Wednesday, December 10, 2008

Exaptation! PT flare up #2

Continuing on with my thoughts about the flare up at Panda's Thumb (part 1 here):

Basically, I think "Green" the anonymous undergrad from a University in the UK, raised a few valid issues that are worth thinking about. A lot of the evolutionists, while I agree with their points on general terms, are not addressing the concern of "Green" directly.

Her main point is (from the comments at Panda's Thumb):

“Co-option may not be the de novo formation of genes, but it still requires mutations (such as, for example, the gain of a cis regulatory region). My whole point was that simultaneous mutations are required for the evolution of the phototransduction cascade. Correct me if I’m wrong, …”

This is in part true, and raises the point that we should be discussing EXAPTATION and not co-option, to most clearly convey the point.

Green is stating that even if all the components of phototransduction are present an ancestral genome that lacks phototransduction, multiple mutations would be required to assemble all those components into a phototransduction cascade. So, multiple co-option events would be required, and this is what she is having a problem with.

HOWEVER, what is false is the requirement for all these mutations to occur simultaneously. Instead, the components could be assembled one by one in a graduated, step-wise (Darwinian) fashion.

Instead of focusing on co-option, Green should focus on "exaptation". Exaptation is the idea (roughly) that features can arise for one function, and then change function later on. In the case of phototransduction, much of the phototransduction cascade originated for another purpose - sensing some signal from outside the cell to elicit changes inside the cell. (And just because a yeast pheromone cascade isn't THE phototransduction precursor, doesn't mean there wasn't one). One response to a signal evolves, changing the signal that is detected (to light) seems pretty surmountable. In fact, this has happened independently in the lineage leading to C. elegans (see my post here).

For another example of exaptation, we've found that many components used in synapses predate synapses themselves. See these posts in pharyngula, Newsweek. The open access paper and other news sites (including radio interview) are here.

6 comments:

T Ryan Gregory said...

I dealt with this fallacy in the paper, although I was discussing organ level components rather than biochemical components. E.g.,

Two important points bear mentioning about the process of indirect evolution through “collage”: (1) the linking of components is not an “all or nothing” process in which two or more already complex structures suddenly are joined—--individual parts, which themselves may variously be simple or relatively complex and functional for something else or nonfunctional, can be added in series, with each new addition leading to a different function for the combined structure and (2) the newly combined structure may carry out its new function rather poorly at first, with subsequent direct adaptation leading to improvement along this novel axis, for example by enhancing the integration of the newly combined components (Fig. 3).

and

Misconception #5 Indirect evolution implies that various preexisting structures are assembled instantaneously into a new organ.

Indirect evolutionary processes such as shifts in function (exaptation) and the combining of existing structures (collage) play important roles in the origin of complex organs. However, this is sometimes misunderstood to imply that all components are (1) already in their final form when assembled together and (2) brought together simultaneously to form a new complex organ. In actuality, the addition of components to an evolving organ may occur in series (i.e., one at a time) and may involve a relatively poor fit at first. Again, the only criteria for such additions to be preserved by natural selection are that they must serve some function, and they must confer an advantage relative to alternatives within the population. Once combined, secondary adaptation may improve the integration of parts and may in the process enable other parts to be added, once again possibly resulting in a shift in function and beginning as a poor fit that is enhanced only later (Fig. 3). Thus, even indirect evolution is gradual in the sense that it proceeds in a stepwise fashion and requires no prohibitively improbable leaps.


I think gene sharing is important in this process as well, because then it can be a change in timing/location of expression rather than mutations to form a new gene.

The larger issue, which I mentioned elsewhere, is that this disagreement misses a significant point, namely that we don't establish the fact of evolution by knowing all the details of the path of evolution. The fact that no reliable observation has ever arisen to refute the idea that eyes are the product of evolution in 150 years even though many new types of data became available (genetics, for one) is strong support. The fact that all of these new data are actually providing very detailed insights into the components of visual systems is even stronger evidence. It is a misunderstanding of the scientific method to assume that one needs to know all the details about the origin of a biochemical pathway to acknowledge that an organ is a result of evolutionary mechanisms.

Anyhow, looks as though we have work to do in better explaining how exaptation operates.

mammuthus said...

Ryan,

You wrote:

In actuality, the addition of components to an evolving organ may occur in series (i.e., one at a time) and may involve a relatively poor fit at first. Again, the only criteria for such additions to be preserved by natural selection are that they must serve some function, and they must confer an advantage relative to alternatives within the population.

Is this the case? Must they serve some function? To elaborate, I mentioned this paper in the comments on the post below:

Ortlund, E.A. et al. (2008) Crystal structure of an ancient protein: evolution by conformational epistasis. Science, 317, 1544-1548.

The authors note the importance of "permissive" mutations that are "substitutions of no immediate consequence, which
stabilize specific elements of the protein and allow it to tolerate subsequent function-switching
changes". This makes a lot of sense to me.

However, the YEC crowd argue against this by saying that the "permissive" mutations envisaged by Ortlund et al would be lost because they confer no immediate selectable advantage. Therefore this mechanism is invalid

http://www.answersingenesis.org/articles/aid/v2/n1/ancient-protein-resurrected

I thought of ways around the problem they raise and it seems to me to ignore the fixation through neutral genetic drift. This paper points out the importance of drift in this context:

Bloom, J.D. et al. (2007) Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution. Biology Direct, 2, 17, doi:10.1186/1745-6150-2-17.

Bloom says:

Overall, experiments have now demonstrated two clear mechanisms by which neutral genetic drift can aid in the evolution of protein functions. In the first mechanism, neutral genetic drift fixes a mutation that increases a protein's stability [24,25,55], thereby improving the protein's tolerance for subsequent mutations [26-28], some of which may confer new or improved functions [28]. In the second mechanism, which was the focus of this work and the recent study by Tawfik and coworkers [44], neutral genetic drift enhances a promiscuous protein function. This enhancement poises the protein to undergo adaptive evolution should a change in selection pressures make the promiscuous function beneficial at some point in the future.

So, given this, could your argument be changed slightly? Is it necessary that additions "must serve some function, and they must confer an advantage relative to alternatives within the population." If it is necessary, is the Ortlund et al paper wrong?

Or, because you are dealing with organ level components rather than the molecular level, does my reasoning not really apply?

Thanks,

-m-

T Ryan Gregory said...

I said they must be functional "to be preserved by natural selection". Drift is another important mechanism, which is why I also discuss non-adaptive processes in the article.

T Ryan Gregory said...

(But your point is well made that selection is not the only mechanism, which is too commonly overlooked.)

RBH said...

Ryan quoted his earlier paper as saying

In actuality, the addition of components to an evolving organ may occur in series (i.e., one at a time) and may involve a relatively poor fit at first. Again, the only criteria for such additions to be preserved by natural selection are that they must serve some function, and they must confer an advantage relative to alternatives within the population. Once combined, secondary adaptation may improve the integration of parts and may in the process enable other parts to be added, once again possibly resulting in a shift in function and beginning as a poor fit that is enhanced only later (Fig. 3).

There is a very nice Youtube video (if one ignores the background music!) based on Nick Matzke's proposal for the evolution of the bacterial flagellum that illustrates that very process beautifully.

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