Saturday, June 14, 2008

Lenski’s E. Coli Experiments

Bacteria Makes "Major" Evolutionary Shift in Dr. Lenski's Lab, is the headline of a recent New Scientist article. An interesting paper has just appeared in the Proceedings of the National Academy of Sciences, It is the "inaugural article" of Richard Lenski, who was recently elected to the National Academy. Lenski, is well known for conducting the longest, most detailed "lab evolution" experiment, growing the E. coli bacteria continuously for about twenty years in his Michigan State lab. For the fast-growing bug, that's over 40,000 generations! E. coli you may recall is the bacteria that are often cited as the cause for food poisoning in humans. Here is an article in New Scientist that discusses the Lenski experiments: http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html;


 

So does this mean the end for Intelligent Design? If a major evolutionary change can take place described as "the first time evolution has been caught in the act of making such a rare and complex new trait", doesn't this doom any claims that Darwinism is wrong? Well, I don't think this is much of a story for a number of reasons. But let me first describe what the Lenski experiments show, and then I will later explain why this is exactly what was described in Prof. Michael Behe's (pro-ID) 'Edge of Evolution' book.


 

The Lenski experiment is fascinating. He examined trillions of E. coli bacteria cells, over 20 years time, resulting in over 44,000 generations. What he did was set up 12 different groups all descended from the Adam E. coli parent. All of the groups developed along similar lines in the ideal lab: they all evolved larger cells; and all developed faster growth rates on the glucose that they were fed. But one of the 12 test groups developed a unique trait – the ability to metabolize citrate, which was a second nutrient (besides the glucose) in all of the cultures. And when the "evolved" E. coli developed the ability to metabolize citrate, it was a beneficial new trait that allowed this group an advantage over the other 11 groups because of its growth in population size.


 

So was this really a "major" evolutionary shift? Was it the development of a new leg, or a proto-eye? What was the "complex new trait" that the E. coli bacteria developed after 40,000 generations? Yes, this "profound change" meant that it could "metabolize" citrate. The article makes it sound like it is a big deal. But consider that E. coli is normally capable of utilizing citrate as an energy source under anaerobic (without oxygen) conditions, with a whole suite of genes involved in its fermentation. In addition, the Krebs cycle (or citric acid cycle, where chemical reactions create energy for the cell to use) for E. coli already generates and utilizes citrate in its normal metabolism of glucose and other carbohydrates. Now is this really a big deal? It doesn't seem like it's a major new step – instead, it appears to be just the re-tooling of machinery inside the E. coli that is already there. Here is the way Prof. Behe describes it: "the wild bacterium lacks an enzyme called a "citrate permease" which can transport citrate from outside the cell through the cell's membrane into its interior. So all the bacterium needed to do to use citrate was to find a way to get it into the cell. The rest of the machinery for its metabolism was already there."


 

So there you have it – The E. coli's major evolutionary shift is to allow citrate to be transported inside the cell membrane so that it can be used. All of the machinery to use citrate was already inside the cell. Yawn, excuse me while I go to sleep…


 

The real question is why are the Darwinists making such a big deal about this? It's obviously because Prof. Behe's pro-ID book "Edge of Evolution' has drawn blood on the dying, critically wounded Theory of Evolution. Louisiana just this past week passed a bill to teach Darwinism critically (like Texas before it), and this seems like it is a growing trend. And the Darwinists will use anything to try and show that observed major evolutionary changes really do take place. That's all well and good, but we still haven't seen any major changes, and the Lenski E. coli experiments certainly are not Darwinism's savior.


 

Instead, this looks like it is exactly along the lines of what is described in Prof. Behe's 'Edge of Evolution' book, where he describes malaria's resistance to drugs used against it, as well as HIV's evolving resistance. In fact, chapter 7 of EoE Prof. Behe actually describes and uses the Lenski experiments in support of his position. He placed the Edge of Evolution at three successive mutations. And the way it is described in the New Scientist article, this appears to be exactly what took place in the Lenski E. coli experiment – one change took place in one of the 12 groups after 20,000 generations. And the new trait was discovered after 30,000 generations. Although there are no details learned of what genetic changes took place, it sounds like these are successive, single point mutations building upon each other, perhaps up to three mutations working together. Professor Behe's full Response is posted in his Amazon blog, which can be found at: http://www.amazon.com/gp/blog/post/PLNK3U696N278Z93O; Thus, it seems just like the other genetic studies reviewed in Prof. Behe's book – no new major evolutionary changes. Instead, just minor mutations that eventually provide a small benefit.


 

So, those of you who distrust the Darwinist fairy tale description of how life developed on Earth, commonly known as Evolution, you have nothing to fear from what is contained in the Lenski E. coli experiments. And it looks much more supportive of Intelligent Design than it does of Darwinism. Here are a few of the reasons why I say this:


 

  • Trillions of cells evolving over 30,000 generations? Look at the math! For humans to evolve anything during this same period (30,000 generations), would be the equivalent of 600,000 years (30,000 generations averaged over 20 years time, a rough estimate of an adult generation). And the ability to metabolize citrate is all that was developed? Darwinism is not at all an effective explanation for how life developed on Earth. Too little change and not enough time. As one blogger writes – "Presumably, the same mechanism that gave E. Coli citrate capability turned a primitive simian ancestor into Beethoven, with orders of magnitude fewer probabilistic resources." This problem of Darwinism sounds very persuasive to me;
  • It looks like mutations that hurt the cell are much more numerous than any possible benefits. Prof. Behe claims that all of the E. coli mutations in the Lenski study are "degradative" (see Behe link, above), making the cells less active. This makes for the exponentially more difficult problem of Darwinism to make for a beneficial mutation;
  • The straightforward ID prediction is that any experimentally demonstrated change in the genome of E. coli will be limited to two, or at the most 3 separate steps, unless the steps can be demonstrated to be sequentially more fit. That's a scientific prediction, if you will, which would seem to make ID a scientific theory. Where are the Darwinists to show that this prediction is wrong?


 

Keep the faith! Happy birthday to my child no. 3, and to me, Jeanne, and Boy George. Enjoy Father's Day tomorrow, all you fathers out there.

32 comments:

edward oleander said...

"... So all the bacterium needed to do to use citrate was to find a way to get it into the cell. The rest of the machinery for its metabolism was already there."

Typical Behe strategy... trivialize what he cannot refute. 2 points:
1) He makes it sound like it was just some tiny change needed to get the citrate through the cell wall under aerobic (oxic) conditions. If he admits what a fiendishly difficult thing this is, he admits it's a major change, so he trivializes it.
2) Of course "the rest of the machinery" was already there. Let's use a car analogy. A Ford muscle car that has been "tweaked" with some new parts for the engine might go a lot faster, and no longer run on regular gas, but it is still 99.9% the same car. Those tiny changes had big impact. Now make lots of those little changes to the engine, tranny, suspension. The car is still a Ford, and recognizable as such, but if you take into the dealership for service, they can't work on it... it is just different enough to be a new species of Ford.

Now to the points you make at the end...

"For humans to evolve anything during this same period (30,000 generations), would be the equivalent of 600,000 years (30,000 generations averaged over 20 years time, a rough estimate of an adult generation). And the ability to metabolize citrate is all that was developed?"

You're extrapolating the rate of change in this bacteria to that in humans. Hasty generalization. Bad logic. Mutation rates vary widely, making such translations as bacteria generations to human generations irrelevant. This is especially true when trying to compare creatures who use different means of reproduction. Sexual reproduction introduces whole new variables into the game.

You're also band-wagoning Behe by saying "all" the E. coli got was the ability to use a food source that was 10 TIMES more plentiful. How can you say that's "All"??? It gave that strain of bug a huge survival advantage! What more could you ask for? Ridiculing and trivializing info you don't like may serve to discredit a fact, and while that is great for debating and useful in a courtroom, it is emotional based and therefore not useful scientifically.

"It looks like mutations that hurt the cell are much more numerous than any possible benefits. Prof. Behe claims that all of the E. coli mutations in the Lenski study are "degradative" (see Behe link, above), making the cells less active. This makes for the exponentially more difficult problem of Darwinism to make for a beneficial mutation;"

These are two separate points. First of all, it's well known that most mutations are harmful. Very, very, VERY few are beneficial. For a crude analogy, look at war. Thousands of bullets are fired for each soldier killed, yet lots of soldiers die, and whole generations of whole nations can be affected. Bottom line, it doesn't take more than a tiny fraction of mutations to be beneficial. Behe is trying to make a given point seem more important than it is.

Second point from above: Behe is playing semantic word games to try and dazzle and misdirect his audience. He calls the mutations degradative as if that is the central point. He seeks to equate a degradative mutation as unable to affect positive change in thr survivability of a species. BAD Zoot! Naugty Zoot! Wicked, evil, NAUGHTY Zoot! (Sorry - can't help the occasional Monty Python reference). The point here is that you need to look at the RESULT of a mutation, not at what scientifically confusing label is placed on it. The RESULT of the mutation(s) is that the bacteria gained a significant advantage over other E. coli in the same environment.

"The straightforward ID prediction is that any experimentally demonstrated change in the genome of E. coli will be limited to two, or at the most 3 separate steps, unless the steps can be demonstrated to be sequentially more fit. That's a scientific prediction, if you will, which would seem to make ID a scientific theory."

You're using the wrong criteria to judge the science-worthiness of ID/Creationism. ANY theory can make predictions. My Theory of Ed's Brain Power predicts that if I sit at a red light and concentrate on it changing to green, it will happen within one minute. Empirical observation in the field backs this up. WOW! My Theory predicts something you see in real life! I'm a Certified Scientific Genius!

Hmmm... We all know that just ain't right...

But why? The reason is that my theory lacks any testable hypothesis of why it works. ID/Creationism has the same problem. It will never be a scientific theory until it comes up with testable hypothesis of how and why it works.

It all comes back to my previous assertions that a real theory has to advocate FOR something. The "theory" of ID is a vehicle to advocate AGAINST evolution. It seems to be unable to come up any evidence FOR anything. Indirect proofs are interesting and even elegant in certain forms of mathmatics (such as geometry). But in biology? Not so much...

We really should do this in person... There's a very complex Straw Man that the ID crowd uses constantly that is just too involved and tangential for this forum... I like the ClayCon idea...

Pax,
~E~
ps: Having that many birthdays on one day in one family is the best evidence you've come up with so far for the existence of the supernatural...
HAPPY BIRTHDAY TO ALL THREE OF YOU!!!

I won't include Boy George. I don't like him. Unlike you, and yours, who I do. A lot. :-)

edward oleander said...

And yes, I know that's technically two families... I meant our larger "pseudo-extended" family...

Did you know that if you put 23 random people in the same room together there will be a 50% chance of two people having the same birthday? We never figured the odds on THREE people in a given group having the same one...

tom wolff said...

Thanks for the Happy Birthday wishes Ed, and for taking the time to look at the Lenski experiment. I hope you would have the courage to read one of Prof. Behe's books before you use such harsh ad hominem attacks. Generally when I see someone using ad hominem attacks it seems to me that either the person does not understand the topic very well, or is simply losing. I hope you agree with me that ad hominems are the weakest form of argument.

Second, when I showed the bacteria mutation rate was far too low to mutate anything useful in mammals, you said "You're extrapolating the rate of change in this bacteria to that in humans. Hasty generalization. Bad logic."

I think if you take a moment to think about what you said, you may wish to withdraw it. Are you saying that humans / mammals have a HIGHER mutation rate than simple bacteria? Of course this is not true as human DNA has much more error correction mechanisms than does bacteria. And simpler organisms simply mutate more than more complex ones, like human DNA. Thus given this, the numbers I used to show that the E. coli mutation rate were too small to do anything of significance for humans / mammals, and that bacteria mutates much more than human DNA, I conclude that the numbers I used were magnitudes too small. Thanks for helping me to make this point.

Finally, on your comment of my "band-wagoning", in trivializing the mutations that the E. coli underwent in the 20 year Lenski experiment, let me say that the puny changes that were observed do nothing to support Darwinism. Ed, consider the Cambrian Explosion. In a mere 3 million year time period life moved from very simple pancake like creatures to EVERY body plan that's been seen on earth. During this time period eyes came into being; spinal columns; circulatory systems; sexual reproduction, and yes I could go on.

Do you really think that seeing a simple 3 step change in the amino acids of a protein over 40,000 generations for 1 trillion organisms, really shows that something like the Cambrian Explosion could have taken place?

I'm sorry to be so blunt but the Darwinist position fails on far too many levels, for someone as logical as you to support it. Observation in the lab shows mutation rates are too small and slow to do any new thing. The fossil record shows sudden appearance with little change, and then disappearance. And logic is also against Darwinism as well - you expect anyone to believe that we go from inaminate objects (like rocks, minerals and water) to living creatures with brains, capable of producing the works of Beethoven, Michaelangelo, and the Mona Lisa? No, without any sort of evidence Darwinism seems to be a completely empty belief system.

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Konrad Zielinski said...

Not very significant ...
come on, the equivalent would be humans gaining the ability to digest cellulose. After all that's just another way of stringing glucose together, and our cells can already use glucose as fuel, we just need away of breaking it out.

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