Behe’s “Multiple mutations needed for E. coli”
| June 9, 2008 | Posted by Patrick under Biology, Darwinism, Evolution, Intelligent Design, Irreducible Complexity, Science |
Multiple mutations needed for E. coli
An interesting paper has just appeared in the Proceedings of the National Academy of Sciences, “Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli”. (1) It is the “inaugural article” of Richard Lenski, who was recently elected to the National Academy. Lenski, of course, is well known for conducting the longest, most detailed “lab evolution” experiment in history, growing the bacterium E. coli continuously for about twenty years in his Michigan State lab. For the fast-growing bug, that’s over 40,000 generations!
I discuss Lenski’s fascinating work in Chapter 7 of The Edge of Evolution, pointing out that all of the beneficial mutations identified from the studies so far seem to have been degradative ones, where functioning genes are knocked out or rendered less active. So random mutation much more easily breaks genes than builds them, even when it helps an organism to survive. That’s a very important point. A process which breaks genes so easily is not one that is going to build up complex coherent molecular systems of many proteins, which fill the cell.
In his new paper Lenski reports that, after 30,000 generations, one of his lines of cells has developed the ability to utilize citrate as a food source in the presence of oxygen. (E. coli in the wild can’t do that.) Now, wild E. coli already has a number of enzymes that normally use citrate and can digest it (it’s not some exotic chemical the bacterium has never seen before). However, 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. As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1)
Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.)
The major point Lenski emphasizes in the paper is the historical contingency of the new ability. It took trillions of cells and 30,000 generations to develop it, and only one of a dozen lines of cells did so. What’s more, Lenski carefully went back to cells from the same line he had frozen away after evolving for fewer generations and showed that, for the most part, only cells that had evolved at least 20,000 generations could give rise to the citrate-using mutation. From this he deduced that a previous, lucky mutation had arisen in the one line, a mutation which was needed before a second mutation could give rise to the new ability. The other lines of cells hadn’t acquired the first, necessary, lucky, “potentiating” (1) mutation, so they couldn’t go on to develop the second mutation that allows citrate use. Lenski argues this supports the view of the late Steven Jay Gould that evolution is quirky and full of contingency. Chance mutations can push the path of evolution one way or another, and if the “tape of life” on earth were re-wound, it’s very likely evolution would take a completely different path than it has.
I think the results fit a lot more easily into the viewpoint of The Edge of Evolution. One of the major points of the book was that if only one mutation is needed to confer some ability, then Darwinian evolution has little problem finding it. But if more than one is needed, the probability of getting all the right ones grows exponentially worse. “If two mutations have to occur before there is a net beneficial effect — if an intermediate state is harmful, or less fit than the starting state — then there is already a big evolutionary problem.” (4) And what if more than two are needed? The task quickly gets out of reach of random mutation.
To get a feel for the clumsy ineffectiveness of random mutation and selection, consider that the workers in Lenski’s lab had routinely been growing E. coli all these years in a soup that contained a small amount of the sugar glucose (which they digest easily), plus about ten times as much citrate. Like so many cellular versions of Tantalus, for tens of thousands of generations trillions of cells were bathed in a solution with an abundance of food — citrate — that was just beyond their reach, outside the cell. Instead of using the unreachable food, however, the cells were condemned to starve after metabolizing the tiny bit of glucose in the medium — until an improbable series of mutations apparently occurred. As Lenski and co-workers observe: (1)
“Such a low rate suggests that the final mutation to Cit+ is not a point mutation but instead involves some rarer class of mutation or perhaps multiple mutations. The possibility of multiple mutations is especially relevant, given our evidence that the emergence of Cit+ colonies on MC plates involved events both during the growth of cultures before plating and during prolonged incubation on the plates.”
In The Edge of Evolution I had argued that the extreme rarity of the development of chloroquine resistance in malaria was likely the result of the need for several mutations to occur before the trait appeared. Even though the evolutionary literature contains discussions of multiple mutations (5), Darwinian reviewers drew back in horror, acted as if I had blasphemed, and argued desperately that a series of single beneficial mutations certainly could do the trick. Now here we have Richard Lenski affirming that the evolution of some pretty simple cellular features likely requires multiple mutations.
If the development of many of the features of the cell required multiple mutations during the course of evolution, then the cell is beyond Darwinian explanation. I show in The Edge of Evolution that it is very reasonable to conclude they did.
References
1. Blount, Z.D., Borland, C.Z., and Lenski, R.E. 2008. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc. Natl. Acad. Sci. U. S. A 105:7899-7906.
2. Hall, B.G. 1982. Chromosomal mutation for citrate utilization by Escherichia coli K-12. J. Bacteriol. 151:269-273.
3. Pos, K.M., Dimroth, P., and Bott, M. 1998. The Escherichia coli citrate carrier CitT: a member of a novel eubacterial transporter family related to the 2-oxoglutarate/malate translocator from spinach chloroplasts. J. Bacteriol. 180:4160-4165.
4. Behe, M.J. 2007. The Edge of Evolution: the search for the limits of Darwinism. Free Press: New York, p. 106.
5. Orr, H.A. 2003. A minimum on the mean number of steps taken in adaptive walks. J. Theor. Biol. 220:241-247.
97 Responses to Behe’s “Multiple mutations needed for E. coli”
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one other comment-
‘no change’ could also mean changes in a “don’t care” region of a word containing an instruction. There are often “don’t care” regions to optimize logic if I’m not mistaken.
So IOW, it should be clearly evident why average SAT scores, the catfish populations in manmade lakes, and the popularity of eastern european folk music are all determined by the exact same fundamental force.
Here is my scenario of what happened:
A mutation occurred at around 20,000 generations and the citrate-eating ability appeared when one of the bacteria bearing that mutation had a different mutation at around 31,500 generations. IMO the first mutation was very unusual or rare because (1) it apparently took about nine years to occur (44,000 generations in 20 years is about 2200 generations per year) and (2) it apparently appeared in only one of twelve lines of bacteria, even though all twelve lines were descended from a single individual. I think that the second mutation is a fairly common one because it was often expressed again in populations started by the unfrozen preserved populations of 20,000 generations or later, and the reason why this second mutation took so long to be expressed the first time — about 11,500 generations (from the 20,000th to the 31,500th) or 5 years — was that bacteria with the preliminary first mutation were scarce because the preliminary first mutation conferred no advantage in survival. After the preliminary first mutation occurs, appearance of the citrate-eating ability would be just a matter of time if the second mutation were a common one.
Also, I am disturbed by numerous claims that the results of this study refute the ideas of Michael Behe — IMO that is not the case.
http://creationontheweb.com/content/view/5827
Just found this thread. Only read the first few of the comments and then searched for these keywords:
- conjugation
- horizontal gene transfer
- gene duplication
- nondisjunction
- polyploidy
And couldn’t find a single comment with these readily observable genetic phenomena, all of which increase the amount of DNA in an organism and most of which are survived just fine.
I really can’t assume there are IDers out there who seriously propose that some magic man added some chromosomes so that the king crab gets 208 then takes away some so the fruit fly only gets 8 and then again adds some such that humans get 48 and then adds some more so the camel gets 60? What are you guys saying that an increase in DNA hasn’t been seen? Genes/chromosomes duplicate all the time and then acquire mutations which change their information. Come on, that’s genetics 101, not rocket science.
Likewise, what’s “beneficial” or “good”? You mean in the lab or in the wild? Under stress or under perfect conditions? Hot or cold? Island or mainland? Freshwater or saltwater? In yeast, 60% of all knocked-out genes do not show any effect in the lab, in mice it’s still 30% of genes. In the genome age we know that many if not most gene knock-outs (depending on the organism) have comparatively small, incremental effects, many of which are buffered out. It’s called degeneracy (no, not redundancy and not the degeneracy of today’s youth, but degenerate as in the degenerate code). So instead of inventing nonsensical nomenclature for mutations, IDers should try to explain degeneracy: if there are intelligent designers out there changing things around in the DNA every once and a while, why is there degeneracy? That would be so totally unnecessary and impractical. The only reason I can see to put degeneracy in the genetic system would be to trick someone to believe the system actually evolved, but I’m sure you can come up with better reasons why degeneracy was chosen by the intelligent designer.
Evolution predicts degeneracy. How does ID predict degeneracy?
Oh and I forgot one other thing: species. What do IDers mean by species? Scientists can’t really agree on what a species is, can IDers?
One common, but by no means uncontested species definition refers to reproductive isolation. According to this definition, speciation has been observed a few times, even in animals (Drosophila comes to mind), but also in plants (grass species on islands). Mind you that certain breeds of dogs would classify as species in this sense, as they would not be able to reproduce with each other naturally (Mastiff and Chihuahua for example), which is exactly why it is contended.
Another regards the fertility/survival of hybrid offspring. However, a mule is a largely sterile hybrid, so according to this definition evolution resulting in horses and donkeys would be absolutely impossible for IDers, even thought they’re so similar.
So maybe species is something that somehow looks different from another? There are many species that nobody denies are very different species (even different orders!) but look very similar, to the extent that even specialists can’t tell them apart easily. So that makes no sense either. What to do?
I have a very practical solution: species in the sense of the biblical “kinds”! IDers could use it to refer to higher up clades such as: kingdom, phylum, class, order, or family?
I suggest IDers use some of the latter to mean species (kinds). This would be very practical, because then they can always retreat to the next higher level when one level has been shown experimentally
“No, no, it’s really kind/family/order/class/etc. what I meant with ‘species’, really!”
Based upon his comments brembs must be new to this debate. His statements about what ID proponents believe are truly off the wall. And the topic he brings up have been addressed many times over. Go back to lurking, brembs. Read some more and once you have something interesting to say perhaps come back.