Living the Scientific Life (Scientist, Interrupted)

Evolution: Random or Directed?

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The common gut bacteria, Escherichia coli, typically known as E. coli.

Image: Dennis Kunkel.

ResearchBlogging.org

Evolution is a random process — or is it? I ask this because we all can name examples of convergent evolution where very different organisms arrived at similar solutions to the challenges they are faced with. One such example is the striking morphological similarities between sharks (marine fishes) and dolphins (marine mammals). Thus, based on observations of convergent evolution, one is tempted to hypothesize that, even if the mutations that underly evolution itself are random, the “end result” of evolution is not. In fact, this is the central premise of an interesting book by Simon Conway Morris, Life’s Solution (Cambridge University Press, 2004), where he postulates that ”the evolutionary routes are many, but the destinations are limited”. This is in direct conflict with the late Stephen Jay Gould’s hypothesis that a far different evolutionary outcome would occur if we could only replay the “tape of life”. So which is it?

Of course, replaying this tape of life is impossible, except when the organisms being studied have a fast enough generation time that we can watch their evolution during our own lifetimes. One scientist, Richard E. Lenski, a professor in the department of Microbiology and Molecular Genetics at Michigan State University, has been conducting this very experiment for the past 20 years. His organism of choice is our own humble gut bacteria, Escherichia coli, which has a generation time of approximately 20 minutes under optimum conditions.

To investigate the repeatability of evolutionary trajectories and outcomes within a population, Lenski set up a long term evolution experiment in 1988 where he obtained twelve founding bacterial lineages from the same clone of E. coli. According to his experimental design, all twlve populations were grown separately from each other under identical conditions for more than 44,000 generations, so far (the experiment is ongoing). At time intervals of 500 generations, samples were collected from each of the twelve lineages and frozen. These samples can later be thawed, revived and grown in culture, providing a glimpse into the evolutionary past for each lineage, revealing a detailed living fossil record of evolutionary changes that occurred in each population, providing researchers with the opportunity to study the contributions from genetic mutation and drift, and of natural selection to evolutionary change.

Part of Lenski’s experimental design was to grow the twelve E coli lineages under poor conditions, where their preferred energy source, glucose, was severely limited. Thus, one of the first characteristics that these bacterial populations evolved was the ability to rapidly metabolize all the available glucose in the culture and then wait patiently for their next daily meal. The culture broth also included a second energy source; citrate. But unlike glucose, which was limited, citrate was present in abundance. At first, the abundance of citrate was unimportant because E coli cannot metabolize this molecule when oxygen is present, and in fact, citrate metabolism (Cit+) is a characteristic that has long been used to differentiate this species from other similar, bacterial species.

Surprisingly, after 31,500 generations had passed, one of the twelve E coli lineages did the impossible: it evolved the capacity to metabolize citrate in the presence of oxygen.

But when exactly, did the citrate metabolic ability first appear? Referring to frozen bacterial stocks for this particular lineage, Lenski’s team discovered that Cit+ variants first appeared after 31,000 generations had passed, but were unable to expand to dominance until a further 2000 generations had passed. This suggests that the Cit+ variants needed to accumulate several more mutations that enhanced their metabolic efficiency so they could out-compete their Cit- relatives.

The long period of time that elapsed before Cit+ appeared within one — and only one — population suggested one of two evolutionary possibilities; either the Cit+ mutational event was especially unusual or the evolution of this particular character is contingent upon a complex series of earlier mutations, at least some of which were not uniquely advantageous to the organisms possessing them. This second, more complex form of evolution is known as contingent adaptation.

To clarify the evolutionary events that underlie the appearance of citrate metabolism, the researchers asked if Cit+ would always arise among descendants from the evolutionary ancestors wihtin this one lineage. In short, would the Cit+ variant always appear in this lineage if the “tape of life” could be replayed? When the researchers replayed the “tape of life” for this lineage by reviving older bacterial stocks and growing them again, they found that Cit+ never appeared in populations grown from samples that were frozen before 20,000 generations had passed, that citrate metabolizers were “extremely rare” in populations grown from samples frozen afterwards up until 27,000 generations had passed, and after that point, citrate metabolizers then were only “rare”. Based on all these data, Lenski’s team concluded that evolution is a process of historical contingencies so that, if one can replay the “tape of life,” the evolutionary trajectory would yield different outcomes.

But what traits had to change before Cit+ arose? To identify the specific mutations that gave rise to Cit+ variants, the team is currently sequencing the entire genome of this bacterial lineage, using samples that were frozen before and after Cit+ appeared. Conveniently, an ecological balance formed in this lineage; even though a large majority of the community consisted of Cit+ specialists, a minority of the bacteria in the population remained Cit- generalists. This fortuitous development allows Lenski’s team to identify specific mutations that contribute to Cit+ by comparing genomic sequence data from Cit- clones to Cit+ after citrate metabolism appeared in the population.

Further, because there are now two subpopulations in this lineage, this experiment presents the unique opportunity for scientists to study population dynamics that govern the emergence of a new character and to understand how one phenotype affects the other under a variety of environmental conditions.

As a result of this experiment, Lenski’s team hypothesizes that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.

Source

Blount, Z.D., Borland, C.Z., Lenski, R.E. (2008). Inaugural Article: Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proceedings of the National Academy of Sciences, 105(23), 7899-7906. DOI: 10.1073/pnas.0803151105

Comments

  1. #1 Bill Dearmore
    June 13, 2008

    I very much enjoyed this article about a fascinating experiment, and I hope to read a lot more like it here. I just have one quibble.

    I believe your original question, “Evolution: Random or Directed?” is misleading. Evolution is seldom if ever random. It is probably always directed.

    Mutations are random, but natural selection is probably aways present to some extent; and it is never random. Natural selection is always directional, in the sense that only the “fittest” are selected. Whether or not it is also directional in any other sense is doubtful, but it’ll be very interesting to see additional results of this experiment.

    Keep up the good reporting.

  2. #2 Drew Wheelan
    June 14, 2008

    Great article!!

  3. #3 biosparite
    June 14, 2008

    G/S,
    Extremely well-written; intelligent and crystal-clear.

  4. #4 "GrrlScientist"
    June 14, 2008

    thank you bill for the clarification. of course, i meant “mutations are random” and evolution acts on those mutations to select for those that provide the organism with the “best fit” for the niche they are living in, but i should have said that!

  5. #5 melior
    June 16, 2008

    One hint that the fitness landscape often has areas with steep plateaus comes from descriptions of the way “invader species” sometimes rapidly assume competitive dominance over well-established native species. If all slopes were gentle one would expect these natives to have already reached the same level as the invaders long ago.

  6. #6 jamirokaki
    June 19, 2008

    very interesting article and experiment, thank you.

    @Bill Dearmore: i think that “best fit” idea is a wrong interpretation of the Darwinism or Neodarwinism.
    In the case of this experiment, all the samples had the same propierties and some where changed to see bacterie’s response, and in fact, the ones who had the aleatory character capable of metabolicing citrate in the presence of oxygen, where the “fittest” for that rule, but we must understand that in natural conditions any habitat, and even more any microhabitat is constantly changing, so the possible “fitest bacteries” could be for lots and lots of diferent elements and conditions, and not to any particular direction.
    i hope i explained myself alright.
    something like that happens with the convergence of some marine mammals and sharks mentioned in the article (and some extinct reptils!) in the case of morphology the most pressuring element in the water is the hidrodinamical shape, so animals wich have in common design could turn into similar outfit, but anyway there are and been million of other diferent ways and forms to fit the navigation in the sea (even in the same scala of this animals we are talking.

  7. #7 genesgalore
    July 27, 2008

    what a silly question. it’s both as are all nature-nuture queries. you can’t one without the other.

  8. #8 brtkrbzhnv
    August 3, 2008

    the evolutionary routes are many, but the destinations are limited

    idk to me the idea that there are “destinations”, which are somehow distinct from “routes”, seems rather strange and quite questionable. If a niche is good enough to be part of a route, it should be good enough to be a destination.

  9. #9 sue
    August 14, 2008

    thank you for making this research accessible to those of us who are educated lay persons. You made the issues, the design of the experiement, and the findings easy to understand.

  10. #10 Shannan Mortimer
    August 14, 2008

    Very well written science writing.
    @ brkrbzhnv
    Regarding the analogy of destinations and routes. That they are different seems perfectly clear to me, it is the term ‘niche’ that is muddies their distinction to mix the metaphor. Organisms from different lineages converge on common morphological solutions again and again. routes are ancestry. The idea of destinations has been also explored in the idea of ‘attractors’.

    Perhaps what is confusing is that destinations are not necessarily final (terminal)from the lineages point of view and that the attractor exists independent of the lineage that stumbles into it.

  11. #11 "GrrlScientist"
    August 14, 2008

    thanks for reading! and yes, i was using “destinations” metaphorically since really, evolution is really a journey with no end (except for those species that become extinct).

  12. #12 genesgalore
    September 5, 2008

    form follows function and function follows form. form will function when the function can form. ;)

  13. #13 Rob W
    October 10, 2008

    I looked askance at the question at first as well… partly because just yesterday I was watching a brief discussion between Richard Dawkins and Ted Haggard (evangelical extraordinaire, now somewhat reduced) where Haggard was saying “now, evolutionists say that the eye, and all these complex things just happened at random, and some people have a hard time believing that” (I’m paraphrasing), and of course Dawkins was incensed; “no actual scientist says that evolution itself is random — it’s extremely directed (reproduce or disappear), through the very simple mechanism of natural selection” (again very much paraphrasing).

    So I’d say maybe even tweak the title… just because there are IDers who are sneaky enough to use your post as an example of “even more proof that real scientists are wondering how evolution can work” or whatever nonsense they want to tag onto it. I suppose I’m paranoid, but you see enough dirty tricks and you start to see them everywhere….

  14. #14 Monado
    November 6, 2008

    Variation is random but selection depends on the conditions – from both the external environment and competition from fellow organisms.

    Think of a sieve. Suppose you have a mixture of dry sand with dried peas and you want to eat the peas without sand. You can pick out the individual peas, which is slow and effortful. Or you can dump the whole lot into a colander and shake it. The motions of the peas and sand grains are effectively random. You can’t predict which sand grain will strike the sieve where or whether it will strike a hole or a solid part. But after a minute, the sand has fallen through and the peas remain.

    The motions of the peas and sand are random variation; the colander is the environment.

    I do this to separate bite-sized bits from chaff when I get to the bottom of a box of cereal.

  15. #15 Dov Henis
    December 30, 2008

    Evolution is biased at genes replication routes, at their alternative-splicing-steps junctions

    A. A reply to one of my posts:

    “Dov, you write: Life’s evolution is not random. It is biased, driven by culture.

    Be sure you understand that Darwin did not say that evolution is random. He said that evolution is not random. It is driven by natural selection.”

    B. I never wrote anything that Darwin said. Here, again, is what I say and wrote:

    Culture is the universal driver of genetic evolution

    The major course of natural selection is not via random mutations followed by survival, but via interdependent, interactive and interenhencing selection of biased genes replication routes at their alternative-splicing-steps junctions, effected by the cultural feedback of the third stratum multicells organism or monocells community to their second and prime strata genome-genes organisms.”

    Dov Henis
    (Comments From The 22nd Century)
    http://blog.360.yahoo.com/blog-P81pQcU1dLBbHgtjQjxG_Q–?cq=1

    Life’s Manifest
    http://www.the-scientist.com/community/posts/list/112.page#578

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