Tuesday, November 27, 2007


It is interesting that evolutionists quite often use the term "lineage" to refer to a clade. I feel I've seen this in many contexts. Gene families may be called a lineage. A clade of species may also be called a lineage.

What is linear about these groups of biological entities? I think almost nothing. A clade of genes or species contains a common ancestor. A line can be drawn from that ancestor to any of the terminals. However, the decision of which line to draw is arbitrary, unless a single gene or species is all that is of interest in the clade.

Clades are not lineages, they are clades. Clades are branching diagrams without any inherent linearity. I think referring to clades as lineages provides yet another example of how linear thinking is embedded in the way people see the world. "Tree thinking" is a skill central to understanding biology. But to achieve this skill requires people to overcome innumerable difficulties. Some, such as referring to clades as lineages, seem subtle, but nevertheless probably have an effect on our ability to see biology as a collection of branching processes.

Monday, November 5, 2007

The iconography of an expectation: Redux

"Scientific illustrations are not frills or summaries; they are foci for modes of thought." -Gould, 1991

Almost certainly, one of Stephen Jay Gould's pet peeves was the human tendency to assume that evolution proceeds like a ladder, from simple to complex species, often culminating in human kind. He spilled a lot of ink trying to dispel this common misunderstanding. His essay "Life's Little Joke", reprinted as Chapter 11 of Bully For Brontosaurus (1991), shows that the classic case of horse evolution is not a trend, as often portrayed. Rather, horses diversified, leaving only a few single-toed, large bodied species survivors.

My favorite example of Gouldian ladder-bashing is Chapter 1 of Wonderful Life (1989) entitled The Iconography of an Expectation. Here, Gould uses figure after figure from popular culture depicting evolution as linear series. Most are variations on the familiar parade of knuckle walking primate (brining up the rear) to modern human (leading the way). These quite commonly end with a joke, such as ending the parade with a modern human crouched over a computer.

A quick search with Google image, using the simple search term "evolution", confirms Gould's observation almost two decades later: The first seven hits were variations on the human walk of progress.

Here is one of the joke variety:

The metaphor even extends beyond living things, in this case to cellular phones:

Perceived evolutionary ladders abound, it's true. So where is the "redux" from the title? Well, I've been noticing that the fallacious ladder of progress not only applies to species, but also applies to traits, like eyes. Here is a recent example from a PNAS paper by Ayala:

Illustrated are the photoreceptive organs of five mollusk species. Like a 'primative' knuckle-walking proto-human, the 'lowly' pigment spot of a limpet begins the parade.
Ever so slightly more complex is a pigment cup, followed by the pin-hole eye of a Nautilus. At the top of this ladder of progress are the lensed eyes of a snail and an octopus. Cephalopod eyes, like that of Octopus, are widely heralded as strongly convergent with our own eyes, where a lens focuses light on a retina at the back of the eye. Thus completes the march of progress, from lowly pigment spot right on up to the most human-like eye of the invertebrate world. Congratulations, humans, we're at the top of the ladder again! Dr. Gould may be rolling in his grave.

There are a lot of extensions to this idea, which I will continue in future posts. I have several examples from eye evolution of iconographic ladders of progress. What are these ladders trying to accomplish, and what is wrong with such a view anyway? Is it really a model of how evolution works?

To be continued.

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.

Tuesday, October 16, 2007

Origins of Genes

Darwin was the first to envisage global common descent for species. Who was the first to make the analagous conceptual leap for genes? In other words, who was the first to propose that all genes originate by duplication of other genes?

I've not yet done a proper historical analysis, but I have made a little progress on these questions. A good place to start with a historical analysis of gene duplication is with a review article that I'm a fan of (Taylor and Raes, 2004). They point out that ideas about the copying of genetic material date back to the early 1900's, especially with studies on chromosome duplication and ploidy changes.

But this is a different question. The idea that chromosomes or even genes can be duplicated is not tantamount to a hypothesis of global common descent for those genes. I've argued, in a paper with Michael Rose, published in Biology Direct, that even if early evolutionists and geneticists recognized gene duplication, they did not often recognize the possibility of the relatedness of all genes. Instead, genes were thought to be molded very quickly by natural selection, such that their history is quickly erased. Here is a graphical representation of this idea:

There are two critical differences in figures A and B above. First, in A, genes have only short histories. Whatever their origins (and often their origins were not contemplated, as genes represented very abstract entities), their history was short. Natural selection should quickly mold gene function to current utility and erase history. Second, in B, genes have a branching history of their own, semi-independent of the branching history of species.

In my initial attempts at understanding the history global common ancestry for genes, I've focused on finding the origin of the idea of separate histories for genes and species. One of the best candidates is a paper by V Ingram in Nature, 1961. (Here is a biography of Ingram, a protein biochemist). Ingram had obtained the first amino acid sequences of hemoglobins. He noticed the similarities of different human hemoglobins (e.g. fetal, adult), and constructed a gene tree of hemoglobins as the only figure in the article (everyone knows the only figure published in Origin of Species, right?). Ingram concludes with the sentence "Such a scheme involves an increase in the number of haemoglobin genes from one to five by repeated gene duplication and translocations; the scheme may thus illustrate a general phenomenon in gene evolution."

Ingram was close. But "general phenomenon" does not equate with an idea that gene duplication is the primary or even sole mechanism for the origin of new genes. Perhaps Ohno (1970) or Zuckerkandl (1975) make the bold leap to common ancestry of all genes. I will have to check into that when I get a chance.

Monday, October 15, 2007

Pluralistic Darwinism

Every year I ask the undergraduate students in my course EEMB 102-Macroevolution the same question. "What do you think of when I say 'Darwin'"?

Some answers are jokes, like "The Darwin Awards". One common answer, "Darwin's Finches", was unexpected to me. But given the ubiquity of these birds in textbooks, perhaps I should not be surprised. Of course the most common answer is "survival of the fittest".

The reason I ask every year is that I like to point out two things in the first lecture of the course. First, that Darwin was not the only one to think up natural selection. A.R. Wallace famously scooped Darwin, and they published their ideas in 1858 at the urging of Charles Lyell. Two others had actually published the idea of natural selection, long before Darwin and Wallace thought of the idea, but in obscure places. I like to cite this when arguing for science as deterministic - a process unto itself that does not depend much on the individuals who practice it.

The second reason I ask is to highlight that Darwinism is so much more than just natural selection - despite most people's tendency to equate the two. All of the above answers (Darwin Awards, Finches, and survival of the fittest) re-enforce the idea that people often equate Darwinism and natural selection. The Darwin Awards go to people who do stupid things, and thereby "improve the species...by accidentally removing themselves from it". The implicit idea is that removing people with genes coding for stupidity will improve the human species. Much research on Darwin's Finches is about documenting natural selection in the wild. And "survival of the fittest" is the most common buzz phrase referring to natural selection.

Never in my (admittedly small number of) years teaching the course has anyone mentioned any of the other Darwinian Theories (see Mayr's classification), besides natural selection. Why should this be, when global common descent is the most profound idea in all of biology? Global common descent provides explanatory power in biology. It is what scares anti-evolutionists the most, as the realization has transformed the view of humankind's place in the natural world from a self-congratulatory perch atop a Scalae Naturae, to an arbitrary outpost alongside other apes as cousins to every conceivable organism, from slime mold to germ.

It makes me wonder. Why is it that global common descent so often gets such a distant second billing to natural selection? Why do people so often equate Darwinism with natural selection, despite the fact that others conceived of natural selection (unlike global common descent, where as far as I know Darwin was the first) and despite the profound implications of common descent?

One idea is that humans - sometimes even practicing evolutionary biologists - have a difficult time coming to grips with global common descent. Perhaps a branching view of time is difficult to internalize compared to linear time. Perhaps it's all just a vestige of the great chain of being concept.

Questions and realizations about common descent are precisely what I want to contemplate in future posts.