- I hope I have read this right, apparently with inside information, our host seems to describe the experiment as just an exercise in breeding bugs that are better at eating glucose, and they are.

That is a gross oversimplification of the experiment, and completely misses the point. The point of the experiment was to demonstrate whether evolution is constrained to a single path. By tracking the evolution of 12 genetically identical clones* in separate but identical environments, they were able to test that question. The ability to metabolize citrate represents a spectacular confirmation that evolution can take multiple paths, but it is not the only result that confirms this.

*except for a marker demonstrated to be neutral in the experimental environment

- It does seem hard to say that no other bug got in from outside the experiment and transferred some useful gene for swallowing citrate to the lab bug population – but apparently it is a combination that has never been found in the great laboratory, the natural world. Having said that, it may be a combination that is not advantageous in the natural world, only in this strange domain of glucose and citrate.

They tested in a great many ways to make sure that nothing got in to contaminate it. While it is not an absolute certainty (no conclusion in science is), they can make that claim with greater confidence than a DNA “fingerprinting” lab could claim that your mother is in fact your mother.

- I hope I have read this right, apparently with inside information, our host seems to describe the experiment as just an exercise in breeding bugs that are better at eating glucose, and they are. That some of them now eat citrate came as a surprise. Better hope they don’t learn to eat glass, or they’ll break out and escape from the lab, leading to catastrophe for spectacle wearers everywhere and the collapse of civilisation (Notice how many leading world politicians wear spectacles…)

- It does seem hard to say that no other bug got in from outside the experiment and transferred some useful gene for swallowing citrate to the lab bug population – but apparently it is a combination that has never been found in the great laboratory, the natural world. Having said that, it may be a combination that is not advantageous in the natural world, only in this strange domain of glucose and citrate.

- Another point about the natural world is that E. coli apparently has been evolving there for way longer than in -this- laboratory. (Although in this laboratory it has surely mutated every single gene it has.) So a mutation that improved glucose digestion -without- impairing uptake of other materials surely would have appeared -already- in the natural world, and would have beat out the rest. So that hypothetical mutation is already present in the initial sample after all. (Unless it’s a very unlikely mutation even on the historic scale – and then it won’t happen in your lab, either.) It only remains for the laboratory bugs to find ways to use glucose better while sacrificing other processes that are important to their cousins outdoors. For instance, if the metaphor applies of the microbe having slots in its skin to take in particular shaped molecules, like a child’s block toy, then one improvement is to have more glucose-shaped slots instead of some of the other shape slots – sacrificing (partially?) the ability to use those other molecules.

The key concept is that the bacteria changed from not being able to eat citrate to being able to eat citrate. No one, not even Larry, doubts this.

If this can happen in the lab with or without a bit of prodding from the experimenters then it can certainly happen outside of the lab.

Whether your world view can grow to encompass this new FACT is an entirely different story. Shooting the messenger doesn’t help.

“He could clarify his statements by saying that Cit+ evolution was one of several goals or was a longshot goal or a secondary goal or was never considered or whatever.”

Did you miss it?

“or was never considered”

He did say it was never considered, when he said that Cit+ was not a goal. So, he did clarify his statement, and your comment is both stupid and meaningless. He is not being evasive, you are being willfully ignorant.

Even if you had done such a thing (you didn’t, but you’re close: you’ve proven that YOU are a jerk), it wouldn’t discredit the paper.

Shut the f*** up.

Shut the f*** up yourself, you lousy sack of %$*&^@. Nothing that the paper says can change the fact that Zachary is posting bullshit on this blog and won’t answer some simple, basic questions.

He could clarify his statements by saying that Cit+ evolution was one of several goals or was a longshot goal or a secondary goal or was never considered or whatever. What if there is another discussion and he only says that Cit+ evolution was never a goal — the statement could mislead people. And he never answered my question of whether favoring Cit+ evolution was a purpose of the glucose cycling. Andy Schlafly at Conservapedia is wasting his time in his futile effort to discredit the paper by asking for all of the raw data — I have discredited the paper right here by showing that one of the principal investigators is an evasive jerk.

Zachary has stated clearly that citrate was included as a chelating agent to assist in iron utilization. He has stated clearly that glucose cycling was included to create selection pressure for any possible mutations favoring reproduction in a carbon-limited environment. He has stated clearly that there was discussion of whether the coli would evolve an ability to utilize that energy-rich citrate – its an obvious thing to wonder about – but that it was not a goal.

Larry keeps whining that Zachary wont take hieriment was. Larry, the world does not revolve around you. Papers are pubished because a LOT of people are interested, and there isnt time in the universe to take every vain, self-glorified, uninformed idiot on the internet and carefully explain to them what they refuse to learn for themselves. There is an expectation that interested people will take the time to educate themselves, so as not to waste the time of the person who did the hard work of carrying out the experiment and COMMUNICATING IT TO THE WORLD BY PUBLISHING IT!!!!

Whining that Zachary wont communicate with you, while you continue to refuse to take advantage of the most fundamental ways in which he has communicated his work to EVERYONE, is simply self-absorbed, intellectually-lazy, time-wasting, conversation-deadening, narcissistic special pleading of the very worst sort. Shut the f*** up.

He won’t read, he can’t think, he doesn’t understand. He blames his huge inadequacies on everybody else. Does he have any positive qualities? Couldn’t evolution come up with something closer to intelligent life? Couldn’t God have created something that was less a waste of space?

Now, can we have som LOLlarries?

Andy Schlafly of Conservapedia has even gone so far as to request the raw data of the experiment.
Read the Pharyngula post, and the comments on it, to learn how stupid this is.

I agree that it is stupid. So?

David Marjanović said (#306) –

Oopsie. Some of the triple blockquotes in my last post didn’t work. But I think it’s pretty obvious who wrote what.

No, it is not obvious who said what, and the problem of determining who said what is not just with the triple blockquotes.

David Marjanović said (#305) –

I said that the glucose cycling tends to reduce silent mutations because the bacteria that can eat only glucose cannot reproduce after the glucose supply is exhausted, and errors in gene duplication during reproduction are a major source of mutations.
Why would that reduce silent mutations?

The statement you quoted answers your question — silent mutations tend to be reduced because errors in gene duplication during reproduction are a major source of mutations, and Cit- bacteria cannot reproduce when there is no glucose to feed on.

Here’s the quote again (from comment #155)
In 1988, Richard Lenski, Michigan State University, East Lansing, founded 12 cultures of E. coli and grew them in a laboratory, generation after generation, for twenty years (he deserves some marks for persistence!). The culture medium had a little glucose but lots more citrate, so once the microbes consumed the glucose, they would continue to grow only if they could evolve some way of using citrate. Lenski expected to see evolution in action. — from
http://creationontheweb.com/content/view/5827
This sounds like the bacteria were expected to eat the citrate. They weren’t. More importantly, it sounds like this was the whole point of the experiment. This is completely wrong. I’m really surprised you still haven’t noticed this.

I never said that Cit+ evolution was the whole point of the experiment. I quoted the above article just to show that others have the same impressions that I had — that Cit+ evolution was a goal of the experiment and that a purpose of the glucose cycling was to favor Cit+ evolution.

Dave Godfrey said (#307) –

I certainly don’t agree with you Larry. . . .I quoted Zachary’s first comment to show the only point that he seemed to be unsure about, (whether Cit+ was postulated at the start) and then his subsequent comment where he corrects himself (yes, but its so rare that it really wasn’t expected).

As I said, rarity or unexpectedness has nothing to do with whether or not it was a “goal.” In searches for the Lost Dutchman Mine or the ivory-billed woodpecker, finding them are “goals.”

Now can we please move on?

You can move on — I am not going to. I am not going to give up so easily after all of the time I have spent pursuing this issue. I showed that according to a standard dictionary’s definition of “goal,” Zachary made confusing, ambiguous, and inconsistent statements about whether Cit+ evolution was a “goal” of the experiment. He failed to clarify those statements. The problem is not just with this comment thread — in other discussions, he could mislead people by just saying that Cit+ evolution was never a goal. He also failed to answer my question of whether a purpose of the glucose cycling was to favor Cit+ evolution.

I would also like to point out that I gave people information for publications (#145 and #147 on Dr. Lenski’s website) that describe the goals of the experiment so that my word wouldn’t have to be taken on the matter.

Zachary

Now can we please move on?

David Marjanović said (comment #233) –

yet you think it is OK to just refer me to a long paper in answering my simple, specific questions.

Yes, it is in fact OK.

It is sometimes OK. It was not OK here.

Telling you to read the paper is always OK, because you are expected to do that anyway. Read the paper, and if you have any questions left then, then come back.

You folks have a double standard. You expect me to give direct answers to your questions but think that bibliography-bluffing is OK in responding to my questions.

Again, why should we bother? You must read the paper anyway.

“Just”? That requires a transporter protein. Why do you think that must be easy to evolve?

It is comparatively easy to evolve.

Why do you think so?

and now you are questioning whether that evolution is “desirable.”

It was not expected to happen. It was a surprise.

But if it was foreseen as a possible and desirable event, then it was a goal. If it was a goal but a long-shot goal, then it should be called a long-shot goal. Anyway, I proposed that we stop using the word “goal” here because you folks don’t understand the word’s meaning.

You are using it the wrong way. If it was foreseen as a possible and desirable event, then it was a possible and desirable outcome. Had Cit+ not evolved and the experiment therefore been considered a failure, then the evolution of Cit+ would have been a goal. When a goal is not attained, that’s a failure. If Cit+ had not evolved, that would not have been a failure; the goal was to watch natural selection in action, and that was reached.

But I have to repeat Tulse and many others: What does it matter if Cit+ evolution was a goal or not? The bacteria aren’t psychics, they didn’t care about the wishes of the experimenters.

No. The purpose was for glucose to be the limiting factor, so that higher efficiency of glucose metabolism would be selected for.

Selection for higher efficiency of glucose metabolism would occur without limiting the glucose supply.

No, why? A truly unlimited supply would not lead to such selection. Selection occurs for the growth-limiting factor.

I assert that it appears that the purpose or one of the purposes of giving an insufficient supply of glucose was to try to promote evolution of citrate-eating bacteria.

It wasn’t, but even if it was*, so what?

* That would be like putting your family underwater for a few hundred millennia and waiting for gills to grow.

How many times do I have to repeat myself? I said that the glucose cycling tends to reduce silent mutations because the bacteria that can eat only glucose cannot reproduce after the glucose supply is exhausted, and errors in gene duplication during reproduction are a major source of mutations. Suppose, for example, instead of starting new populations every day, the populations were kept for a year and were still given just a few hours of glucose supply. That would make it quite obvious that the glucose cycling tends to reduce silent mutations in the bacteria that can eat only glucose.

Why would that reduce silent mutations? It wouldn’t, because silent mutations are by definition silent, which means they are neutral — they don’t have any effect on the phenotype and therefore are neither beneficial nor detrimental, which means natural selection is completely blind to them. They absolutely don’t matter.

You linked to it in comment 155 and quoted it.
So how does the article misinterpret the experiment?

Here’s the quote again:

In 1988, Richard Lenski, Michigan State University, East Lansing, founded 12 cultures of E. coli and grew them in a laboratory, generation after generation, for twenty years (he deserves some marks for persistence!). The culture medium had a little glucose but lots more citrate, so once the microbes consumed the glucose, they would continue to grow only if they could evolve some way of using citrate. Lenski expected to see evolution in action.

This sounds like the bacteria were expected to eat the citrate. They weren’t. More importantly, it sounds like this was the whole point of the experiment. This is completely wrong. I’m really surprised you still haven’t noticed this.

The rest of your comment (#233) is a response to another commenter.

That’s why it’s separated by a line of ———.

You ought to identify who you are responding to so that people won’t think that you are responding to me (especially when your comment starts with responses to me). It is especiall annoying that some people may think that I made statements that another commenter made.

I am a scientist. I don’t respond to people, I respond to questions, statements, hypotheses. I respond to what people say. Who says it doesn’t matter; it has no effect on the credibility of what is said, for example.

Anyway, as I said, IMO we should stop using the term “goal” here because you folks can’t understand its meaning.

And it has never occurred to you that if 15 people agree with each other and disagree with you that perhaps you are the one who’s wrong?

Andy Schlafly of Conservapedia has even gone so far as to request the raw data of the experiment.

Read the Pharyngula post, and the comments on it, to learn how stupid this is.

Why do I have to wade through a lot of stuff unrelated to my questions?

It isn’t unrelated. It is necessary background — necessary for you to understand your own questions and the answers to them.