenski's cockroach squasher: (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.

A PNAS paper: The pykF gene encodes one of two pyruvate kinases that catalyze the conversion of phosphoenolpyruvate (PEP) and ADP into pyruvate and ATP. PEP is also used by the phosphotransferase system (PTS) to transport glucose into the cell. By slowing the conversion of PEP to pyruvate, mutations in pykF might make more PEP available to drive the PTS-mediated uptake of glucose, which is the limiting resource in the environment of the long-term evolution experiment. As noted, nadR encodes a bi-functional protein that is involved in several aspects of NAD metabolism, itself a key metabolite important in many different pathways. Several genes involved in NAD synthesis and recycling are repressed by the NadR protein, and mutations in nadR might increase their expression and the resulting intracellular concentration of NAD.

Didn't recognize the E. coli mutations and so looked them up. FYI. The roaches are being silly. One can get E. coli K12 anywhere, ATCC or any one of countless biotech supply companies. This is the white mouse of the biotech and molbio fields.

Frank J · 24 June 2008

C'mon now. Do I have to be the one to say it?

After 20 years it's still a germ. ;-)

raven · 24 June 2008

J Bacteriol. 1982 Jul;151(1):269-73. Links Chromosomal mutation for citrate utilization by Escherichia coli K-12.Hall BG. A mutant strain of Escherichia coli K-12 that utilizes citrate as a sole source of carbon and energy was isolated. Citrate utilization arose as the consequence of two mutations in genes citA and citB, which are linked to the gal operon. The mutant strain expresses a semiconstitutive citrate transport system, and it utilizes both citrate and isocitrate as carbon and energy sources. It is capable of utilizing cis- and trans-aconitate, but only if it is preinduced by growth on citrate.

While we are stepping on cockroaches. Lenski's work has already been independently reproduced more or less. Hall isolated cit+ E. coli in 1982, way before Lenski. He says that it required 2 mutations. Given the methodological differences, plates incubated for a long time in a start and end point procedure versus serial liquid culture, he might well have missed one or more "potentiating" mutations. Lenski's first mutation was "potentiating" but otherwise without phenotype. My wild guess is he picked up a mutator as 1/3 of his lines acquired a mut+ phenotype. mutator=mutations causing higher mutation rates. Seen commonly when cultures are under severe physiological stress and possibly an example of "adaptive mutation."

iml8 · 24 June 2008

DavidK said: These creationists wouldn't have the foggiest idea what to do with the stuff.

Do we HAVE to spell it out? (HINT: What did P.T. Barnum say was born every minute?) Y'know, after all these years people are *STILL* not wise to "Dr. Richard Paley". A few years back "Dr. Paley" was making a fuss about some Satanic plot by Apple Computer. It got to Dawkins and he saw the gag immediately. White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

raven · 24 June 2008

Andy Schlafy's and his flunkies goal in life are to be malevolent, destructive, insane cockroaches. Whatever, it is a free country.

I can't see how it has anything whatsoever to do with xianity. There is no commandment that says:

Thou shalt be a malevolent, crazy cockroach. Go forth and hinder the progress of humankind.

Steve s · 24 June 2008

raven said: Lenski used a sledge hammer on a cockroach. Conservapedia is misnamed anyway. The real name is Lieapedia.

Yeah, modern conservatism may have it's flaws, but I'm not going to blame them for this guy. That site should be called RighteousIdiotOpedia.

Raging Bee · 24 June 2008

raven: knowing Conservapedia, their version of the Bible would probably have just such a passage inserted in one of the Gospels, if not an Umpteenth Commandment.

tacitus · 24 June 2008

LOL! I just came across this wonderful example of the type of "scientific research" Schlafly conducts, this one concerning the "Mystery [of] Young Hollywood Breast Cancer Victims":

http://www.conservapedia.com/Mystery:Young_Hollywood_Breast_Cancer_Victims

And don't miss the Talk page where he defends his pathetic attempt at science.

And this man thinks to lecture a real scientist on how he should manage the data of his research? I see the problem here. Schlafly doesn't even understand the concept of scientific data.

Schlafly is beyond a joke.

_Arthur · 24 June 2008

"Hall isolated cit+ E. coli in 1982, way before Lenski. He says that it required 2 mutations."

Raven, Lenski's Ecolis and Hall's Ecolis may very well (almost certainly) have evolved _different_ mutations. There are many ways to skin a cat, or to metabolize a citrate.

We will know more when Lenski swings the budget to sequence his critters.

Of course, the fact that several different multi-mutation pathways can achieve a new biological functionality flies in the face of creationists and the Dembsi sect of IDers.

AL · 24 June 2008

Is this the same Dr. Richard Paley of Objective Ministries?

RBH · 24 June 2008

Anyone know what link was deleted from Lenski's second email?

The spam filter blocked it because it consists of a link previously determined by this site to be unacceptable.--Aschlafly 08:08, 24 June 2008 (EDT)

The loons are speculating (search on "link missing") that Lenski inserted a link to a porn site to pollute "family friendly" Conservapedia:

...we can assume it was a shock site, foul language, pornography, or something in that line. Since Lenski knew that his response would be posted on this family-friendly encyclopedia, he would have purposefully put the link in to aggravate readers. That tells us a lot about his attitude, and by keeping the link intact, we let him "win".

raven · 24 June 2008

Arthur: Raven, Lenski’s Ecolis and Hall’s Ecolis may very well (almost certainly) have evolved _different_ mutations. There are many ways to skin a cat, or to metabolize a citrate.

Sure. The Hall work in 1982 was a single paper without much, if any, followup. He indicates a transport system but doesn't have any of the molecular data we would like today. Wonder if he still has those cit+ mutants? It has been 26 years.

raven · 24 June 2008

Anyone know what link was deleted from Lenski’s second email?

The names of a few good psychiatrists. Actually on the PZ thread, someone determined it goes to RationalWiki, a site that makes fun of Schlafly a lot.

iml8 · 24 June 2008

AL said: Is this the same Dr. Richard Paley of Objective Ministries?

Well, since there is really no such person that is a very interesting question. But if you read through the citation in the comments at top by "Dr. Paley" with the thought in mind that the author may not be quite what he seems to be, it performs a sudden and drastic change in meaning. "I recognize the lion by his paw." White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

tacitus · 24 June 2008

Note that the loons are even afraid to mention RationalWiki by name in their comments. The closest they are able to come is "RW" in fear of instant bannination.

It really is too pathetic.

Torbjörn Larsson, OM · 24 June 2008

A good trouncing. Frank J will find this Pharyngula comment a treat, I'm sure:

I love this exchange. What else is in the woodwork? "Really? He said he would put the data on his website, and I think Behe meets Lenski's three qualifications for a scientist to whom he would release the bacteria. Drochld 10:55, 24 June 2008 (EDT)

Behe? Are you serious? He's supposed to be a Creation Scientist? The guy believes in the big bang, an earth billions of years old, and evolution. He does not believe in a young Earth, Adam and Eve, or the true word of the Bible. He's an evolutionist who happens to say "oh yeah, God guided evolution." As if there was anything on the Earth not guided by God! Just because he's one of the few scientists who isn't an atheist he's supposed to be one of us? No thanks. I'd rather go with someone who didn't drink the Old Earth Kool-aid. TonyT 11:41, 24 June 2008 (EDT)

Btw, RationalWiki on the censored link:

Keen readers at Conservapedia noticed that the the phrase [Ed.: citation omitted due to spam filter] is contained in the second of the Professor's replies. Inquires about this withholding of information were made by some readers at Conservapedia. After at least two users were blocked for pursuing the issue it was revealed that the offending link was to none other than a certain RW. It was further established that the initials RW referred to a "Wiki claimed to be Rational".

This ironic failure to reveal data caused some interest both at Conservapedia and RationalWiki. Our article above has the full information included in the professor's reply as we do not believe in withholding public information. For those who are interested, the link Conservapedia censored is http://rationalwiki.com/wiki/Expelled:_No_Intelligence_Allowed

Wesley R. Elsberry · 24 June 2008

According to RationalWiki, the deleted link was http://rationalwiki.com/wiki/Expelled:_No_Intelligence_Allowed.

_Arthur · 24 June 2008

What is the ballpark cost to sequence a whole E. coli genome (several times) ?

As far as I know, sequencing a single, known, gene is quite cheap, but sequencing a whole genome is very costly and time-consuming.

So far, I understand Lenski has had no opportunity to do sequencing, or to pinpoint the location of the genes involved in citrate metabolization.

There are dozens of possible research projects, using Lenski's biological specimens, if funding can be found.

Julie Stahlhut · 24 June 2008

“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."

I doubt Schlafly's home is equipped with a -80ºC freezer for maintaining glycerol stocks, so the image of his living room, bedroom, and den overflowing with thousands of overripe Petri dishes is curiously amusing.

iml8 · 24 June 2008

Julie Stahlhut said: I doubt Schlafly's home is equipped with a -80ºC freezer for maintaining glycerol stocks, so the image of his living room, bedroom, and den overflowing with thousands of overripe Petri dishes is curiously amusing.

It leads to an even more amusing scenario of what his home would look like if Lenski had been working with the *Drosophila melanogaster* fruitfly. "There's a fly whisk at the door if you would like it." White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

John Kwok · 24 June 2008

Dear Mike, It's a sad, but rather true observation of yours:

Mike O'Risal said: It often occurs to me that a lot of the Creationist wackaloons think that scientists work like they do in movies about mad scientists. As if material is just sent out to whomever we happen to like best, as if our work isn't subject to independent review. Frankly, it sounds a lot more like the way religious figures work than it does like the way scientists collaborate and communicate, examine and critique, in the real world. What Schlafly is requesting is tantamount to being allowed into a laboratory while work is in progress so that he can stand around, kibbitz, make notes about things he doesn't understand and demand answers to whatever question pops into his mind. Like any bully, he'll soon throw a tantrum when he doesn't get his way.

Am sure someone like my friend Abbie Smith would love to show Schlafly around, demonstrating how scientists REALLY work. And if you really believe that, then there's a bridge that spans the East River between Manhattan and Brooklyn that I would love to sell you. Cheers, John

_Arthur · 24 June 2008

bigbang said: plus RM+NS has had all those parasites over the past 10,000 years or so to get past sickle cell (itself the result of a degradatory mutation), and it still hasn’t come up with anything

How would you know ?

iml8 · 24 June 2008

bigbang said: BTW, P. Z., I’m disappointed that you didn’t intervene in your Ham-Nightmare thread and explain to your fellow Darwinians there, who claim to believe in God, that believers are “credulous idiots” that don’t comprehend that the “dominant source of their credulity in our culture” is indeed “dangerous and a lie,” and that their belief in a god qualifies, as Dawkins notes, as a delusion, or, at best, is “wishy-washy.”

Man, you just don't know what you're missing until you finally switch to the decaf. White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

raven · 24 June 2008

What is the ballpark cost to sequence a whole E. coli genome (several times) ?

Whole genome sequencing costs continue to fall: $300 million in 2003, $1 million 2007, $60,000 now, $5000 by year end Several companies are sequencing the human genome for about $60,000 to $100,000 and taking about 4 weeks. Whole genome sequencing could be $5000 or less and take 24 hours or less by the end of 2008. Inexpensive costs that will accelerate the transformation of medicine into personal genomics and personal medicine. Prices are going to keep falling with better nanopore and highly parallel approaches.

Hard to say right now. Depends on your setup and which advertisements you read and believe. The human genome is running $100K but that is 2 billion nukes versus E. coli 4 million. It would have been standard but nontrivial to clone citA citB in 1982. For all I know it is almost certainly in a database somewhere now since E. coli has long been completely sequenced.

Nomad · 24 June 2008

Wow, the convervapedia people really are scary obsessive. That bit where the link was censored and they immediately assume it must have been a porn site is just amazing. These people really do think that scientific researches have horns and smell of sulfur, don't they?

raven · 24 June 2008

That bit where the link was censored and they immediately assume it must have been a porn site is just amazing.

I'm sure they have a world class collection of porn site links already and don't need any help. The hypocracy of these sorts of loons is legendary and very predictable. They are always getting busted for kiddie porn (The Freshwater hangeron), cruising the wrong restrooms (a US senator), snorting meth with male escorts (Haggard), dying with large collections of sex toys around them (deep south minister) and on and on.

PvM · 24 June 2008

_Arthur said:
bigbang said: plus RM+NS has had all those parasites over the past 10,000 years or so to get past sickle cell (itself the result of a degradatory mutation), and it still hasn’t come up with anything
How would you know ?

Funny, in another posting Bigbang claims he is far more intellectually honest that me. Seems that all must be quite relative in his world.

tacitus · 24 June 2008

Nomad, to creationists, anything that even hints at being related to real science is worse than porn.

Viewing porn merely risks giving them a few minutes of self-loathing and sinful entertainment from which they can repent with a quick prayer the following Sunday. Viewing science, on the other hand, risks realizing that their faith is built upon a foundation of quicksand and thus (they believe) risks losing their faith in the Bible altogether. They believe that if Genesis is wrong, then there is no basis for believing anything the Bible says.

Wesley R. Elsberry · 24 June 2008

I got the deleted link directly from Lenski, and it is http://rationalwiki.com/wiki/Lenski_affair.

jeffinrr · 24 June 2008

raven said: Andy Schlafy's and his flunkies goal in life are to be malevolent, destructive, insane cockroaches. Whatever, it is a free country. I can't see how it has anything whatsoever to do with xianity. There is no commandment that says: Thou shalt be a malevolent, crazy cockroach. Go forth and hinder the progress of humankind.

No matter how low the guys may go, please don't call them cockroaches. It evokes imagery from the genocide in Rwanda, where the Hutus dehumanized the minority Tutsis by repeatedly equating them with cockroaches. Then the calls to squash the cockroaches preceded the mass murder of the Tutsis. If we want this dialog to be more than just a pissing match, or worse, we need to rise above dehumanizing our opponents regardless of how reprehensible their actions are. Besides when we dehumanize them, we play right into their delusion that we’re the genocidal Nazis and they’re the faithful martyrs.

hje · 24 June 2008

No matter how low the guys may go, please don’t call them cockroaches. It evokes imagery from the genocide in Rwanda, where the Hutus dehumanized the minority Tutsis by repeatedly equating them with cockroaches. Then the calls to squash the cockroaches preceded the mass murder of the Tutsis.

There is a key difference here. The term is meant as a simple insult, it is NOT being used as a metaphor to justify extermination. In the case of Rwanda, the desire to kill came first, then the metaphor simply justified the actions.

Do you really think raven really has murderous intent? Please. I find it hard to imagine a lynch mob comprised of scientists.

How about comparing them to mosquitos? Aphids? Or in non-metaphorical terms, just plain annoying.

BTW, have you ever read K. Eaton's rants here or on Pharyngula? Now I find his diatribes just plain scary.

Art · 24 June 2008

bigbang said: ....As Behe notes in his Edge of Evolution, N.J. White determined that it took RM+NS around 10^20 malaria parasites b/f it finally developed the two or so degradatory mutations required to provide it with CQ resistance;

And as I explained here, Behe got the story wrong. Here is what White really said:

"Chloroquine resistance in P. falciparum may be multigenic and is initially conferred by mutations in a gene encoding a transporter (PfCRT) (13). In the presence of PfCRT mutations, mutations in a second transporter (PfMDR1) modulate the level of resistance in vitro, but the role of PfMDR1 mutations in determining the therapeutic response following chloroquine treatment remains unclear (13). At least one other as-yet unidentified gene is thought to be involved. Resistance to chloroquine in P. falciparum has arisen spontaneously less than ten times in the past fifty years (14). This suggests that the per-parasite probability of developing resistance de novo is on the order of 1 in 10^20 parasite multiplications. “

Care to count the number of genetic changes White is speaking about, anyone? Care to comment on how many of these were "degradatory"?

harold · 24 June 2008

Bigbang -

I agree with Lenski that that certainly is a lot of opportunity for RM+NS (and drift & contingency, etc.). Any thoughts on why we don’t currently see a lot more evolution than we see in all the various microbes out there in the wild, other than a few simple things like say the nylon eating bacteria that most probably developed as a resulted of a single step mutation? Shouldn’t we be seeing much more than we’ve seen here in Lenski’s laboratory induced evolution of E. coli that resulted in a rather simple mechanism to absorb citrate that apparently resulted from two or three mutations; and the above mentioned nylon eating bacteria hat evolved in the wild?

I am glad to see that you have completely changed your arguments. You previously claimed to be skeptical that "RM and NS", as you inaccurately put it, were "sufficient" for evolution, and that magic must be required for the appearance of new species. I hope this paraphrase is fair. You now seem to think that there is so much mutation and selection going on that "there should be more" evolution, and that something magical must holding it back! At any rate, the reason modern bacteria populations may show the appearance of genetic stability over time, on human time scales, in static environments, is that they are adapted to their environments, and most mutations either have no impact on the phenotype, or are selected against. Please note that the theory of evolution suggests that populations WILL become adapted to their environment and may show relative stasis in a stable environment, NOT the opposite. (Please also note that no environment is permanently stable.) However, when stressors like antibiotics or low glucose conditions are introduced into the environments of bacteria, evolution that can easily be observed on a human time scale results. The massive diversity that life on earth has achieved since its origin is rather obvious evidence that evolutionary processes lead to remarkable changes over long periods of time.

Ron Okimoto · 24 June 2008

I sort of hope that someone is preserving the Conservapedia junk. Someone with time on their hands and that has to do some humorous historical PhD thesis could use the material someday and have to try to explain how so much crap settled into one place.

The wonders of the internet.

iml8 · 24 June 2008

Art said: Care to count the number of genetic changes White is speaking about, anyone? Care to comment on how many of these were "degradatory"?

And then there's the related issue of why *P. falciparum* hasn't evolved to defeat the sickle-cell defense over a matter of millennia when it can defeat chloroquine in a matter of generations. Defeating a toxin or the like is fairly "straightforward" from an evolutionary point of view. From what I scraped up in an admittedly inexpert way, the sickle-cell defense is not so "straighforward" to defeat. It seems that there is not entire agreement over how the defense works, but one plausible mechanism is that the cell tends to sickle easily when infected by *P. falciparum* and is then scavenged up (along with its parasites) by the immune system. So to defeat the defense, *P. falciparum* has to put the red blood cell on life-support so it doesn't sickle. This is obviously a much more complicated thing than neutralizing a toxin and implies construction of a "complex" system where it is hard (if not impossible) to see how it could arise through functional intermediates. "The difficult we do today, the impossible takes a little longer." Of course this argument dodges the fact inconvenient to Darwin-bashers that the sickle-cell mutation is "beneficial" -- but only in a particular circumstance and then with nasty side-effects. Obviously it's not something anyone's going to play up as evidence of Design. I know Behe has made a fuss about *P. falciparum*, but does he use the "malaria should have defeated the sickle-cell defense" gimmick? Given his complexity arguments it would be ironic, since those same arguments suggest why it hasn't ... hoisted by his own petard. White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.htmle

George · 24 June 2008

Dr. Lenski's approach to sharing samples from his collection is an outstanding idea. His experiment would be very hard to duplicate in whole and the results should be different, especially over time.

This such an important work. Getting confirmations from independent labs will be of great value.

It is also wonderful to see a scientist do the long, tedious experiment like this. We all gain such profound knowledge from this work. This is the work of a visionary who sees the big picture and is so confident in understanding of nature to invest 20 plus years to this work.

And yet so see such wondrous changes in the mere blink of the eye in time while working with an extremely limited ecosystem (low diversity) is outstanding. It becomes much easier to imagine how these creatures might change in 1M or 1 billion years when in the rich, complex and diverse ecosystem of the earth.

Unsympathetic reader · 24 June 2008

George, just to note: Prof. Lenski's offer to release strains to interested, responsible labs is standard practice in the field.

Doc Bill · 24 June 2008

George,

I hate to rain on your parade, although I'd love to rain and hail on Schafly's, but only a loser lab would have an interest in "confirming" Lenski's results.

Lenski's methodology, previous papers, score of grad students and all speak for themselves. Build on the work, yes. Confirm it, a waste of time.

For creationists, what Lenski's work does is blow the lid off the micro-macro evolution argument, while simultaneously destroying Behe's argument, not that Behe had an argument in the first place. Lenski's work also wipes out the creationist whine of no experiments that demonstrate evolution.

If you want to talk about confirming work, then go no farther than Cold Fusion which was thrust upon the scene with no mechanism, dubious procedures and vague data. Or, Raelean human cloning, all claims, no data. Extraordinary claims require extraordinary proof and confirmation.

Lenski's work is not extraordinary in that sense, rather it represents a meticulous daily grind, the total work represented being mind-numbing. But, it is unassailable because of that meticulous methodology. Thus, both creationists and ID are totally screwed by Lenski's results.

So, how many proofs does a creationist need? All of them. (And, it has to be in the Bible.) There you have it.

swbarnes2 · 24 June 2008

_Arthur said: What is the ballpark cost to sequence a whole E. coli genome (several times) ? As far as I know, sequencing a single, known, gene is quite cheap, but sequencing a whole genome is very costly and time-consuming.

Just this year, there are at least three new instruments that can sequence bacteria really, really fast, and pretty cheap. The cost is in the ballpark of $1000 a sample, I think. I'm familiar with the Solexa, and you can do E.coli in two weeks, tops. A few days to prep the DNA, a day to put the DNA bits on their chip, and at least 3 days for the instrument to collect the data, (or 2x as long to collect 2x the data). The Solexa yields about 5 million little sequences 36 bases long. That yields a whole lot of coverage at each base, enough to see if there are differences beween what you expect, and what's there. So half a day or more for the software to turn 1 TB of raw data into DNA reads, and then maybe a week to put together what all those reads are telling you. The other virtue of this kind of sequencng is that if there is some kind of contamination, like a plasmid, you'll see it. With standard sequencing, it's hard to find things you aren't looking for.

There are dozens of possible research projects, using Lenski's biological specimens, if funding can be found.

In theory, a Creationist could request the samples, and send them to a professional sequencing company, one that has a bunch of the kinds of instruments I described above. In practice, I bet Lenski want's to find the mutations himself, so if there's any outsourcing to be done, he'll do it. He's not going to give the samples to someone else to scoop him. But once those mutations are published, Creationists could pore over the sequences all they liked, since they'll probably make all the sequencing data available.

raven · 24 June 2008

AS I already posted earlier, the broad conclusions of Lenski's work have already been confirmed, absolutely independently by time travelers.

In 1982 no less, before he even started. Yes you can evolve cit+ E. coli and it takes at least 2 mutations.

Unsympathetic reader · 24 June 2008

Dang right Lenski wants the sequences. That information could be a major part of several future papers, a grant or two, and research projects for a graduate/post-doc or two.

Note that the whole-genome sequencing is for identifying the Cit+ related mutations. What Schlafly needs is different. He only has to sequence the markers in a couple loci to confirm the lineage of the strains (as described in the paper). That's trivial -- One only needs a couple pairs of oligos for that (I think the selective agar plating data would have been sufficient for most microbiologists).

Of course, if one believes that deities zot new organisms into existence, how are you going to convince a Creationist that the shared markers in the Cit+ strains weren't the result of 'common design' by a creator who happened to stuff new bacteria into the culture flask while Lenski's back was turned?

raven · 24 June 2008

For those who want to take a break from feeding the repetitive troll, there is a whole mini-field in evolving bacteria to metabolize novel substrates. Nylonase, ebg evolved beta gal., and so on. In the example below 3 mutations were required to convert bacteria to xylitol metabolizers by evolution of a new pathway. Which involved duplication and then mutation of one copy. Lenkski's work is well within the envelope of what we already know (evolution happens, duh!) and the Lieapedia trolls are just being trolls by hinting at fraud.

Xylitol is also not normally metabolized, but Mortlock and his colleagues were able to develop strains (generally through spontaneous mutations, but sometimes with u.v. ray or chemical induced mutations) that could use it because ribitol dehydrogenase (which is usually present in the cells to convert ribitol to D-ribulose) was able to slightly speed up the conversion of xylitol to D-xylulose, for which metabolic pathways already exist. The ability of the strains to utilize xylitol was increased as much as 20 fold when first production of ribitol dehydrogenase was deregulated (the enzyme was produced all the time, not just when ribitol was present), then duplication of the ribitol dehydrogenase genes occurred, then the structure of the enzyme was changed such that its efficiency at working with xylitol was improved, and finally, in at least one case, a line regained control of the modified ribitol dehydrogenase gene so that the enzyme was only produced in the presence of xylitol. Here we have a complete example of a new metabolic pathway being developed through duplication and modification of an existing pathway.

Reed · 24 June 2008

In practice, I bet Lenski want's to find the mutations himself

In fact, whole genome sequencing is on their agenda. From the papers Discussion and Future Directions section:

To find the relevant mutations, we will perform whole-genome resequencing, which has become a powerful approach that is well suited to experimental evolution

Zachary Blount (co-author of the original paper) commented

As to your question [why whole genome sequencing], we decided on whole genome sequencing because it is fairly cheap and time-saving at this point while giving us a lot of information that genetic crosses and transduction experiments would not.

For anyone who missed it the first time around, the actual paper can be found at http://myxo.css.msu.edu/lenski/pdf/2008,%20PNAS,%20Blount%20et%20al.pdf

_Arthur · 24 June 2008

Lenski will certainly do the sequencingof the initial (clonal) strain, and compare it to the current-day strain.

I don't know what method Lenski will use to pinpoint the genes actually involved in metabolizing the citrate. There's a lot of genes in E.coli, and I expect his strain to have mutated a lot since the start of the experiment. A lot of genes involved in fighting off other bacteria have probably been ditched or switched off.

Can microarrays give a hint on what proteins are expressed ?

Crudely Wrott · 24 June 2008

Eloquence is so fine. It wields a feather and a short length of iron pipe.

The feather along the ribs will just tickle you to death and the pipe upside the head will make you shut up and pay attention.

Lenski's tone and content are so nicely balanced; but I can't help worrying that the message will be lost upon its recipients.

Pete Dunkelberg · 24 June 2008

Conservatism is just too deep.

Ichthyic · 24 June 2008

that sounds scarily like some of the more "energetic" people I've run across on animal use protocol boards at various universities.

Joel Eissenberg · 24 June 2008

Well, I don't have the time to waste on the inane attacks on evolution. I'm just posting to say that I went to grad school with Rich Lenski and have followed his extraordinary career since he left Chapel Hill. He is a first-rate scientist and a super person.

Unsympathetic reader · 24 June 2008

Regarding Zachary Blount's account of P1 mapping: Interesting. As he says, they are probably expecting at least three mutations ('potentiator' plus two others). Hopefully the clues will pop out from the genome sequencing 'cause otherwise, it's going to be a bitch to identify the key mutations out of the background.

iml8 · 24 June 2008

Crudely Wrott said: Lenski's tone and content are so nicely balanced; but I can't help worrying that the message will be lost upon its recipients.

Ahhhhhh ... well, look at it like this, if a small noisy dog is barking away at you, it usually doesn't pay much mind to what you say to it. However, Lenski's response stands on its own considerable merits. White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

Torbach · 24 June 2008

After being home schooled I accept any child to assume the outside worlds eduction lacks solipsism. call it Allegory-of-the-caveapedia. Obviously the THE REST OF THE WORLD must have the bias..... Tell them to Go break a mirror.

Why do they get to gleefully call themselves conservative? We let them have that dignity?
Science is conservative, it has remained intact, with its rigorous analysis and shall remain rigorous as it grows with wisdom, never altering its foundation. These people are pre-conservative.

Wesley R. Elsberry · 24 June 2008

I apparently missed a level of indirection in Lenski's email to me. The link I posted originally (about a quarter hour after Larsson) is the one that was in Lenski's original reply. The later link just links to everything about the incident.

RBH · 24 June 2008

Bigbang asked

Art says: “Care to comment on how many of these were “degradatory”?” . Thanks for responding Art. If they weren’t degradatory, then why, after CQ isn’t used for a few years, does the CQ resistant strain of malaria tend to disappear?

Because fitness is a property of the intersection of environment and genome. In a CQ environment, CQ resistance is adaptive -- reproductively superior. In a non-CQ environment, it's not. Once again, "fitness" is not an intrinsic property of a gene or allele or phenotype. It's a property of a variant in a specified environment. Creationists (and others) seem to regard "fitness" as being like length. It's not. It's always a property of a variant in a particular selective environment.

Eric · 25 June 2008

bigbang said: ...then why, after CQ isn’t used for a few years, does the CQ resistant strain of malaria tend to disappear?

What an obvious question. Spending resources to create unused structures is wasteful, i.e. unfit. When the need for something disappears, mutations that deactivate it will propagate through the population. This leads to a direct prediction and counter-prediction between creationism and evolution. Evolution predicts that unused capability will disappear over generations (i.e. mutate into uselessness), while design theories predict (or, at least they should predict, but they refuse to make predictions) that capabilities useful in the future should be preserved. Several hundred years after the bubonic plague wiped out 1/3 of Europe, most of us have no immunity to it. Hmmm....

PvM · 25 June 2008

On UcD Bill Dembski, obviously envious of Lenski's ability to control his anger and not proclaim a Waterloo for his opponents, wonders if Lenski's measured response betrays strength or weakness. For someone who published a farting video, I'd say that in Bill's world, any ability to apply logic and reason in an argument would undoubtably be seen as a weakness. Such is the world of ID, scientifically vacuous.

Of course, unlike Lenski, Dembski has contributed little more than ignorance to our understanding of evolution.

CDV · 25 June 2008

Since there has been some talk of "Fitness" and "degradative" changes, I thought this little story might make some sense here -

Day 1 - Man's horse runs away. His neighbours gather around and express their condolences that a major resource has been lost and the consequently the reproductive success of his lineage has been compromised. Man gives a Zen reply - " Good luck, bad luck. Who knows ? "

Day 2 - Man's horse returns to stable bringing along a huge herd of wild horses from the nearby forest. Man's neighbours congratulate him on the increased resources he now has and the increased reproductive success this will bring to his lineage. Man, somewhat predictably repeats - " Good luck, bad luck. Who knows ? "

Day 3 - Man's only son tries to unsuccessfully harness one of the new horses,- this results in major blunt force trauma to the son's foot - making it clear he will walk all his life with a limp. The neighbours discuss privately among themselves how Man's lineage has lost its reproductive advantage. To emphasize the point, all the Man's horses run away that night. - Man goes to bed intoning " Good luck, bad luck. Who knows ? "

Day 365 - Drafting orders arrive in the village. All able bodied males are conscripted into the King's army for the unending distant war. Man's son is exempted, on account of his bad leg.

Day 366 - The neighbour's daughters have all decided that Man Junior has a certain charm, something they notice clearly now that he is the only young man left in the village.......

Rolf · 25 June 2008

tacitus said: Nomad, to creationists, anything that even hints at being related to real science is worse than porn. Viewing porn merely risks giving them a few minutes of self-loathing and sinful entertainment from which they can repent with a quick prayer the following Sunday. Viewing science, on the other hand, risks realizing that their faith is built upon a foundation of quicksand and thus (they believe) risks losing their faith in the Bible altogether. They believe that if Genesis is wrong, then there is no basis for believing anything the Bible says.

(My bold) You hit the nail right on the head. That is all there is to it, and as long as they have that problem, "our" problem will continue.

Ichthyic · 25 June 2008

Of course, unlike Lenski, Dembski has contributed ~~little more than~~ [nothing but] ignorance to our understanding of evolution.

or was there something I missed?

Nigel D · 25 June 2008

Nomad said: Wow, the convervapedia people really are scary obsessive. That bit where the link was censored and they immediately assume it must have been a porn site is just amazing. These people really do think that scientific researches have horns and smell of sulfur, don't they?

Nomad, yeah, once you've used ethane dithiol, the smell never really goes away... http://en.wikipedia.org/wiki/1%2C2-Ethanedithiol but Wiki does not seem to mention the stench. Ethane dithiol can be detected by the human olfactory system at parts per billion, and the pure liquid has the most intensely unpleasant smell I have ever encountered.

Kevin B · 25 June 2008

Ichthyic said: Of course, unlike Lenski, Dembski has contributed ~~little more than~~ [nothing but] ignorance to our understanding of evolution. or was there something I missed?

There was the flatulent video clip..... I suspect that some of the people admiring Lenski's prose style have not recognised the genre. Lenski's scalpel blade has no doubt been honed for the cut-and-thrust of academic bureaucracy. Demski is bound to be jealous; after all, did he not meet his Waterloo as a result of one of his memos?

Stephen · 25 June 2008

The original paper isn't hard to refute or confirm. You don't even need the original e. coli. It's not like this stuff is rare. Everyone reading this already has plenty of samples. And you should get positive results by 2028, or non-confirming results, say, ten years later. Instead of 12 batches from one clone, you might start with 100 batches each from 100 original clones. You might get cit+ much quicker, and overall, it might be cheaper. And, you wouldn't have to do as much paperwork to get it. [obvious paperwork joke omitted.]

Eric · 25 June 2008

bigbang said: All examples of RM+NS degrading things, and not providing mechanisms that contribute to overall fitness (or elegance).

If you're going to respond to one of my posts, it might be nice if you read its first sentence. Not building a useless* structure contributes to fitness. So RM+NS contributes to fitness. Elegance...where does that come from? Do you have some scientific theory of conservation of elegance you'd like to share with us? What am I thinking, you never propose alternative theories, as you don't want to admit your only alternative consists of "God put his finger in the petri dish, and lo, the E Coli could eat citrate." (* "useless" within a specific ecological context. Thanks CDV for keeping me honest)

PvM · 25 June 2008

Bigbang: All examples of RM+NS degrading things, and not providing mechanisms that contribute to overall fitness (or elegance).

That's such a foolish and ignorant statement. RM+NS cannot (in general) lead to lower overall fitness since selection increases fitness. As to the concept of elegance, that's an even more ignorant and undeveloped concept. Is this the best ID Creationists have to offer? A mindless repetition of a flawed understanding of the basic mechanisms of evolution? No wonder, ID has failed to contribute anything non-trivial to our scientific knowledge. Bigbang's contributions make this extremely clear and for that I thank my Christian brother.

jasonmitchell · 25 June 2008

Nigel D said:
Nomad said: Wow, the convervapedia people really are scary obsessive. That bit where the link was censored and they immediately assume it must have been a porn site is just amazing. These people really do think that scientific researches have horns and smell of sulfur, don't they?
Nomad, yeah, once you've used ethane dithiol, the smell never really goes away... http://en.wikipedia.org/wiki/1%2C2-Ethanedithiol but Wiki does not seem to mention the stench. Ethane dithiol can be detected by the human olfactory system at parts per billion, and the pure liquid has the most intensely unpleasant smell I have ever encountered.

I thought ethane dithiol was orderless? BME on the other hand - foul smelling stuff http://en.wikipedia.org/wiki/Beta_mercaptoethanol

jasonmitchell · 25 June 2008

jasonmitchell said:
Nigel D said:
Nomad said: Wow, the convervapedia people really are scary obsessive. That bit where the link was censored and they immediately assume it must have been a porn site is just amazing. These people really do think that scientific researches have horns and smell of sulfur, don't they?
Nomad, yeah, once you've used ethane dithiol, the smell never really goes away... http://en.wikipedia.org/wiki/1%2C2-Ethanedithiol but Wiki does not seem to mention the stench. Ethane dithiol can be detected by the human olfactory system at parts per billion, and the pure liquid has the most intensely unpleasant smell I have ever encountered.
I thought ethane dithiol was orderless? BME on the other hand - foul smelling stuff http://en.wikipedia.org/wiki/Beta_mercaptoethanol

retraction - I was thinking of something else - but BME is foul (and ironically found in human flattus (flatti?))

angst · 25 June 2008

PvM said: No wonder, ID has failed to contribute anything non-trivial to our scientific knowledge. Bigbang's contributions make this extremely clear and for that I thank my Christian brother.

Has ID even made trivial contributions to scientific knowledge?

James F · 25 June 2008

It has actually detracted from scientific knowledge, wasting people's time and energy with neocreationist arguments.

angst said:
PvM said: No wonder, ID has failed to contribute anything non-trivial to our scientific knowledge. Bigbang's contributions make this extremely clear and for that I thank my Christian brother.
Has ID even made trivial contributions to scientific knowledge?

Frank B · 25 June 2008

Big(little)bang said

plus RM+NS has had all those parasites over the past 10,000 years or so to get past sickle cell (itself the result of a degradatory mutation), and it still hasn’t come up with anything

The sickling of red cells infested with malaria is a physical act that malaria may never be able to prevent. It is totally different from chemical defenses. For example, our body's immune system can not stop a bullet or a knife. Behe was showing his ignorance using that as an example, and apparently you know less than he.

_Arthur · 25 June 2008

Lenski failed to surround his experiment apparatus with big **GODS KEEP OUT** signs, (or to keep it within a pentagram, whatever works), so one can never tell if a passing angel/designer didn't bestow the citrate genes to the hapless ecolis.

Flint · 25 June 2008

one can never tell if a passing angel/designer didn’t bestow the citrate genes to the hapless ecolis.

I prefer to think that Lenski caught the Designer in flagrante delicto. Now we've seen Design in action, right in the petri dish. Behe should be overjoyed. The "interdependent arrangement of parts" now occurs through the actual mechanism of Designer diddling. Behe could probably get a sample of the Designer's direct handiwork if he asked nicely and had the appropriate environment for preserving and examining it.

iml8 · 25 June 2008

Frank B said: The sickling of red cells infested with malaria is a physical act that malaria may never be able to prevent. It is totally different from chemical defenses. For example, our body's immune system can not stop a bullet or a knife. Behe was showing his ignorance using that as an example, and apparently you know less than he.

The interesting thing is that for *P. falciparum* to do so, it would have to be attentive to the health of the red blood cell. That is somewhat counterproductive to the whole notion of the term "parasite", though it does suggest, if it were to do so, that *P. falciparum* could become a symbiotic partner with our blood system. Of course, this is a mere idle thought for its amusement value. This argument is just a red herring: "Did you check past records in your report? Did you do do a patent search? Did you run it through a group review? Did you do carbon dating? WHAT!? No carbon dating!? So what are you wasting my time for?!" When I was in Corporate customer service every very rare now and then we'd get a customer who would ask for help and do everything to be uncooperative when we gave it to him. After about three cycles of this we'd get wise and then bluntly start grilling the customer to figure out where he was coming from. Very often it was someone trying to get materials for a lawsuit against the company. We'd tell him to contact Corporate Legal and then refuse to talk to him further. White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

dhogaza · 25 June 2008

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'm surprised no one has pointed out that Schafly is simply ripping off Steve McIntyre's (of Climate Audit infamy) incessant attack on Lonnie Thompson's ice core data tracking CO2 concentrations in the atmosphere over the last few hundreds of thousands of years. McIntyre's attack on Thompson's been going on for years, including demands made to the University Thomspon works for, journals, PNAS, etc. It's a technique that's a bit reminiscent of SLAPP suits ... attacking the scientist in an effort to discredit them, bog them down in an effort to fight back, etc etc. McIntyre's efforts against Thompson are actually a bit scary, because he's skilled at being nasty. Scharfly's just a clown. But the rip-off of the technique is interesting.

Stanton · 25 June 2008

As far as I know, the nature of the defective hemoglobin causes afflicted red blood cells to be brittle and unelastic, as compared to to normal elastic, and resilient red blood cells. Imagine how long rubber innertubes and plastic milk cartons would last filled with water, while being bounced around inside a complex of pipes. Even if Plasmodium sp could promote the health of their host red blood cell, they could do nothing to prolong the lifespan of a sickle-cell red blood cell, as the blood cell is already sickle-celled to begin with. A sickled red blood cell kills any Plasmodium parasites in it by dying, either by rupturing do to some adverse condition, whether from the parasite consuming its hemoglobin, or due to anaerobic metabolism events, or when the sickled red blood cell gets lodged in some nook, cranny or capillary, and dies (the elasticity of a health red blood cell prevents this from occurring).

iml8 said:
Frank B said: The sickling of red cells infested with malaria is a physical act that malaria may never be able to prevent. It is totally different from chemical defenses. For example, our body's immune system can not stop a bullet or a knife. Behe was showing his ignorance using that as an example, and apparently you know less than he.
The interesting thing is that for *P. falciparum* to do so, it would have to be attentive to the health of the red blood cell. That is somewhat counterproductive to the whole notion of the term "parasite", though it does suggest, if it were to do so, that *P. falciparum* could become a symbiotic partner with our blood system.

iml8 · 25 June 2008

Stanton said: Even if Plasmodium sp could promote the health of their host red blood cell, they could do nothing to prolong the lifespan of a sickle-cell red blood cell, as the blood cell is already sickle-celled to begin with.

Hmm? I may be under a false impression, but from what I know about sickle-cell anemia if you have only one single-cell allele the red blood cells look healthy normally. However, they tend to sickle relatively easily under stress (as in being attacked by malevolent protozoans). Now get a double dose of the sickle-cell allele you get sickled red blood cells normally and you are not a happy person at any time. I have heard that, though we generally associate sickle-cell anemia with black folk, it occurs among non-black populations in regions where malaria is common. Another interesting question is whether they have the same mutations ... reminiscent of the data item that there are at least four separate mutations for lactose tolerance. Heh! I was lurking in an Amazon.com discussion in which a fellow named Nguyen was promoting the "no constructive mutations" argument. I had to think: OK, so why am I lactose-tolerant and as an East Asian you are by a very good bet not? White Rabbit (Greg Goebel) http://www.vectorsite.net

iml8 · 25 June 2008

Duh, when all else fails (and only if all else fails) check
Wikipedia ... there's only one mutation but it occurs in four
separate populations and may have arisen four times. Those with
only one sickle-cell allele may have a small proportion of
sickle cells among a healthy population of red blood cells.
The actual mechanism of resistance I mentioned earlier is apparently
speculative. That there is resistance there is no doubt.

White Rabbit (Greg Goebel) http://www.vectorsite.net

Stanton · 25 June 2008

iml8 said: I may be under a false impression, but from what I know about sickle-cell anemia if you have only one single-cell allele the red blood cells look healthy normally. However, they tend to sickle relatively easily under stress (as in being attacked by malevolent protozoans). Now get a double dose of the sickle-cell allele you get sickled red blood cells normally and you are not a happy person at any time.

From what I was taught, the sickle-cells are produced already sickled: they rupture when they're under stress, whether they're exposed to anaerobic metabolism, or being invaded by Plasmodium (remember that there are at least 4 different species of importance in humans). Remember that you only need one copy of a gene to make the correct protein: hemoglobin is one of those traits that have both copies of the gene active at the same time, so that carriers of sickle cell anemia make both sickle and normal red blood cells.

I had to think: OK, so why am I lactose-tolerant and as an East Asian you are by a very good bet not? White Rabbit (Greg Goebel) http://www.vectorsite.net

You're lactose-tolerant because you're probably descended from one of the two major human populations that have developed faulty lactase inhibitors (either Northern Europeans, or the Masai cattle-herders). I'm half-Taiwanese, actually, so, while ice cream, as my mother puts it, doesn't talk to my mother, I'm still on speaking terms with dairy products, sort of. It's a quarrelous relationship, mind you.

iml8 · 25 June 2008

Stanton said:
iml8 said: From what I was taught, the sickle-cells are produced already sickled: they rupture when they're under stress, whether they're exposed to anaerobic metabolism, or being invaded by Plasmodium (remember that there are at least 4 different species of importance in humans). Remember that you only need one copy of a gene to make the correct protein: hemoglobin is one of those traits that have both copies of the gene active at the same time, so that carriers of sickle cell anemia make both sickle and normal red blood cells.
Sigh, if you have a double allele you have sickle-cell anemia, no argument. The issue is that if you have only one allele, you have resistance to malaria but do not have sickle-cell anemia. The sickle-cell allele is not *completely* recessive but its operation in that case is unclear. One speculation, discussed earlier, is that it makes seemingly healthy red blood cells more prone to sickling under stress, at which time they die or are killed off by the immune system. White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

iml8 · 25 June 2008

Stanton said: From what I was taught, the sickle-cells are produced already sickled: they rupture when they're under stress, whether they're exposed to anaerobic metabolism, or being invaded by Plasmodium (remember that there are at least 4 different species of importance in humans). Remember that you only need one copy of a gene to make the correct protein: hemoglobin is one of those traits that have both copies of the gene active at the same time, so that carriers of sickle cell anemia make both sickle and normal red blood cells.

Sigh, if you have a double dose of the sickle-cell trait, you have sickle-cell anemia. No argument. If you have a *single* dose, you don't have sickle-cell anemia and your red blood cells look (mostly) healthy -- but you have resistance to malaria. Nobody is quite sure why, but one theory offered here earlier says that infected cells sickle easily and fall by the wayside. The sickle-cell gene is not completely recessive. Being of Anglo-Germanic ancestry I can assume I have one particular mutation for lactose tolerance. Lactose-tolerant Africans can have one or more of three other mutations for the trait. White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

Frank B · 25 June 2008

When a person has sickle-cell trait, I believe they produce equal amounts of the hemoglobin A (normal) and hemoglobin S (sickle-cell). At 50% the red cell will not sickle under most conditions. Being infected with malarial organisms is one exception, and extreme medical conditions (anoxia) is another.
Infants and newborns need to be transfused with blood testing negative for hemoglobin S to avoid the risk of sickling red cells.

trrll · 25 June 2008

I agree with Lenski that that certainly is a lot of opportunity for RM+NS (and drift & contingency, etc.). Any thoughts on why we don’t currently see a lot more evolution than we see in all the various microbes out there in the wild, other than a few simple things like say the nylon eating bacteria that most probably developed as a resulted of a single step mutation? Shouldn’t we be seeing much more than we’ve seen here in Lenski’s laboratory induced evolution of E. coli that resulted in a rather simple mechanism to absorb citrate that apparently resulted from two or three mutations; and the above mentioned nylon eating bacteria hat evolved in the wild?

Bacteria evolve so fast that they are expected to be pretty much at an evolutionary optimum for their ecological niche. After all, in view of numbers, they are perhaps the most successful organisms on earth. There is not really much selective advantage for evolving into other types of creatures, such as multicellular organisms, because those ecological niches are already occupied. So one would not expect to see much evolutionary change in bacteria unless they have to deal with some sort of environmental perturbation.

trrll · 25 June 2008

And then there’s the related issue of why *P. falciparum* hasn’t evolved to defeat the sickle-cell defense over a matter of millennia when it can defeat chloroquine in a matter of generations.

The selective pressures are very asymmetrical. Since malaria greatly reduces fitness, there is a big selective advantage to malaria resistance--enough to balance the loss in fitness due to occasional mating of heterozygotes to produce homozygotes with sickle cell disease. But the latter means that the sickle cell allele will not take over a population, because as the frequency of the sickle allele in the population increases, its fitness penalty also increases, because heterozygotes become more likely to mate with one another. At the limit of everybody being a heterozygote, the penalty is 25%, which is a substantial loss in fertility. So the sickle cell allele is self-limited in the population to a frequency at which the selective advantage to malaria resistance just balances the selective penalty of occasionally producing homozygotes. What this means is that P. falciparum doesn't really need to defeat the sickle resistance--there will always be plenty of nonresistant hosts to propagate the parasite. Defeating sickle cell resistance would not be worth even a small loss in overall fitness to P. falciparum.

_Arthur · 25 June 2008

Bigbang's argument "Plasmodium failed to evolve ... [this or that characteristic]" is a common gambit amongst ID creationists. Failure live up to an IDer imaginary non-expectation is the weakest argument possible.

I expected E.coli to metabolize fluor, and corrode Dr. Lenski glass dishes, to escape its 20-tears confinement.

E.coli bacteria's failure to escape the petri dishes clearly show where the edge of evolution is.

raven · 25 June 2008

The shorter answer is that we are in a coevolutionary arms race with the pathogens. Sometimes we win, sometimes they win. Just simple, basic biology.

We managed to wipe out one perennial lethal disease, smallpox. Another bug jumped the species barrier and we are now battling HIV. SARS came close but a lot of clever people were able to defeat it.

Evolutionary biology predicts that there will be another emerging disease sooner or later. If it was up to the creos, we would be the equivalent of a bunny sitting in the middle of the road while distant headlights get closer and closer.

_Arthur · 25 June 2008

raven said: The shorter answer is that we are in a coevolutionary arms race with the pathogens. Sometimes we win, sometimes they win. Just simple, basic biology.

And most of the times, a metastable equilibrium is reached. No obvious winner or loser.

Nigel D · 26 June 2008

jasonmitchell said:
jasonmitchell said: I thought ethane dithiol was orderless? BME on the other hand - foul smelling stuff http://en.wikipedia.org/wiki/Beta_mercaptoethanol
retraction - I was thinking of something else - but BME is foul (and ironically found in human flattus (flatti?))

Retraction accepted, Jason. My head nearly exploded when I read your thought that ethane dithiol was odourless! Now, try to imagine 2-ME as the definition of a "sweet" odour; ethane dithiol is foul by comparison. In structure, 2-ME and ethane dithiol are very similar - the only difference being that where 2-ME has an atom of O, ethane dithiol has a second S. Believe me when I say that the human olfactory system is exquisitely sensitive to the difference between oxygen and sulphur*! Despite them being adjacent in Group VI of the periodic table.

Stanton · 26 June 2008

~~bigbang~~Bigot lied: Alas, ultimately it all seems so utterly pointless, doesn’t it? No wonder the emotionally fragile among us, like PvM, feels a need to invent a god to have faith in, in his case an unreal, non-existent god that is “hidden” in a “permanent gap of ignorance.” I apologize to PvM that I made fun of his faith.

Your gross insincerity is deafening, Bigot.

Eric · 26 June 2008

bigbang said: Alas, ultimately it all seems so utterly pointless, doesn’t it?

I find it pointless that my speed is restricted to c. Unfortunately for me, "pointless" provides no evidence of "incorrect." Are you coming around, Bigbang? Your last post almost sounded like you accept common descent and the development of multicellular species via natural selection.

Mike from Oz · 26 June 2008

Having read through the whole saga now, including the astonishing ignorance and, quite frankly, unbelievable gall of the crowd at Conservapedia, I must say that if I was Andy "whadya mean I have to actually read your paper before I attempt to trash it?" Schlafly, I'd go and hide under a rock somewhere.

This thing is scattered far and wide across the web now, and it doesn't make the Creo crowd look good at all.

Stanton · 26 June 2008

Eric said: Are you coming around, Bigbang? Your last post almost sounded like you accept common descent and the development of multicellular species via natural selection.

Highly unlikely. The bigot is just being snide: if he were sincerely trying to come around, he would have attempted to sound civil, rather than continue his insufferably pretentious and arrogantly ignorant tone of voice.

iml8 · 26 June 2008

Frank B said: When a person has sickle-cell trait, I believe they produce equal amounts of the hemoglobin A (normal) and hemoglobin S (sickle-cell). At 50% the red cell will not sickle under most conditions. Being infected with malarial organisms is one exception, and extreme medical conditions (anoxia) is another. Infants and newborns need to be transfused with blood testing negative for hemoglobin S to avoid the risk of sickling red cells.

*Very* interesting -- both genes are fully operational (isn't there a clumsy term called "codominant" for that?) but they do not carry the same weight in terms of their effect. Now I am definitely pushing the limits of my knowledge of genetics here, but would it be ridiculous to speculate that a gene duplication could produce a coupled trait in which both forms of hemoglobin were synthesized? This would be more "difficult" in evolutionary terms since gene duplications are much rarer than single-point mutations, but it suggests the possibility of a human population whose red blood cells are neatly optimized to make life harder for the plasmodium parasites but which does not suffer from sickle-cell anemia. If this sounds ignorant, I beg forgiveness, but I offer the idea in hopes of learning something from it. White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

iml8 · 26 June 2008

bigbang said: Too bad, b/c it’s actually a rather significant reality with significant implications . . . as is the reality that I’ve always accepted common descent, but then you don’t really seem to be all that concerned about such realities. Hey, you may be a perfect candidate for faith in PvM’s god, an unreal god that PvM says is hidden in a permanent gap of ignorance.

I say it over and over, but you really *can* find decaffienated coffee that tastes as good as the real thing. Honest! White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

Stanton · 26 June 2008

~~bigbang~~Bigot said: OK Stanton, I’ll make you a deal----you be civil and I’ll be civil; but you go first, and remember that, considering all your rants in your various posts, you have a lot of bad history to overcome; so forgive me if I remain skeptical.

Why should I be civil to you or any other maliciously moronic troll, Bigot? You were never civil before, and it's quite obvious that you never intend to be civil to anyone. You are the one who came to Panda's Thumb in order to spread your malevolent stupidity and engage in your abominably incompetent attempts at character assassinations, and you don't care that all of your posts make it crystal clear that you not only do not care about truth or facts, but, you could not tell the truth if the truth landed on your face and infected you with kala azar. Honestly, I can not understand how you can be so proud of yourself when fortune cookie fortunes are exponentially more sincere and more honest than you.

Eric · 26 June 2008

bigbang said: ...as is the reality that I’ve always accepted common descent,

Really? In your first post on this thread you brought up Behe's edge of evolution and stated your opinion that we should be seeing much more evolution (in bacteria) than we do. "Where's the arms race?" you asked. Then you went on for a couple posts about RM+NS only being able to degrade DNA (and not be elegant). These posts clearly imply that you think RM+NS can't build anything new. So how exactly do these posts square with your belief in common descent? Can natural selection create new information? Can it produce new species? Yes or no? Your position isn't clear. (In contrast, I think you've been pretty clear on your views on Darwin, and Mayr, and Dawkins. While it seems terribly important to you that some scientists are athiests that think poorly of religion while other scientists are religious, please, there's no need to repeat your views on this.)

but then you don’t really seem to be all that concerned about such realities. Hey, you may be a perfect candidate for faith in PvM’s god, an unreal god that PvM says is hidden in a permanent gap of ignorance.

Okay...from now on I'll keep in mind that you accept common descent. Is that real enough for you, or do you want to take a few more potshots at me before answering my question about what you think the limits of evolution actually are?

aaron shuman · 26 June 2008

I enjoyed very much this lucid response to Andy Schafly and his acolytes. This response is certainly more than they deserve. But the fact that this is posted publicly to help maintain a public dialogue on the issue is appreciated. This sort of honest openness is invaluable to a thinking society. Nicely done, Dr. Lenski.

trrll · 26 June 2008

Alas, ultimately it all seems so utterly pointless, doesn’t it?

I've heard people say this kind of thing, but it never has made sense to me. What is a "point," and why should one need it? I can only speculate that people who feel this way must lead sad, colorless lives, and be searching for something outside their own experience to give them a reason for living. I've never known a scientist who felt this way, probably because we are all so fascinated with the endless wonder and complexity of the natural world that it never occurs us to seek a "point."

iml8 · 26 June 2008

aaron shuman said: I enjoyed very much this lucid response to Andy Schafly and his acolytes. This response is certainly more than they deserve. But the fact that this is posted publicly to help maintain a public dialogue on the issue is appreciated. This sort of honest openness is invaluable to a thinking society. Nicely done, Dr. Lenski.

Do not overlook the sly way "Dr. Richard Paley" handed Lenski a nice big stick to hit them over the head with ... which Lenski used with good effect without, it seems, ever suspecting that "Dr. Paley" was really on his side. White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

iml8 · 26 June 2008

trrll said: I've heard people say this kind of thing, but it never has made sense to me. What is a "point," and why should one need it?

"Everybody should believe in something. I believe I'll have another drink." (WC Fields, cited in a number of variations) White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

raven · 27 June 2008

bigbang said: Alas, ultimately it all seems so utterly pointless, doesn’t it?

This is so pathetic it is amazing. According to the creos, god created a universe 6,000 years ago that looks like it is 13.7 billion light years across and old with billions of galaxies. We however, knock around on a tiny planet completely fooled by the old trickster with the kid with an ant farm mentality. But he will show up any day now and destroy everything and kill everyone so nothing is important. That they think this is a happy event shows how desperately empty and meaningless their lives are. This isn't xianity either, it is suicidal solipsistic Nihilism. One scientific viewpoint is that the small corner of the galaxy we see appears to be empty. Our distant descendants could spread out and own it all. As a transitional species, since all species are transitional, our descendants could be far smarter, far less destructive, and even immortal. Being intelligent tool users gives us choices and whatever we choose, it will have been a dramatic ride.

Nigel D · 27 June 2008

Why should I be civil to you or any other maliciously moronic troll, Bigot? You were never civil before, and it’s quite obvious that you never intend to be civil to anyone. You are the one who came to Panda’s Thumb in order to spread your malevolent stupidity and engage in your abominably incompetent attempts at character assassinations, and you don’t care that all of your posts make it crystal clear that you not only do not care about truth or facts, but, you could not tell the truth if the truth landed on your face and infected you with kala azar.
— Stanton, responding to the resident hypocrite

Nicely put, Stanton. BTW, I've given up reading bigbang's comments. This was because I learned that reading his comments is a waste of my time.

fnxtr · 27 June 2008

I think I get it now. It thinks it's being droll, wry, and witty, and doesn't realize it's just annoying.

I've read Mark Twain, bigbang, and you, sir, are no Mark Twain (pace Bentsen).

Interrobang · 27 June 2008

Steve s said: Yeah, modern conservatism may have it's flaws, but I'm not going to blame them for this guy...

Considering who Andy Schafly's mother is (that would be the infamous Phyllis Schlafly, one of the ideological ancestors of modern conservatism or radical right-wingery), you're entirely too charitable. Andy Schafly is modern conservatism, all the way from wingnut-welfare cradle to inevitable grave. By handing this guy his rump neatly sliced as asshimi, Lenski has also made a distinct political point about the intellectual bankruptcy of the modern far right.

Eric · 27 June 2008

bigbang said: I doubt you’d ask what is a purpose or a meaning, and why should one need it.

If by "one" you mean "humans," its debatable. If by "one" you mean hurricane Katrina, then yes, I doubt. Please explain to me why hurricane Katrina needs a purpose, and why, in terms of needing meaning or purpose, you think natural selection is more like a human than a hurricane.

scientists continuously seek the purpose and/or meaning of new and unexpected things that they find

We do? What major scientific journal publishes on the subject of purpose? What NSF grants are given to study it? Why do I spend so much time reading Nature when clearly deep down inside I want to read Purpose? I submit to you that there is an hypothesis that explains all these observations: scientists don't seek purpose, and don't find it interesting as a research topic. (Caveat: unless there's beer involved.)

Consider the unlikelihood of origin of life. Does that mean something?

I'm considering. It means, IMO, that Bigbang doesn't understand the flaws in the anthropic argument. [Apologies if this posts twice]

PvM · 27 June 2008

Now that's ironic. Bigbang seems to be white-washing his own history which is far worse. Shame on you.

bigbang said: Stanton complains: if he [bigbang] were sincerely trying to come around, he would have attempted to sound civil” . OK Stanton, I’ll make you a deal----you be civil and I’ll be civil; but you go first, and remember that, considering all your rants in your various posts, you have a lot of bad history to overcome; so forgive me if I remain skeptical.

trrll · 27 June 2008

Instead of pointless, perhaps I should have used a word like purposeless, or meaningless. I doubt you’d ask what is a purpose or a meaning, and why should one need it.

Certainly I understand purpose and meaning--they are internal constructs that I create in my own mind to guide my actions and to aid my own understanding. But the idea that the universe should have a purpose or meaning sounds nonsensical. Why should it, and why should I care if it did? It's like asking what the "purpose" of my car is. My car doesn't have a purpose. The people who made it had a purpose, and I have a purpose for owning it, but my car doesn't have any purpose--it's an inanimate object operating according to the laws of physics, and it doesn't have a brain in which to conceive a purpose. If the universe had something like a brain, and was capable of conceiving a purpose, then that would be of interest to me if knowing that purpose helped me to figure out how things work. But its purposes would not be mine, and I would certainly not be happier living in a universe with a purpose than in one without.

Sure, scientists, as most all of us, are fascinated by the endless wonder and complexity of the world; and yet, in spite of that wonder and complexity, scientists continuously seek the purpose and/or meaning of new and unexpected things that they find that may not readily fit in with what we currently know or understand about the world, or think we know or understand.

Not me. When I do science I am interested in function--how things work. Something doesn't have to have a "point" or "purpose" to function. In biology, particularly, expecting things to have a "purpose" generally leads one into mistakes, because selective pressures shift over time, and the function of a structure or reaction today is likely to be completely unrelated to why it provided a selective advantage when it initially evolved. Thinking in terms of "purpose" leads to a narrow, simple-minded view of biology that misses much of the richness and complexity of function that is actually there.

That’s how our understanding evolves. When the redshifts were first observed, Hubble considered the meaning of that discovery—-Hubble’s law and the BB model resulted.

I would say rather that he considered what that evidence told him about how the universe works, now its "meaning." Does an expanding universe "mean" something different than a contracting universe or a static universe? Not to me.

Consider the unlikelihood of origin of life.

I can consider the hypothesis that the origin of life was unlikely. I find it doubtful that the origin of life here on earth was unlikely, because the "waiting time" from when the earth calmed down enough to support life was rather short. So the default hypothesis is that under appropriate conditions, the origin of life is highly probable. Of course data from other worlds is needed to confirm that, and also to find out how broad the range of "appropriate conditions" might be.

Does that mean something? Koonin thinks it means that there’s some sort of infinite, eternal multiverse; where all things and all universes are not only possible, they’re inevitable.

Improbable events happen sometimes. There is no meaning to that; it is simply the nature of statistics. If it turns out to be true that the origin of life was improbable, then it could suggest multiple hypotheses that would make it less improbable: a universe large enough to render even such improbable events likely, or some variant of the multiple universes hypothesis. I can't say that any of these hypotheses has a "meaning;" they are just different ideas of how the universe might work.

iml8 · 27 June 2008

Consider the unlikelihood of origin of life.

Well, since we don't have strong data on its origins, the probabilities could range from extremely low to extremely high. Of course, it would be interesting to calculate the probability of the origins of life in supernatural terms. The only basis we have for such a calculation is the number of supernatural events that have occurred in provable terms. This number being zero, the calculation is, as the math boys and girls put it, "trivial". And AGAIN ... do give the decaf a try. White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

fnxtr · 27 June 2008

Now you are being deliberately evasive, and equivocating on the definition of 'meaning'. I expect you deny this, of course, notmarktwain, but everyone else can see it too.

trrll · 27 June 2008

Well, that’s rather naive. Last I checked an expanding universe does mean something different than a static universe to scientists.

Really? And what "meaning" do you imagine that an expanding universe has to scientists, beyond the trivial meaning of the words "expanding" and "static" themselves? Returning to your original wording, would you say that an expanding universe is more or less "pointless" (or "meaningless" if you prefer) than a static one?

Did Darwin’s (and others) observations and conclusions regarding similarities and variations in various aspects of life mean or imply something? Yeah: Darwin called it common descent.

That's funny. A while ago, you referred to natural selection as "pointless," and when I questioned what this meant, you offered "meaningless" as a synonym. Yet now you are insisting that it has meaning. Perhaps you would be less confused if you were to make up your mind which of the definitions of "meaning" you want to use, and stick to it.

Science Avenger · 27 June 2008

trrll said: Perhaps you would be less confused if you were to make up your mind which of the definitions of "meaning" you want to use, and stick to it.

You mean "whichever serves my rhetorical purposes at the moment" is not sufficient?

Stanton · 27 June 2008

Science Avenger said:
trrll said: Perhaps you would be less confused if you were to make up your mind which of the definitions of "meaning" you want to use, and stick to it.
You mean "whichever serves my rhetorical purposes at the moment" is not sufficient?

And this is the primary reason why I affix the adjective of "perfidious" to ~~bigbang~~Bigot.

Science Avenger · 28 June 2008

bigbang said: And indeed that is what Darwinism unavoidably means, or implies, that our existence is little more than an accident of sorts that has no ultimate meaning or purpose, that human life has no more intrinsic value than say a cockroach’s.

It doesn't, whether "Darwinism" is true or not. Deal.

trrll · 28 June 2008

Science says it means that, unlike a static universe, an expanding universe means that the universe, space-time itself, is not infinite and eternal, but rather that it has a finite age, currently estimated around 14 billion years, that it had a beginning from some sort of singularly; it means that there are cosmological horizons; it means that it’s a universe that explains things like CMBR, redshifts, etc., etc.

Yes, this is a description of an expanding universe. But you didn't answer my question. Is this more or less "pointless" (or meaningless, if you prefer) than a static universe?

And indeed that is what Darwinism unavoidably means, or implies, that our existence is little more than an accident of sorts that has no ultimate meaning or purpose, that human life has no more intrinsic value than say a cockroach’s.

So you are saying that you would be happier if your were serving some other creature's purposes rather than your own? You are certainly reinforcing my impression that those who seek after an external "point" to give their lives "meaning" or "value" must lead terribly sad, colorless lives.

Stanton · 28 June 2008

trrll said: So you are saying that you would be happier if your were serving some other creature's purposes rather than your own? You are certainly reinforcing my impression that those who seek after an external "point" to give their lives "meaning" or "value" must lead terribly sad, colorless lives.

~~bigbang~~Bigot must lead a catastrophically dreary life if the only way he can bring meaning to his existence is by engaging in crude, and sloppy word-lawyering, as well as incompetently childish character assassinations.

trrll · 28 June 2008

In your Darwinian world, humans no more serve their own purpose than do bacteria or cockroaches; although I suppose one might argue that in the Darwinian world humans do seem to posses a rather unique brain that generates an illusion of free will (apparently b/c such a an illusion confers some sort of fitness benefit), and that often also generates illusions of purpose and/or meaning; and in the case of Darwinians like PvM, it generates delusions of a nonexistent god hidden in permanent gap of ignorance.

My purposes most certainly guide my actions. Are you arguing that a purpose must be magical to be real? I imagine that my purposes reflect my genetics, my experiences, and doubtless chance fluctuations in my nervous system, all of which are unique to me. Whether or not you choose call that "free will" seems to me to be a content-free exercise in semantics.

OTOH, trrll, if you feel that say Einstein’s “spirit vastly superior to that of man,” or Planck’s “ Mind that is the matrix of all matter” would make your life sad and colorless, then by all means, stick with the Darwinism that tells you that your life is and accident, having no ultimate meaning or purpose and that human life has no more intrinsic value that say a cockroach’s, a view that unavoidably engenders atheism.

You can tell that somebody is getting really desperate when they cite Einstein as a supporter of the view that human life has no value unless it serves the purpose of some nonhuman entity .

Stanton · 28 June 2008

You also notice how ~~bigbang~~Bigot never gives a specific citation whenever he claims that "Darwinists" (sic) claim that human life has as much value as that of a cockroach?

(He doesn't provide a citation supporting his claim that Stalin supported "Darwinism" (sic) either.)

trrll · 28 June 2008

Sure, in your Darwinian world, free will is an illusion, and your “purposes” are little more than the result of some sorts of evolved algorithms, somehow embedded in your genetics.

So what? My sense of personal value is not founded upon my accomplishments and my relationships with other human beings, not upon the belief that my purposes are magical. It is difficult for me to imagine how little sense of self-worth a person must have to feel that their personal value derives from serving the purposes of some nonhuman entity.

PZ Myers · 29 June 2008

Notice: I will be purging this thread of sockpuppets for the usual lying creationist later today.

trrll · 29 June 2008

In your Darwinian world your sense of “self worth” or “personal value” is nothing more than an illusion of sorts, something magical as it were; a useful illusion perhaps, but an illusion nonetheless

Illusion of what? My sense of self worth is a function of my own nervous system. What is the illusion there?

your life has no more intrinsic value or meaning than say a cockroach or a bacterium

"Intrinsic value" is a meaningless concept. Value needs a referent--value to whom? My life is more valuable to me and to the people whose opinions I care about than that of a cockroach or bacteria.

although, FWIW, their kind will most likely be around far longer than will yours.

That may or may not be true, but I don't see what it has to do with "value" or "meaning." Would you really feel that your life has more value if your kind are around longer than the bacteria? That sounds crazy to me.

trrll · 29 June 2008

I agree that “intrinsic value” of human life is typically seen as a meaningless concept in the world of atheists and nihilists.

This seems to me to be quite separate from questions of a/theism. Even if gods or other nonhuman "supernatural" entities exist, why should they be the arbiters of the value of life? It seems to me that only humans are qualified to judge the value of human life.

trrll · 29 June 2008

I agree that “intrinsic value” of human life is typically seen as a meaningless concept in the world of atheists and nihilists.

Nigel D · 30 June 2008

PZ Myers said: Notice: I will be purging this thread of sockpuppets for the usual lying creationist later today.

Thanks, PZ. That's much better now.

Sean · 30 June 2008

Some cheese to go with your whine Bigot?

Sean · 30 June 2008

Some cheese to go with your whine Bigot?

J. Biggs · 30 June 2008

Nigel D said:
PZ Myers said: Notice: I will be purging this thread of sockpuppets for the usual lying creationist later today.
Thanks, PZ. That's much better now.

Truthfully, you don't even need to see the bb's original comments as they are re-posted ad nauseum by other commenter's intent on refuting what s/he posts. I have come to recognize that bb's posts consist mainly of making mendacious unsupported claims then repeating them ad nauseum; and then, a dodge to a new equally dishonest claim after a thorough refutation of the previous one again repeated ad nauseum. You have to admit, bb is very good at disrupting what started as a decent thread.

Green Eagle · 30 June 2008

Here's a good Paley quote that I found: "Even Jews, being imperfect pre-Christians, have in them the potential to share in this, our common, foundational American value, should they stop their obstinate refusal to acknowledge Jesus as Messiah. Patience is a virtue that we Americans are happy to show them."

Nice guy. It always comes down to this sort of bigotry in the end. I wonder how he feels about mud people.

AL · 2 July 2008

Green Eagle,
I think it's been established that Paley is a Poe.

AL · 2 July 2008

Green Eagle said: Here's a good Paley quote that I found: "Even Jews, being imperfect pre-Christians, have in them the potential to share in this, our common, foundational American value, should they stop their obstinate refusal to acknowledge Jesus as Messiah. Patience is a virtue that we Americans are happy to show them." Nice guy. It always comes down to this sort of bigotry in the end. I wonder how he feels about mud people.

Green Eagle, I think it's been established that Paley is a Poe.

Tyler · 7 July 2008

Sometimes I think it would be better for the scientific establishment to build 'doubter' labs, equipped with skilled scientists, access to equipment, grad students, etc, and directlyemployable by these vocal 'skeptic' groups.

If it came down to these groups having recourse and being personally responsible for funding the experiments necessary to test the conclusions of other scientists, I should think they would either shut up very quickly or improve science, either by confirming old results or casting doubt on them.

Of course, who would want to work at the behest of a bunch of crackpots that apparently can't read, and not do any original work?

Henry J · 7 July 2008

Of course, who would want to work at the behest of a bunch of crackpots that apparently can’t read, and not do any original work?

Must be all those ID theorists that we keep hearing about but for which we never seem to get names or publication references... Henry

Jordan · 18 July 2008

I'm really, really impressed with the civility and class Dr. Lenski showed in his first response to Conservapedia's request. It can be hard to keep levelheaded and civil when talking to creationists, but it's absolutely critical to do so for observers who see the correspondence, and could be convinced to join the debate on the pro-science, pro-reality side. Well done, Dr. Lenski.

Ray T. Perreault · 14 February 2009

Stanton said: You also notice how ~~bigbang~~Bigot never gives a specific citation whenever he claims that "Darwinists" (sic) claim that human life has as much value as that of a cockroach? \Why not? There are plenty of Creationist quotes available, just not anything factual. (He doesn't provide a citation supporting his claim that Stalin supported "Darwinism" (sic) either.)

\Won't find one, either. Geneticists (Russian term for Darwinian biologists) were decreed "bourgeois" by Stalin. Trofim Lysenko was peasant born uneducated, therefore perfect for the new proletarian world. As Commissar of Agronomy, he imposed his delusional proletarian evolutionary theory, and the geneticists were off to the gulags (literally). To Lysenko, heredity was in the cytoplasm, DNA not being involved. Lysenko' stupidity caused the starvation of over 20,000,000 Russian citizens. \Creationists regularly show Stalin style agitprop, one article I read last year even called for violent elimination of the 'evolutionist class'. One of the principle IDiots, Jonathan Wells, repeats Lysenko's drool verbatim. Wells is DI's token Moonie. Ray

Ray T. Perreault · 15 February 2009

Mike from Oz said: Having read through the whole saga now, including the astonishing ignorance and, quite frankly, unbelievable gall of the crowd at Conservapedia, I must say that if I was Andy "whadya mean I have to actually read your paper before I attempt to trash it?" Schlafly, I'd go and hide under a rock somewhere. This thing is scattered far and wide across the web now, and it doesn't make the Creo crowd look good at all.

\Schlafly is the same genius who posted the North Pacific Arboreal Octopus site as real science for 4 years, in spite of its only natural enemy being Bigfoot, and sponsored in part by People for the Ethical Treatment of Pumpkins. \Of course, Conservapedia is the sourcebook for ideologically correct Respublikanskoi Parti propagandists.

Doris Tracey · 21 October 2009

This is great news, I always new homo-sapiens were not created by God,only the sons and daughters of light were a creation of God... Made in his image and after his likeness.Unfortunately to do a rescue mission, the sons and daughters of light had to descend into the matter spheres and take on the gross bodies of the homosapiens.It appears there were two creations. The sons and daughters of light were created by the Eloheim and the homosapiens were a creation of the fallin angels. The angels had the power to co-create everything, but a living soul.

Greg D · 17 November 2009

It's bad enough that in the face of all rational thought,there are still folk out there who need the existence of God to explain the universe.
But it is beyond understanding that they also need to pretend that evolution is not an established fact despite all the evidence.
It would not surprise me if they also believe that the Nazi Holocaustin Europe did not occur.
What a world!

Lenski gives Conservap&aelig;dia a lesson

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Lenski gives Conservapædia a lesson