Changes

:“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. ...”  

:“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?   

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:

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:

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'''.  

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!'''  [ https://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.  [ https://en.wikipedia.org/wiki/Allusion]

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!'''  [ https://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.  [ https://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:

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.”  

:“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 exactly the 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.  

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 exactly the 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.  

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.

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.

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,

Sincerely,

<br>  Richard Lenski

<br>  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.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.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!'''  [ https://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.S. You may be unable to understand, or unwilling to accept, that evolution occurs.  '''And yet, life evolves!'''  [ https://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.

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.

The biologist [[Michael Behe]] criticized Richard Lenski's claims concerning the significance of his experiment (see: [http://behe.uncommondescent.com/2008/06/multiple-mutations-needed-for-e-coli/ Multiple Mutations Needed for E. Coli] by Michael Behe).

The biologist [[Michael Behe]] criticized Richard Lenski's claims concerning the significance of his experiment (see: [http://behe.uncommondescent.com/2008/06/multiple-mutations-needed-for-e-coli/ Multiple Mutations Needed for E. Coli] by Michael Behe).

Jonathon Witt of the [[Discovery Institute]] indicates that the biologist Dustin Van Hofwegen punctured the evolutionists' claims for Richard Lenski’s long-term evolution experiment (see: [https://evolutionnews.org/2021/06/biologist-dustin-van-hofwegen-punctures-claims-for-lenskis-long-term-evolution-experiment/ Biologist Dustin Van Hofwegen Punctures Claims for Lenski’s Long-Term Evolution Experiment]).

Jonathon Witt of the [[Discovery Institute]] indicates that the biologist Dustin Van Hofwegen punctured the evolutionists' claims for Richard Lenski's long-term evolution experiment (see: [https://evolutionnews.org/2021/06/biologist-dustin-van-hofwegen-punctures-claims-for-lenskis-long-term-evolution-experiment/ Biologist Dustin Van Hofwegen Punctures Claims for Lenski’s Long-Term Evolution Experiment]).

[[Category:Evolution]]

[[Category:Evolution]]