[_ Old Earth _] More evolution witnessed in labs

[Free]

Is there a point to all of this off-topic rhetoric?

 

[Jayls5]

Is there a point to all of this off-topic rhetoric?

Which?

The thread had already gone south, so I figured I may as well point out more areas where people refuse to take it literally.

 

[freeway]

Sorry guys this is not evolution, God has given his creation the ability to adapt, and man in all his wisdom can and has altered their environment, but until it grows legs and jumps off the table as a new species.............its creation.. :wink:

 

[Barbarian]

Sorry guys this is not evolution,

Evolution is defined by scientists as a "change in allele frequency over time." So yes, it's evolution. That's what evolution is. If you want your own theory, get your own name for it.

God has given his creation the ability to adapt, and man in all his wisdom can and has altered their environment, but until it grows legs and jumps off the table as a new species.............its creation..

Yep. Evolution is God's creation. And new species occur regularly. Would you like to learn about some of them?

 

[freeway]

"Jayls5"]http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html

A major evolutionary innovation has unfurled right in front of researchers' eyes. It's the first time evolution has been caught in the act of making such a rare and complex new trait.

you can go back and re read the whole post if needed...


but what about this....
Now the popularist treatments of this research (e.g. in New Scientist) give the impression that the E. coli developed the ability to metabolize citrate, whereas it supposedly could not do so before. However, this is clearly not the case, because the citric acid, tricarboxcylic acid (TCA), or Krebs, cycle (all names for the same thing) generates and utilizes citrate in its normal oxidative metabolism of glucose and other carbohydrates.5

Furthermore, E. coli is normally capable of utilizing citrate as an energy source under anaerobic conditions, with a whole suite of genes involved in its fermentation. This includes a citrate transporter gene that codes for a transporter protein embedded in the cell wall that takes citrate into the cell.6 This suite of genes (operon) is normally only activated under anaerobic conditions.

this would be the sort of thing that mutations are good at: destroying things

So what happened? It is not yet clear from the published information, but a likely scenario is that mutations jammed the regulation of this operon so that the bacteria produce citrate transporter regardless of the oxidative state of the bacterium’s environment (that is, it is permanently switched on). This can be likened to having a light that switches on when the sun goes downâ€â€a sensor detects the lack of light and turns the light on. A fault in the sensor could result in the light being on all the time. That is the sort of change we are talking about.

http://www.creationontheweb.com/content/view/5827/

 

[Jayls5]

"Jayls5"]http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html

A major evolutionary innovation has unfurled right in front of researchers' eyes. It's the first time evolution has been caught in the act of making such a rare and complex new trait.

you can go back and re read the whole post if needed...

The first time for such a rare and complex trait, not the first time witnessing evolution.

but what about this....
Now the popularist treatments of this research (e.g. in New Scientist) give the impression that the E. coli developed the ability to metabolize citrate, whereas it supposedly could not do so before. However, this is clearly not the case, because the citric acid, tricarboxcylic acid (TCA), or Krebs, cycle (all names for the same thing) generates and utilizes citrate in its normal oxidative metabolism of glucose and other carbohydrates.5

Furthermore, E. coli is normally capable of utilizing citrate as an energy source under anaerobic conditions, with a whole suite of genes involved in its fermentation. This includes a citrate transporter gene that codes for a transporter protein embedded in the cell wall that takes citrate into the cell.6 This suite of genes (operon) is normally only activated under anaerobic conditions.

this would be the sort of thing that mutations are good at: destroying things

So what happened? It is not yet clear from the published information, but a likely scenario is that mutations jammed the regulation of this operon so that the bacteria produce citrate transporter regardless of the oxidative state of the bacterium’s environment (that is, it is permanently switched on). This can be likened to having a light that switches on when the sun goes downâ€â€a sensor detects the lack of light and turns the light on. A fault in the sensor could result in the light being on all the time. That is the sort of change we are talking about.

http://www.creationontheweb.com/content/view/5827/

I posted this article over on another forum I frequent, and I thought I'd show the immediate replies I received. The first one covers the structure of the argument in the article.

CalvinDooglas wrote: I'm no biologist, but as a particularly critical reader, I see a few dead giveaways that show their complete ignorance of scientific method, or the point of this study, and their lack of journalistic experience/ethics.

First, they keep bringing up the red herring of humanity. We are not involved in this study, and it sort of begs the question "how does this apply to humans?", by vaguely insinuating that only evolution in humans counts. Of course this does not apply directly to humans, but an unskeptical reader would not see that the begged question is entirely irrelevant.

Next, the author attributes a motive of expectation to Lenski, which I seriously doubt was gained from a source, or is true at all. They make it appear as though he had a personal, emotional stake in this experiment, the kind that compromises validity. This helps to paint him as "neo-Darwinist", which implies that he has built his worldview around the idea of Darwinism. If anyone who believes that species evolves is a neo-Darwinist, then I guess most of us are also neo-Gravitationists and neo-Heliocentrists.

Further on, they continue to downplay the significance of aerobic metabolism, which is ridiculous. I know from my small understanding of biology, chemistry, and athletics that the presence of oxygen in living things makes an incredible difference, and that biological processes need oxygen like a car needs gas. The author says that it's no big deal because it was a simple matter of keeping the citric acid cycle running without O2, which I am under the impression is like saying "Well, humans being able to breathe underwater isn't a big deal because they could already metabolize oxygen in air".

"So what happened? We don't know, but we're going to assume, and then talk about what's wrong with what we assumed happened." Big strawman and appeal to their own authority.

Ultimately, the entire pseudoscientific subculture built around creationism show they do not understand the point of science except as a tool in for their debate. They continually seek dictate "limits" of science, and insist that theories, at least this one in particular, are sets of rules that affect the world outwardly, when in reality, theories are meticulous descriptions of the changing world we see. In astrophysics, these people would decry General Relativity because it does not explain how their car runs. Behe implies that evolution is supposed to be a force driving itself, which is absolutely untrue. Evolution is a process observed as a byproduct of regular biological function, not something that happens "to" a species by altering biological function. These creationists are stuck in the mindset that organisms are mechanical; that, like a car, a part cannot be changed without affecting the total functionality, and especially not with the engine running.

The biggest fallacy that creation scientists commit (enjoy) is parrying scientific jabs by asking for evidence that evolution is an external, predictable force that acts with intent of improvement alone. We say that evolution has occurred, and they don't ask how, but why.

The long and short of this response is "Yeah, well, we're just not convinced". This whole thing, like everything else creationists publish, is not intended to inform, but simply to market the idea by casting doubt on an absurdly small evidence gap. If the enzyme doesn't fit, you must acquit.

Jeremiah Smith covers the crappy content:

Another possibility is that an existing transporter gene, such as the one that normally takes up tartrate,3 which does not normally transport citrate, mutated such that it lost specificity and could then transport citrate into the cell. Such a loss of specificity is also an expected outcome of random mutations. A loss of specificity equals a loss of information

This one is a favorite. You see, after Dembski mixed Jesus with math, creationists are enamoured with information theory, and so try to phrase all their comments about mutations in the manner of information theory. They try to claim that mutations can't create information, only destroy it, not understanding just how information is actually defined in information theory.

(A quick disproof: A mutation that switched a T nucleotide with an A nucleotide would, to a creationist, be a loss of information, so the original sequence, with a T, would have more information than the mutant sequence with the A. But what mutations can do, mutations can undo, and it's not implausible that the base could mutate back from an A to a T. Since all mutations are a loss of information, this means that the mutant sequence with an A has more information than the original sequence with the T, which as we saw earlier, has more information than the mutant sequence with the A!)

Enzyme specificity refers to how specific the enzyme is at binding to another molecule. An enzyme with high specificity will only bind to a very small set of molecules, maybe just one, while one with low specificity will bind to many various molecules. When it comes to specificity, creationists love to have it both ways. To hear creationists tell it, when an enzyme loses specificity, it's lost the information needed to pick out specific enzymes, while when an enzyme gains specificity, it has lost the information needed to bind to all the other molecules! It is a "heads I win tails you lose" proposition.

However, mutations are good at destroying things, not creating them.

Another lie of creationists, because they have no concept of what mutations actually do or how proteins actually work, instead relying on silly metaphors to machines. Most mutations have little to no effect on a protein, some will indeed ruin its functionality, but there are also mutations that alter the protein's function in such a way as to benefit the organism.

Any time you see a creationist saying that mutations can only destroy genes, you should mentally replace their words with that HLAUGLHAUGLUBABULGUHAG noise that Jerkcity uses to denote (something you can't talk about on this forum). :

 

[freeway]

"Jayls5"]http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html

A major evolutionary innovation has unfurled right in front of researchers' eyes. It's the first time evolution has been caught in the act of making such a rare and complex new trait.

you can go back and re read the whole post if needed...

The first time for such a rare and complex trait, not the first time witnessing evolution.

but what about this....
Now the popularist treatments of this research (e.g. in New Scientist) give the impression that the E. coli developed the ability to metabolize citrate, whereas it supposedly could not do so before. However, this is clearly not the case, because the citric acid, tricarboxcylic acid (TCA), or Krebs, cycle (all names for the same thing) generates and utilizes citrate in its normal oxidative metabolism of glucose and other carbohydrates.5

Furthermore, E. coli is normally capable of utilizing citrate as an energy source under anaerobic conditions, with a whole suite of genes involved in its fermentation. This includes a citrate transporter gene that codes for a transporter protein embedded in the cell wall that takes citrate into the cell.6 This suite of genes (operon) is normally only activated under anaerobic conditions.

this would be the sort of thing that mutations are good at: destroying things

So what happened? It is not yet clear from the published information, but a likely scenario is that mutations jammed the regulation of this operon so that the bacteria produce citrate transporter regardless of the oxidative state of the bacterium’s environment (that is, it is permanently switched on). This can be likened to having a light that switches on when the sun goes downâ€â€a sensor detects the lack of light and turns the light on. A fault in the sensor could result in the light being on all the time. That is the sort of change we are talking about.

http://www.creationontheweb.com/content/view/5827/

I posted this article over on another forum I frequent, and I thought I'd show the immediate replies I received. The first one covers the structure of the argument in the article.

CalvinDooglas wrote: I'm no biologist, but as a particularly critical reader, I see a few dead giveaways that show their complete ignorance of scientific method, or the point of this study, and their lack of journalistic experience/ethics.

First, they keep bringing up the red herring of humanity. We are not involved in this study, and it sort of begs the question "how does this apply to humans?", by vaguely insinuating that only evolution in humans counts. Of course this does not apply directly to humans, but an unskeptical reader would not see that the begged question is entirely irrelevant.

Next, the author attributes a motive of expectation to Lenski, which I seriously doubt was gained from a source, or is true at all. They make it appear as though he had a personal, emotional stake in this experiment, the kind that compromises validity. This helps to paint him as "neo-Darwinist", which implies that he has built his worldview around the idea of Darwinism. If anyone who believes that species evolves is a neo-Darwinist, then I guess most of us are also neo-Gravitationists and neo-Heliocentrists.

Further on, they continue to downplay the significance of aerobic metabolism, which is ridiculous. I know from my small understanding of biology, chemistry, and athletics that the presence of oxygen in living things makes an incredible difference, and that biological processes need oxygen like a car needs gas. The author says that it's no big deal because it was a simple matter of keeping the citric acid cycle running without O2, which I am under the impression is like saying "Well, humans being able to breathe underwater isn't a big deal because they could already metabolize oxygen in air".

"So what happened? We don't know, but we're going to assume, and then talk about what's wrong with what we assumed happened." Big strawman and appeal to their own authority.

Ultimately, the entire pseudoscientific subculture built around creationism show they do not understand the point of science except as a tool in for their debate. They continually seek dictate "limits" of science, and insist that theories, at least this one in particular, are sets of rules that affect the world outwardly, when in reality, theories are meticulous descriptions of the changing world we see. In astrophysics, these people would decry General Relativity because it does not explain how their car runs. Behe implies that evolution is supposed to be a force driving itself, which is absolutely untrue. Evolution is a process observed as a byproduct of regular biological function, not something that happens "to" a species by altering biological function. These creationists are stuck in the mindset that organisms are mechanical; that, like a car, a part cannot be changed without affecting the total functionality, and especially not with the engine running.

The biggest fallacy that creation scientists commit (enjoy) is parrying scientific jabs by asking for evidence that evolution is an external, predictable force that acts with intent of improvement alone. We say that evolution has occurred, and they don't ask how, but why.

The long and short of this response is "Yeah, well, we're just not convinced". This whole thing, like everything else creationists publish, is not intended to inform, but simply to market the idea by casting doubt on an absurdly small evidence gap. If the enzyme doesn't fit, you must acquit.

Jeremiah Smith covers the crappy content:

Another possibility is that an existing transporter gene, such as the one that normally takes up tartrate,3 which does not normally transport citrate, mutated such that it lost specificity and could then transport citrate into the cell. Such a loss of specificity is also an expected outcome of random mutations. A loss of specificity equals a loss of information

This one is a favorite. You see, after Dembski mixed Jesus with math, creationists are enamoured with information theory, and so try to phrase all their comments about mutations in the manner of information theory. They try to claim that mutations can't create information, only destroy it, not understanding just how information is actually defined in information theory.

(A quick disproof: A mutation that switched a T nucleotide with an A nucleotide would, to a creationist, be a loss of information, so the original sequence, with a T, would have more information than the mutant sequence with the A. But what mutations can do, mutations can undo, and it's not implausible that the base could mutate back from an A to a T. Since all mutations are a loss of information, this means that the mutant sequence with an A has more information than the original sequence with the T, which as we saw earlier, has more information than the mutant sequence with the A!)

Enzyme specificity refers to how specific the enzyme is at binding to another molecule. An enzyme with high specificity will only bind to a very small set of molecules, maybe just one, while one with low specificity will bind to many various molecules. When it comes to specificity, creationists love to have it both ways. To hear creationists tell it, when an enzyme loses specificity, it's lost the information needed to pick out specific enzymes, while when an enzyme gains specificity, it has lost the information needed to bind to all the other molecules! It is a "heads I win tails you lose" proposition.

However, mutations are good at destroying things, not creating them.

Another lie of creationists, because they have no concept of what mutations actually do or how proteins actually work, instead relying on silly metaphors to machines. Most mutations have little to no effect on a protein, some will indeed ruin its functionality, but there are also mutations that alter the protein's function in such a way as to benefit the organism.

Any time you see a creationist saying that mutations can only destroy genes, you should mentally replace their words with that HLAUGLHAUGLUBABULGUHAG noise that Jerkcity uses to denote (something you can't talk about on this forum). :

Well I've read your post over a couple of times just to see if I missed something important....and seeing how you are using what others say to help back your theory....
Without just reposting or digging up more to disprove your hope and dreams to your god Darwin and his dying child "evolution". Freeway01 will be sitting watching and waiting for this petri tube specimen to grows legs and jump out..... waiting.............waiting.....yawn....waiting....

 

[Jayls5]

Well I've read your post over a couple of times just to see if I missed something important....and seeing how you are using what others say to help back your theory....
Without just reposting or digging up more to disprove your hope and dreams to your god Darwin and his dying child "evolution". Freeway01 will be sitting watching and waiting for this petri tube specimen to grows legs and jump out..... waiting.............waiting.....yawn....waiting....

You're waiting.... waiting...... waiting..... for something that has nothing to do with the theory you want to disprove.

So the punchline of this post is, "You used a post of someone else which you stated explicitly before doing."

Captain obvious to the rescue there. You want to address what was said now? It basically single handedly shows the fallacy of the main assumption in the article.

 

[freeway]

Well I've read your post over a couple of times just to see if I missed something important....and seeing how you are using what others say to help back your theory....
Without just reposting or digging up more to disprove your hope and dreams to your god Darwin and his dying child "evolution". Freeway01 will be sitting watching and waiting for this petri tube specimen to grows legs and jump out..... waiting.............waiting.....yawn....waiting....

You're waiting.... waiting...... waiting..... for something that has nothing to do with the theory you want to disprove.

So the punchline of this post is, "You used a post of someone else which you stated explicitly before doing."

Captain obvious to the rescue there. You want to address what was said now? It basically single handedly shows the fallacy of the main assumption in the article.

man thats sad all your hopes, dreams and beliefs and faith in a test tube... now thats exciting.... :
as I said before nothing new here..... same old, gee we finally proved we don't need God.. isn't that what its all about for you anyway....because we now have that hard evidence to get rid of God once and for all.......NOT.... 8-)

 

[jmm9683]

Well I've read your post over a couple of times just to see if I missed something important....and seeing how you are using what others say to help back your theory....
Without just reposting or digging up more to disprove your hope and dreams to your god Darwin and his dying child "evolution". Freeway01 will be sitting watching and waiting for this petri tube specimen to grows legs and jump out..... waiting.............waiting.....yawn....waiting....

You're waiting.... waiting...... waiting..... for something that has nothing to do with the theory you want to disprove.

So the punchline of this post is, "You used a post of someone else which you stated explicitly before doing."

Captain obvious to the rescue there. You want to address what was said now? It basically single handedly shows the fallacy of the main assumption in the article.

man thats sad all your hopes, dreams and beliefs and faith in a test tube... now thats exciting.... :
as I said before nothing new here..... same old, gee we finally proved we don't need God.. isn't that what its all about for you anyway....because we now have that hard evidence to get rid of God once and for all.......NOT.... 8-)

The point of biology isn't to disprove religion, no matter how much you want to misconstrue it like that.

 

[freeway]

yea but truth be known,,, isn't that what you and the rest of the religion of evolution group want... to finally disprove the existence to God... Jesus... sorry not going to happen in your life time partner... 8-) 8-) 8-)

 

[jmm9683]

yea but truth be known,,, isn't that what you and the rest of the religion of evolution group want... to finally disprove the existence to God... Jesus... sorry not going to happen in your life time partner... 8-) 8-) 8-)

Not really, you can't prove a negative. I'd like someone to prove there is one though, not gonna happen in your life time partner.

 

[Jayls5]

Well I've read your post over a couple of times just to see if I missed something important....and seeing how you are using what others say to help back your theory....
Without just reposting or digging up more to disprove your hope and dreams to your god Darwin and his dying child "evolution". Freeway01 will be sitting watching and waiting for this petri tube specimen to grows legs and jump out..... waiting.............waiting.....yawn....waiting....

You're waiting.... waiting...... waiting..... for something that has nothing to do with the theory you want to disprove.

So the punchline of this post is, "You used a post of someone else which you stated explicitly before doing."

Captain obvious to the rescue there. You want to address what was said now? It basically single handedly shows the fallacy of the main assumption in the article.

man thats sad all your hopes, dreams and beliefs and faith in a test tube... now thats exciting.... :
as I said before nothing new here..... same old, gee we finally proved we don't need God.. isn't that what its all about for you anyway....because we now have that hard evidence to get rid of God once and for all.......NOT.... 8-)

I see words, but I don't see much argument here. Try again?

 

[Barbarian]

yea but truth be known,,, isn't that what you and the rest of the religion of evolution group want...

The "religion of evolution" group are entirely creationists, who are either dumb enough to think there is such a thing, or hope other people are dumb enough to believe it.

Some of the greatest scientists in evolution, such as Francisco Ayala, Francis Collins, and Theodosious Dobzhansky are devout Christians. Even Darwin, in The Origin of Species, attributed the origin of life to God.

And even Dawkins openly admits that science can't disprove God. That's not what it's for. As usual, the enemy for you is ignorance, not science.

 

[freeway]

yea but truth be known,,, isn't that what you and the rest of the religion of evolution group want...

The "religion of evolution" group are entirely creationists, who are either dumb enough to think there is such a thing, or hope other people are dumb enough to believe it.

Some of the greatest scientists in evolution, such as Francisco Ayala, Francis Collins, and Theodosious Dobzhansky are devout Christians. Even Darwin, in The Origin of Species, attributed the origin of life to God.

And even Dawkins openly admits that science can't disprove God. That's not what it's for. As usual, the enemy for you is ignorance, not science.

you want cheese with that wine..... again evolution is a way to get God out of the picture, pure and simple ... admit you will feel better.... 8-) 8-) 8-)

oh, enough said in this thread.....

 

[Deep Thought]

you want cheese with that wine..... again evolution is a way to get God out of the picture, pure and simple ... admit you will feel better.... 8-) 8-) 8-)

That really is a load of nonsense. Are you saying the millions of Christians (or Muslims for that matter) are trying to get God out of the picture? I think that is quite insulting to those millions of people.

 

[Barbarian]

Yep. He really is saying that. Even though two Christians established modern evolutionary theory, even though many of the greatest evolutionary scientists today are Christians, creationists desperately want it to be about disproving God.

What really bothers them is that evolution (and indeed all of creation) shows God to be much greater and more intelligent than they would like Him to be.

Creationism is another futile attempt to whittle Him down to a comfortable size.

 

[VaultZero4Me]

yea but truth be known,,, isn't that what you and the rest of the religion of evolution group want...

The "religion of evolution" group are entirely creationists, who are either dumb enough to think there is such a thing, or hope other people are dumb enough to believe it.

Some of the greatest scientists in evolution, such as Francisco Ayala, Francis Collins, and Theodosious Dobzhansky are devout Christians. Even Darwin, in The Origin of Species, attributed the origin of life to God.

And even Dawkins openly admits that science can't disprove God. That's not what it's for. As usual, the enemy for you is ignorance, not science.

you want cheese with that wine..... again evolution is a way to get God out of the picture, pure and simple ... admit you will feel better.... 8-) 8-) 8-)

oh, enough said in this thread.....

If someone lost faith in religion due to evolution, then they were weak to begin with.

'nough said.

 

[Barbarian]

When I was in graduate school, I saw a lot of it. If you are raised with the idea that creationism is a Christian doctrine, when you learn the truth, you can easily lose your faith. And not just stupid people. Here's the testimony of a geologist:

But eventually, by 1994 I was through with young-earth creationISM. Nothing that young-earth creationists had taught me about geology turned out to be true. I took a poll of my ICR graduate friends who have worked in the oil industry. I asked them one question.

"From your oil industry experience, did any fact that you were taught at ICR, which challenged current geological thinking, turn out in the long run to be true? ,"

That is a very simple question. One man, Steve Robertson, who worked for Shell grew real silent on the phone, sighed and softly said 'No!' A very close friend that I had hired at Arco, after hearing the question, exclaimed, "Wait a minute. There has to be one!" But he could not name one. I can not name one. No one else could either. One man I could not reach, to ask that question, had a crisis of faith about two years after coming into the oil industry. I do not know what his spiritual state is now but he was in bad shape the last time I talked to him.

And being through with creationism, I very nearly became through with Christianity. I was on the very verge of becoming an atheist. During that time, I re-read a book I had reviewed prior to its publication. It was Alan Hayward's Creation/Evolution. Even though I had reviewed it 1984 prior to its publication in 1985, I hadn't been ready for the views he expressed. He presented a wonderful Days of Proclamation view which pulled me back from the edge of atheism.
http://home.entouch.net/dmd/gstory.htm

ID/Creationism is an efficient atheist-maker.

 

[Jayls5]

The main scientist finally wrote a rebuttal to the attack campaign. It was mainly on conservepedia, but it also deals with the article posted here:

Dr. Lenski posted:

Dear Mr. Schlafly:

I tried to be polite, civil and respectful in my reply to your first email, despite its rude tone and uninformed content. Given the continued rudeness of your second email, and the willfully ignorant and slanderous content on your website, my second response will be less polite. I expect you to post my response in its entirety; if not, I will make sure that is made publicly available through other channels.

I offer this lengthy reply because I am an educator as well as a scientist. It is my sincere hope that some readers might learn something from this exchange, even if you do not.

First, it seems that reading might not be your strongest suit given your initial letter, which showed that you had not read our paper, and given subsequent conversations with your followers, in which you wrote that you still had not bothered to read our paper. You wrote: “I did skim Lenski’s paper …†If you have not even read the original paper, how do you have any basis of understanding from which to question, much less criticize, the data that are presented therein?

Second, your capacity to misinterpret and/or misrepresent facts is plain in the third request in your first letter, where you said: “In addition, there is skepticism that 3 new and useful proteins appeared in the colony around generation 20,000.†That statement was followed by a link to a news article from NewScientist that briefly reported on our work. I assumed you had simply misunderstood that article, because there is not even a mention of proteins anywhere in the news article. As I replied, “We make no such claim anywhere in our paper, nor do I think it is correct. Proteins do not ‘appear out of the blue’, in any case.†So where did your confused assertion come from? It appears to have come from one of your earlier discussions, in which an acoltye (Able806, who to his credit at least seems to have attempted to read our paper) wrote:
“I think it might be best to clarify some of Richard's work. He started his E.Coli project in 1988 and has been running the project for 20 years now; his protocols are available to the general public. The New Scientist article is not very technical but the paper at PNAS is. The change was based on one of his colonies developing the ability to absorb citrate, something not found in wild E.Coli. This occurred around 31,500 generations and is based on the development of 3 proteins in the E.Coli genome. What his future work will be is to look at what caused the development of these 3 proteins around generation 20,000 of that particular colony. ...â€Â

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.â€Â

(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 shownâ€Â, 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] needâ€Â. 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.â€Â

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 rld 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.