Science Literature

An important paper has appeared recently on the way organisms have adapted their vision to dim light. The authors point out that the first vertebrates appearing in the fossil record lived in shallow water, open shelf marine environments. Many animals living in these environments today have rhodopsin molecules with their greatest sensitivity to light of about 500 nm, which matches what we know of spectral intensities at dusk. This, then, becomes the baseline figure for light sensitivity, and the authors have identified other maximum sensitivities ([lambda]max) that are representative of animals from different ecological niches.

"According to their [lambda]maxs and light environments, rhodopsins are classified into four groups: deep-sea (480-485 nm), intermediate (490-495 nm), surface (500-507 nm), and red-shifted (525 nm) rhodopsins."

Rhodopsin, a dim-light photoreceptor (Source here)

A major achievement of the research is the identification of modification to rhodopsins that have contributed to wavelength sensitivity. "[T]he [lambda]maxs of most contemporary rhodopsins can be explained largely by a total of 15 amino acid replacements at 12 sites." The authors could, like many others have done, assume that these 15 amino acid changes are the result of positive (Darwinian) selection. However, they did not make this assumption but set out to test for positive selection using various methods. This is where there were some unexpected findings. The surprises are well expressed by Hughes in a commentary essay:

"In fact, the results showed that the codon-based methods were 100% off target. When Bayesian methods were applied to a set of closely related rhodopsin sequences, eight sites were identified as "positively selected." Yet not one of these sites was among the 12 sites known to be involved in adaptive changes in rhodopsin sensitivity. Moreover, amino acid changes at these sites were shown experimentally to have no effect on [lambda]max and thus almost certainly to lack any adaptive significance."

This is a remarkable finding. Adaptation has occurred, but evidence of positive (Darwinian) selection lacks confirmation. At very least, it demonstrates that the Darwinian mechanism of survival of the fittest is not the key to understanding adaptation of dim-light vision. As we shall see (in a separate blog), Hughes goes much further than that.

It is worth noting that the phenotypic adaptations analysed in this research would be regarded as microevolution by many scientists. We are not considering variations needed to form new functionality, but rather the fine-tuning of existing functionality. As such, these findings are no more supportive of evolutionary biology than they are of ID biology or even Creation-orientated biology. However, since the research demonstrates adaptation without positive selection, is this evidence for neutral evolution? Serious questions about this can be raised because of convergence:

"4 of the 15 critical amino acid replacements occurred multiple times during rhodopsin evolution: [. . .]. Such extensive parallel changes strongly implicate the importance of these and other amino acid replacements at the 12 sites in the functional adaptation of vertebrate dim-light vision." [. . .] "In vertebrate rhodopsins, several amino acid replacements occurred multiple times and, furthermore, the biologically significant [lambda]max shifts occurred on at least 18 separate occasions."

This points us away from stochastic processes towards something more structural. In turn, this raises the question whether mechanisms for variation are designed rather than deterministic or stochastic. But this question cannot even be considered by those who reject design on ideological grounds. Here is yet another example of where design perspectives open up novel aspects of research to explain data that does not fit comfortably into the reigning paradigm.

Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates
Shozo Yokoyama, Takashi Tada, Huan Zhang, and Lyle Britt
Proceedings of the National Academy of Sciences, 105(36), 13480-13485, September 9, 2008 | doi:10.1073/pnas.0802426105.

Vertebrate ancestors appeared in a uniform, shallow water environment, but modern species flourish in highly variable niches. A striking array of phenotypes exhibited by contemporary animals is assumed to have evolved by accumulating a series of selectively advantageous mutations. However, the experimental test of such adaptive events at the molecular level is remarkably difficult. One testable phenotype, dim-light vision, is mediated by rhodopsins. Here, we engineered 11 ancestral rhodopsins and show that those in early ancestors absorbed light maximally ([lambda]max) at 500 nm, from which contemporary rhodopsins with variable [lambda]maxs of 480-525 nm evolved on at least 18 separate occasions. These highly environment-specific adaptations seem to have occurred largely by amino acid replacements at 12 sites, and most of those at the remaining 191 (~94%) sites have undergone neutral evolution. The comparison between these results and those inferred by commonly-used parsimony and Bayesian methods demonstrates that statistical tests of positive selection can be misleading without experimental support and that the molecular basis of spectral tuning in rhodopsins should be elucidated by mutagenesis analyses using ancestral pigments.

See also:

Hughes, A.L. The origin of adaptive phenotypes, Proceedings of the National Academy of Sciences, 105(36), 13193-13194, September 9, 2008 | doi: 10.1073/pnas.0807440105.

Coppedge, D.F. How Not to Prove Positive Selection (Creation-Evolution Headlines, Sept 5, 2008).