Yeast experiment demonstrates convergent evolution

_{Denyse O'Leary

September 21, 2014

Convergent evolution, News}

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In his fourth-floor lab at Harvard University, Michael Desai has created hundreds of identical worlds in order to watch evolution at work. Each of his meticulously controlled environments is home to a separate strain of baker’s yeast. Every 12 hours, Desai’s robot assistants pluck out the fastest-growing yeast in each world — selecting the fittest to live on — and discard the rest. Desai then monitors the strains as they evolve over the course of 500 generations. His experiment, which other scientists say is unprecedented in scale, seeks to gain insight into a question that has long bedeviled biologists: If we could start the world over again, would life evolve the same way?

Many biologists argue that it would not, that chance mutations early in the evolutionary journey of a species will profoundly influence its fate. “If you replay the tape of life, you might have one initial mutation that takes you in a totally different direction,” Desai said, paraphrasing an idea first put forth by the biologist Stephen Jay Gould in the 1980s.

Desai’s yeast cells call this belief into question. According to results published in Science in June, all of Desai’s yeast varieties arrived at roughly the same evolutionary endpoint (as measured by their ability to grow under specific lab conditions) regardless of which precise genetic path each strain took. It’s as if 100 New York City taxis agreed to take separate highways in a race to the Pacific Ocean, and 50 hours later they all converged at the Santa Monica pier. More.

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Comparing 500 generations of yeast breeding to that of dogs . . . According to a CNN article,
By 14,000 years ago, "dogs had become a consistent component of human settlements and were subject to deliberate burial themselves and were included in human graves," the PLOS One study said.
Assuming selective breeding started around that time and that a new dog generation started after an average of two years, we could estimate around 7,000 generations of canis familiaris. By that measure, 500 generations of yeast is not microevolution, espcially when considering that each dog generation is exposed to more than 700 times the ionizing radiation experienced by the yeast. Just sayin' -QQuerius_{September 22, 2014
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I wholeheartedly agree with Barry. There is not enough information here to evaluate the claim. Claiming this to be an example of anything but microevolution seems a bit premature. Besides, he determined what kind of change would be encouraged - only change that resulted from fast growing yeasts. That eliminated a lot of other options. In nature, this kind of artificial selection does not happen so I question the legitimacy of this experiment. If anything, it shows that evolution needs help!tjguy_{September 22, 2014
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I find all of this interesting:
Scientists don’t know why all genetic roads in yeast seem to arrive at the same endpoint, a question that Desai and others in the field find particularly intriguing. The yeast developed mutations in many different genes, and scientists found no obvious link among them, so it’s unclear how these genes interact in the cell, if they do at all. “Perhaps there is another layer of metabolism that no one has a handle on,” said Vaughn Cooper, a biologist at the University of New Hampshire who was not involved in the study. It’s also not yet clear whether Desai’s carefully controlled results are applicable to more complex organisms or to the chaotic real world, where both the organism and its environment are constantly changing. “In the real world, organisms get good at different things, partitioning the environment,” Travisano said. He predicts that populations within those ecological niches would still be subject to diminishing returns, particularly as they undergo adaptation. But it remains an open question, he said. Nevertheless, there are hints that complex organisms can also quickly evolve to become more alike. A study published in May analyzed groups of genetically distinct fruit flies as they adapted to a new environment. Despite traveling along different evolutionary trajectories, the groups developed similarities in attributes such as fecundity and body size after just 22 generations. “I think many people think about one gene for one trait, a deterministic way of evolution solving problems,” said David Reznick, a biologist at the University of California, Riverside. “This says that’s not true; you can evolve to be better suited to the environment in many ways.”
It is experiments such as this that have made me unwilling to expend time and energy on furthering my understanding of population genetics. As someone surmises, there could be completely different levels of metabolic control and networking that ties an organism together. While I have the floor, let me just add this: In the early sixties they ran an experiment where they used various means to cause the common fly to mutate in every conceivable way. They ran out of different phenotypes that they could develop. The results: (1) the fly was always a fly, (2) the absolute majority of mutations were deleterious. There was only so much they could do to the fly genetically, and only so many disformities it could assume. Evolutionary biologists have been missing the forest for the trees for over a century now. Maybe this "physicist" turned "biologist" will help them catch sight of a larger reality.PaV_{September 22, 2014
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B-A "I’m curious. If at the end of 500 generations the organisms were all still the same species of yeast, in what sense was this “evolution” other than the garden variety “variation within a type” that we see all the time? And if it is that, how are these results different from the finch results (beaks get bigger in bad times; revert to normal in good times)." os·cil·la·tion is a dirty curse word on steroids to an evolutionist .DavidD_{September 21, 2014
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Besides the fact they proved randomness was not driving the changes in the Yeast, I have no reason, especially in the laboratory environment, to believe any functional information, over and above what was already present in wild type yeast, 'evolved'. The laboratory environment, where single celled creatures are 'cuddled', is not nearly as demanding as the wild environment is as far as fitness for single celled creatures is concerned. Michael Behe did a survey of 4 decades worth of laboratory evolution experiments and found 'the great majority of helpful mutations degrade the genome to a greater or lesser extent'.
“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/
Lenski's Long Term Evolution Experiment (LTEE) is fairly good at illustrating what happens to 'cuddled' bacteria in the lab:
Lenski's Long-Term Evolution Experiment: 25 Years and Counting - Michael Behe - November 21, 2013 Excerpt: Twenty-five years later the culture -- a cumulative total of trillions of cells -- has been going for an astounding 58,000 generations and counting. As the article points out, that's equivalent to a million years in the lineage of a large animal such as humans.,,, ,,,its mutation rate has increased some 150-fold. As Lenski's work showed, that's due to a mutation (dubbed mutT) that degrades an enzyme that rids the cell of damaged guanine nucleotides, preventing their misincorporation into DNA. Loss of function of a second enzyme (MutY), which removes mispaired bases from DNA, also increases the mutation rate when it occurs by itself. However, when the two mutations, mutT and mutY, occur together, the mutation rate decreases by half of what it is in the presence of mutT alone -- that is, it is 75-fold greater than the unmutated case. Lenski is an optimistic man, and always accentuates the positive. In the paper on mutT and mutY, the stress is on how the bacterium has improved with the second mutation. Heavily unemphasized is the ominous fact that one loss of function mutation is "improved" by another loss of function mutation -- by degrading a second gene. Anyone who is interested in long-term evolution should see this as a baleful portent for any theory of evolution that relies exclusively on blind, undirected processes. ,,,for proponents of intelligent design the bottom line is that the great majority of even beneficial mutations have turned out to be due to the breaking, degrading, or minor tweaking of pre-existing genes or regulatory regions (Behe 2010). There have been no mutations or series of mutations identified that appear to be on their way to constructing elegant new molecular machinery of the kind that fills every cell. For example, the genes making the bacterial flagellum are consistently turned off by a beneficial mutation (apparently it saves cells energy used in constructing flagella). The suite of genes used to make the sugar ribose is the uniform target of a destructive mutation, which somehow helps the bacterium grow more quickly in the laboratory. Degrading a host of other genes leads to beneficial effects, too.,,, - http://www.evolutionnews.org/2013/11/richard_lenskis079401.html
Dr. Behe comments on a Yeast study, that was touted as proof of evolution, here
More Darwinian Degradation: Much Ado about Yeast - Michael Behe - January 2012 Excerpt: "It seems to me that Richard Lenski, who knows how to get the most publicity out of exceedingly modest laboratory results, has taught his student well. In fact, the results can be regarded as the loss of two pre-existing abilities: 1) the loss of the ability to separate from the mother cell during cell division; and 2) the loss of control of apoptosis. The authors did not analyze the genetic changes that occurred in the cells, but I strongly suspect that if and when they do, they'll discover that functioning genes or regulatory regions were broken or degraded. This would be just one more example of evolution by loss of pre-existing systems, at which we already knew that Darwinian processes excel. The apparently insurmountable problem for Darwinism is to build new systems." http://www.evolutionnews.org/2012/01/more_darwinian055511.html
supplemental notes:
Mutations : when benefits level off - June 2011 - negative epistasis (Lenski's e-coli after 50,000 generations) Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually. http://www2.cnrs.fr/en/1867.htm?theme1=7 Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - May 2013 Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11]. 1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696. 2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19. 3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358. 4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144. 5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47. 6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. 7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117. 8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526. 9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685. 10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079. 11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 Is Antibiotic Resistance evidence for evolution? - video https://www.youtube.com/watch?v=rYaU4moNEBU
bornagain77_{September 21, 2014
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If Michael Desai had increased the background radiation to boost the mutations over time, he might have arrived at something significant. As it is, he merely replicated what humans have been doing to domesticated animals for quote some time. -QQuerius_{September 21, 2014
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It's also a pretty creative definition of "convergent" too, no?drc466_{September 21, 2014
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I'm curious. If at the end of 500 generations the organisms were all still the same species of yeast, in what sense was this "evolution" other than the garden variety "variation within a type" that we see all the time? And if it is that, how are these results different from the finch results (beaks get bigger in bad times; revert to normal in good times).Barry Arrington_{September 21, 2014
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