Saturday, October 27, 2007

From the Cutting Room Floor

I spend a lot of time re-writing. I wrangle with the text. It rarely just flows. Not uncommonly, I scrap entire paragraphs or sections, sometimes after considerable effort. This can be hard for me to do - I often like the doomed sections, but perhaps they just don't fit, or perhaps the focus changes. Well, just as directors have started adding deleted scenes to DVD's, I've decided to post here an earlier version of a forthcoming Evolution and Development "Highlights" contribution. I was invited to write this "Highlights" paper; the goal to draw attention to recent literature. I chose to write about recent work that increases our understanding of the evolution of lenses in the eyes of a squid. At the last minute, I changed the focus of the paper. I decided to make it more topical by putting the work in the context of a currently hot topic in evolutionary biology research, the molecular basis for evolutionary change. But this new focus came at the expense of a previous version that argued that the genes of the squid lens evolved as an adaptive radiation. I really like this idea - thinking about genes as undergoing adaptive radiations. So instead of leaving it to degrade on my hard drive for eternity, I post the idea here, where there is a chance someone might stumble upon it.

Evolution of aquatic lenses by an adaptive radiation of genes

"Adaptive radiation" is usually used to describe explosive bursts of speciation that occur in concert with phenotypic adaptation to divergent environments. Below, I will recount an amazing tale of an adaptive radiation - not of species, but of genes - which allowed for the evolution of novel lenses in squid.
Lenses like those of a squid eye that exist and function in water have high demands compared to lenses that function in air. This demand is rooted in the fact that cells are composed mainly of water. As such, aquatic lenses cannot take advantage of the transition of light entering watery cells of the eye from the external air, which bends the light. Instead, aquatic lenses must be very powerful. But the more powerful a lens, the more it must be curved and the more curved a lens, the more aberration results in the image for a lens of a given size. Luckily for fish and squid, there is a solution to these demands, called the graded refractive index lens. These lenses can be compared to an onion, containing a central core and concentric layers surrounding that core. The core bends light very significantly (i.e. it has a high refractive index), while each layer outside the core bends light less and less, with the outer layer having the lowest refractive index. The rings of the “onion” thus form a graded series from high refraction in the middle to low refraction on the outside. These types of lenses achieve high power, with little aberration. How might these rather complicated and precise lenses have evolved? How did this novelty originate? Was it a linear transformation as often envisioned by evolutionists (see future post entitled The Iconography of Expectation). In fact, a linear transformation was envisioned by Nilsson and Pelger, as part of their gradual series from photoreceptive spot to camera-type eye. Dawkins described the models this way:

“ The results were swift and decisive. A trajectory of steadily mounting acuity led unhesitatingly from the flat beginning through a shallow indentation to a steadily deepening cup, as the shape of the model eye deformed itself on the computer screen. The transparent layer thickened to fill the cup and smoothly bulged its outer surface in a curve. And then, almost like a conjuring trick, a portion of this transparent filling condensed into a local, spherical subregion of higher refractive index. Not uniformly higher, but a gradient of refractive index such that the spherical region functioned as an excellent graded-index lens.”

- Dawkins, Richard, Where d'you get those peepers?., Vol. 8, New Statesman & Society, 06-16-1995, pp 29

“Conjuring trick”, indeed: How does an eye "deform itself"? How does a “portion of transparent filling” condense into a local region with higher refractive index? What, for example, are the genetic changes? Do the morphological changes occur gradually, as envisioned by Darwin, Nilsson, and Dawkins? And do genetic changes show a similar pattern? Or have changes occurred in discrete, quantum steps? These questions have been addressed in squid lenses by Alison Sweeney and colleagues in the lab of Sonke Johnsen. Amazingly, the results indicate an adaptive gene radiation was fundamental to the origin of squid lenses.

The rapid radiation in question involves structural lens proteins called crystallins. Crystallins are not a homologous group of proteins, but rather are a functional class, sharing high expression in the lens. Crystallins are well studied proteins that belong to a number of different families; often one protein will have dual functions, acting not only as structural proteins of the lens, but also as enzymes in other tissues. In the lens the crystallins are densely expressed, essentially mimicking glass-like transparency. Lenses of the squid Loligo opalescens are composed primarily of crystallins of a single gene family. Can we conclude that the Loligo crystalline gene family represents an adaptive radiation?
Dolph Schluter, in his book devoted to adaptive radiation, suggests four criteria are required for status as an adaptive radiation. Although he was describing species radiations, these criteria can just as easily apply to genes. First, the units of an adaptive radiation - be they species or genes - must share common ancestry. This is a bit ambiguous since all species, and presumably all genes, share common ancestry. Schluter actually means a recent common ancestry. Second, there must exist a correlation between phenotype and environment. Like species, genes also have phenotypes and environments. A gene's phenotype may be a particular biochemical property of the protein it encodes and its environment may be a specific location of expression within the organism. Third, the phenotype that correlates with environment must have utility specifically for that environment. For example, in Darwin's finches, bill size correlates with habitat - tree dwellers have smaller bills and ground dwellers have larger bills. Larger bills have utility for ground dwelling, because larger bills are more effective at breaking seeds, a food source encountered by ground dwellers. Finally, adaptive radiation requires rapid lineage bifurcation. Despite an intense interest in adaptive radiations, establishing all four of these criteria has been rare; only a few clades including Darwin’s finches, stickleback fishes, columbine and silversword flowering plants, and anolis lizards – have been studied in sufficient detail. Amazingly, squid lens crystallin evolution fits well each of these four criteria for adaptive radiation.
Squid lens proteins easily satisfy the first criterion of common ancestry. The squid lens is dominated by S-crystallins, but not just one gene, rather about 25 related genes are expressed only in the lens at high concentration. These genes are in fact about 80% similar to each other in amino acid sequence, and probably form a monophyletic group that is closely related to a liver-expressed enzyme. All of these genes form a group that can be traced back to a single common ancestor and excludes any other genes. In other words, the genes are a monophyletic clade. Schluter’s first criterion is met with flying colors. The genes of the squid lens have a recent common ancestry.
How do squid crystallins meet the criterion of a correlation between phenotype and environment analogous to the correlation between beak size and habitat in Darwin’s finches? Clearly, proteins have phenotypes; namely their biochemical and molecular structures, properties and functions. Proteins also have environments, the specific location where they are used. In the case squid lenses, proteins expressed closer to the center of the lens have on average higher electrostatic charges compared to proteins expressed at the periphery of the lens. The average phenotype of the genes tends to change in a graded fashion from center to edge of the lens, a clear correlation between phenotype and environment not unlike the preference for large-beaked finches to live on the ground while small-beaked finches live in the trees.
Not only is the phenotype-environment correlation met, but also the phenotype has demonstrable utility for the environment of the proteins. The graded index lens of squids and octopuses is established by a gradient of protein concentration: Higher protein concentrations lead to higher refractive power. Squid crystallins’ molecular phenotypes (charge and length) have utility in allowing for different protein concentrations at different locations in the lens (the genes’ environments). The higher electrostatic charge of the proteins causes them to repel each other, resulting in a less densely packed group of proteins and lower refractive index. Just as large beaks afford greater seed-crushing power, useful for living on the ground where seeds can be found, squid lens crystalline phenotypes have utility for generating different refractive indexes.

I am so taken with these results because they so clearly illustrate what evolutionists ignored for so long - the origins of variation. Focusing on models where eyes gradually increase in complexity, driven by natural selection, misses a crucial part of the equation. Variation is simply assumed. But how did those variations originate? In squid lenses, those variations were gene duplications, changes in duplicated proteins, and changes in the place of expression of those proteins. By opening this black box of variation, evolutionists can now begin to ask new questions, and gain a deeper understanding of the processes that have created the amazing diversity of life we see everyday.

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