I posted this some years ago elsewhere, but it’s apposite to bring it here, not least to provide those who paid attention in class with the means to destroy the usual tiresome canards about eye evolution, peddled with masturbatory zeal by the usual suspects among the mythology fanboys. Now that we have a shiny new forum supporting all the tags I need, it’s time to launch this here.
Bear in mind, that there’s a 32,000 character post limit on these forums, which means that this exposition will be spread across multiple posts.
So, without further ado, I bring you …
The Grand Eye Evolution Exposition
Eye evolution is one of those vexed topics that continues to resurface on forums such as this, and indeed, will probably continue to resurface, courtesy not only of the wilful ignorance (not to mention ideologically motivated discoursive duplicity) of critics of evolutionary theory (Darwin quote mines, anyone?), but because incredulity still persists with respect to this topic. Therefore, I thought it apposite to collect, in one place, as large a body of scientific work on eye evolution, with reference to as many relevant scientific papers as possible, that can be fitted into the confines of posts within these forums. Among those papers are a brace of papers on blind cave fishes, which are particularly apposite with respect to eye evolution, and the illumination of relevant processes and relevant genes.
Having engaged in a literature search on the Mexican Blind Cave Characin, Astyanax mexicanus, for another thread elsewhere, I thought I would bring the material over here, as it makes compelling reading. I found several interesting papers, and provide links to those that can be downloaded in full, and quotes from abstracts where appropriate in order to highlight specific points. Where possible, I shall also provide detailed exposition of the contents of some papers. As a consequence, this is going to be a long post.
Basically, the development of the eye in Astyanax mexicanus is controlled by the genes Pax6, shh and twhh among others, though these are, thus far, the ones principally implicated. I suspect that somewhere along the lines, a linkage with HOX genes and possibly even bmp signalling may prove to be part of the total picture once the requisite research is performed - it wouldn’t surprise me if this was the case, given how HOX genes and bmp signalling turn up in a diverse range of other developmental mechanisms, but for now, shh and twhh appear to be the prime movers signalling wise.
So, on to the papers! First …
Evidence for Multiple Genetic Forms With Similar Eyeless Phenotypes In The Blind Cavefish, Astyanax mexicanus by Thomas E. Dowling, David P. Martasian and William R. Jeffery, Molecular Biology & Evolution, 19(4): 446-455 (2002), which can be downloaded in full and read at leisure as a PDF document from here, and the abstract reads thus:
Other interesting papers include:
Genetic Analysis of Cavefish Reveals Molecular Convergence in the Evolution of Albinism by Meredith E. Protas, Candace Hershey, Dawn Kochanek, Yi Zhou, Horst Wilkens, William R. Jeffery, Leonard I. Zon, Richard Borowsky and Clifford J. Tabin, Nature Genetics, 38(1): 107-111 (January 2006) which can be downloaded in full from here;
Hedgehog Signalling Controls Eye Degeneration in Blind Cavefish by Yoshiyuki Yamamoto, David W. Stock and William R. Jeffery, Nature, 431: 844-847 (19 July 2004) (not a free download but the abstract is online).
From the latter paper about Hedgehog signalling, I provide the abstract:
So it transpires that if you transplant an embryonic lens taken from a surface-dwelling Astyanax mexicanus with normal eyes into the optic cup of an embryonic blind cavefish, normal eye development resumes. Interesting is it not? And, by manipulating the shh and twhh gene expression in surface-dwelling eyed fishes during embryonic development, the scientists were able to reproduce the eye apoptosis seen in the cave dwelling fishes.
An additional paper (downloadable in full from here) is this one:
Early and Late Changes in Pax6 Experession Accompany Eye Degeneration During Blind Cavefish Development by Allen G. Strickler, Yoshiyuki Yamamoto and William R. Jeffery, Development, Genes & Evolution, 211(3): 138-144 (March 2001)
in which the role of the Pax6 gene (which is common to eye development across a wide range of organisms) is examined with respect to the differences in development between the surface-dwelling form of Astyanax mexicanus and the cave-dwelling forms.
At this point, I’ll end Part 1, and reconvene with Part 2, which will be a long post covering one paper in detail …
Eyed Cave Fish In A Karst Window by Luis Espinasa and Richard Borowsky, Journal of Cave and Karst Studies, 62(3): 180-183 (2000)
which describes the co-existence of eyed and eyeless forms in a cave with a karst window, and the abstract makes VERY interesting reading indeed - namely:
So here, we have the first cited evidence that when a blind cave population was, by a serendipitous accident, granted readmission to daytime light sources, some of the blind cave fishes regained their eyes over time.
Indeed, I’ll cover this paper in more detail, as it makes interesting reading to put it mildly. The paper opens as follows:
So, there exists a cave in Mexico called Caballo Moro, that has a karst window admitting light, and within this cave, within reach of the light admitted by the karst window, there is a population of Astyanax mexicanus. This population contains fishes that have lost their eyes, conforming to the phenotype that was once described via the taxon Anophthichthys jordani, that taxon now recognised as a junior ynonym of Astyanax mexicanus. However, the population contains fishes with functioning eyes. It is tempting to think that the eyed fishes are members of a surface-dwelling population that have become intermingled with the cave fishes, and, courtesy of still having access to light, retained their eyes. The population genetics of Astyanax mexicanus have been extensively studied, and as a consequence, a great deal is known about the surface-dwelling and cave-dwelling populations of these fishes, including the fact that there exist distinct genetic markers for distinct populations, allowing scientists to alight upon the fact that the eye-loss phenotype has arisen in multiple separate populations independently, via a range of acquired mutations. The relevant paper containing evidence for this is one I’ve already cited above, namely:
Evidence For Multiple Genetic Forms With Similar Eyeless Phenotypes In The Blind Cavefish, Astyanax mexicanus by Thomas E. Dowling, David P. Martasian and William R. Jeffery, Molecular & Biological Evolution, 19(4): 446-455 (2002)
I’ll leave that paper aside for the moment, as I can always return to it in detail in another post. However, that paper establishes that different cave populations of Astyanax mexicanus possess an eyeless phenotype arising via different sets of mutations in the genes responsible for eye development (namely Pax6, shh and twhh, about which I have posted elsewhere in the past, including the paper covering Pax6 as a master gene in eye development - more on this shortly!). Likewise, populations of the surface dwelling eyed phenotype have genetic markers identifying them as belonging to particular populations, where those populations experience little or no gene flow with other populations, and consequently, the provenance of a fish can be determined with reasonable precision by appropriate genetic analysis. The authors of the paper I am covering here have established that the eyed phenotype fishes in the Caballo Moro karst window cave possess genetic markers identifying them as having derived from ancestral eyeless stock. Which means that these fishes had eyeless ancestors, and consequently regained functioning eyes once light was present.
So, it remains to cover the present paper in more detail, and examine the evidence presented therein. Let’s do that shall we?
And thus, the groundwork is laid for what follows. Namely, that there is no obvious source of eyed fishes from surface or epigean populations, with the cave running for 11 Km underground, without capturing a surface stream between the cave’s entrance pit and the karst window illuminating the population of interest. Moreover, the nearest population of epigean fishes is 4 Km distant from the cave, and there is no obvious connection between the body of water containing that epigean population, and the mixed population of fishes in the karst window lake, which comprises a mixture of epigean and hypogean (cave-phenotype) fishes. So, the possibilities are:
 The epigean phenotype fishes (possessing pigmentation and functional eyes) are a recent arrival, courtesy of an as yet unknown connection between the cave system and a surface body of water supplying these fishes;
 The epigean phenotype fishes have coexisted with the hypogean phenotype (eyeless and depigmented) fishes for an extended period of time with little or no interbreeding;
 The epigean phenotype fishes have arisen from hypogean ancestors.
 is considered unlikely by the authors, given the known geography of the cave system, but is required to be ruled out evidentially.  poses problems with respect to the appearance of an isolating mechanism between the two phenotypes, given that prior breeding experiments have established that epigean and hypogean fishes are capable of mating and producing offspring. , meanwhile, would provide an extremely interesting example of evolution reversing a character change that had previously occurred in these fishes, but requires evidential support before the postulate can be considered valid. So, let’s see what the authors discovered upon further analysis! First, the authors outline their experimental procedures:
Now, comes the analytical results!
Indeed, the accompanying figure is quite impressive (see Table 1 charting the RAPD bands for the various populations). The Caballo Moro fishes are manifestly members of a well-defined and genetically distinct grouping, exhibit a well-defined clustering of bands from the DNA analysis that are only partially shared with individuals from the Molino and Vasquez caves (the other two cave populations sampled), and there are marked differences between the Río Frío, Río Boquillas and Rio Comandante fishes and those from Caballo Moro.
Basically, the above tests establish that the Caballo Moro fish form a genetically distinct group, and that furthermore, there exists an interesting set of relations between the eyed and eyeless fishes, which closely matches that of a Monte Carlo simulation of the emergence of eyed and eyeless fishes in that group.
With that, it’s time to move on to the authors’ discussion of their results:
Now the authors are being appropriately cautious here, with respect to the data that they have obtained, but, that data is more consistent with the hypothesis of the eyed fishes of Caballo Moro having arisen from eyeless ancestors, than it is with competing hypotheses. Which means, if confirmed by more in-depth study involving larger data sets, that the eyed specimens of Astyanax mexicanus resident in the Caballo Moro karst window lake are fishes that have regained functional eyes, courtesy of appropriate mutations being positively selected for in their lineage. It would be interesting to examine the genetic data for the Pax6, shh and twhh genes for these fishes, as, given their known role in the appearance of the eyeless phenotype in other hypogean lineages of Astyanax mexicanus.
Now, aside from the fact that the above refutes wholesale any notion that selection cannot affect the dissemination of particular genes, or shape the inheritance thereof (which as susu.exp has already noted on numerous occasions elsewhere, is based upon a singularly woeful lack of understanding of basic biology - some critics of evolution apparently hasn’t heard of meiosis, apart from anything else), the above findings also drive a tank battalion through creationist quote mining of Crow’s paper, because here we have an instance of purported ‘genetic deterioration’ being thrown into full reverse by evolutionary processes, something which creationist assertions about “genomic entropy” claim simply cannot happen. Once again, the real world demonstrates that blind creationist assertion is nothing more than that - blind assertion.
So, looks like the evidence for the active evolution of these fishes is pretty compelling.
Meanwhile, it’s time to move on from the blind cave fishes somewhat, and concentrate upon Pax6. The papers extant in this area are very interesting. Indeed, as if yet more evidence for the importance of Pax6 was needed, here is the Ensembl page covering the Pax6 gene and the oculorhombin protein that it codes for. That page notes that the following diseases are caused by mutations in Pax6:
 Aniridia type II - partial or complete absence of the iris, absence of the fovea and malformations of the lens (among other structural malformations). Approximately 67% of these defects are familial, and the inheritance mechanism is autosomal dominant;
 Peter’s Anomaly - the site describes this condition thus:
In other words, more severe eye defects;
 Ectopia pupillae - failure of the pupil to be properly centred;
 Foveal hypoplasia - failure of the fovea to develop fully during embryogenesis, inheritance again autosomal dominant;
 Autosomal dominant keratitis - opacity of the cornea with accompanying vascularisation, often associated with foveal hypoplasia above;
 Ocular coloboma - abnormal development of the optic cup and stalk, accompanied by holes appearing in various eye structures;
 Bilateral optic nerve hypoplasia - failure of the optic nerve to develop properly, again with autosomal dominant inheritance;
Here’s the human Pax6 gene, formatted using my nice Visual Basic applet:
Now already we know something is wrong here because the gene is a different size. But the BIG surprise is what happens when we look at the protein it codes for …
Oops. MAJOR malfunction here!
Basically, this mutant form of the gene fails to code for a working protein full stop. The transcription process hits an Ochre stop codon at the third coding triplet.
Furthermore, the extant online gene databases inform me that there are variations as follows associated with Peter’s Anomaly:
 Substitution of codon triplet for W (tryptophan) replacing G (glycine) at codon position 18 (bp 52-54);
 Subsititution of codon triplet for R (arginine) replacing G (glycine) at codon position 26 (bp 76-78);
 Substitution of codon triplet for V (valine) replacing D (aspartic acid) at codon position 53 (bp 157-159) - found principally in Japanese human lineages manifesting the disease (ethnospecific), also associated with congenital cataract and foveal hypoplasia in affected individuals;
 Substitution of codon triplet for S (serine) replacing P (proline) at codon position 363 (bp 727-729);
So, it looks once again as if real science knows a LOT more about eye evolution than mendacious propagandists for creationist fantasies dare to even imagine it is possible to know.
Meanwhile, I’ll also reprise this material - apologies if I repeat citations of papers cited above here:
Adaptive Evolution of Eye Degeneration in the Mexican Blind Caveﬁsh by W. R. Jeffrey, journal of Heredity, 96(3): 185-196 (Jan 2005) - explains how selection is a key factor in the evolution of eye degeneration in cave fishes
Cavefish as a Model System in Evolutionary Developmental Biology by William R. Jeffrey, Developmental Biology, 231:, 1-12 (1 Mar 2001) - contains experimental tests of hypotheses about eye evolution
Hedgehog Signalling Controls Eye Degeneration in Blind Cavefish by Yoshiyuki Yamamoto, David W. Stock and William R. Jeffery, Nature, 431: 844-847 (14 Oct 2004) - direct experimental test of theories about eye evolution and the elucidation of the controlling genes involved
The Master Control Gene For Morphogenesis And Evolution Of The Eye by Walter J. Gehrig, Genes to Cells, 1: 11-15, 1996 - direct experimental test of hypotheses concerning eye evolution including the elucidation of the connection between the Droso gene and eye morphogenesis, and the experimental manipulation of that gene to control eye development
Why cavefish are blind by Natasha .M. Tian & David .J. Price, Bioessays, 27: 235-238 (Mar 2005) - also reports on the connection between the Pax6 and hedgehog signalling genes and how these are subject to selection over time
Let’s have a look at some of the contents of those papers shall we?
Oh dear. The hard evidence from the real world supports evolution. Let’s look at the next paper:
Oh look. More hard evidence from the real world supporting eye evolution. Namely that:
 Different cave fish populations evolved the eye apoptosis mechanism independently, and have different mutations coding for this;
 Other senses, particularly those connected with feeding efficiency, are enhanced in the blind cave populations of Astyanax mexicanus, and the underlying genetic mechanism for this is being elucidated, with special reference to the Prox 1 gene;
 In embryonic fishes, eye formation begins normally, but then undergoes reversal because of cell apoptosis controlled by signalling from the lens tissues, and experimental transplantation of a normal lens from a sighted embryo into an optic cup belonging to a cave dwelling embryo results in the restoration of normal eye formation;
 The genes involved in this process are now known, and the Pax6 gene, which has been demonstrated experimentally to be the master control gene for eye morphogenesis, is involved in the differential formation of eyes in cave dwelling Astyanax mexicanus populations.
One of the best papers I can present with respect to the above issues is this - the very paper that supports the statement I have just made above about the role of Pax6, namely:
The Master Control Gene For Morphgenesis And Evolution Of The Eye by Walter J. Gehrig, Genes To Cells, 1: 11-15, 1996.
However, the best part is when we look at the article in detail …
Oh dear. We know rather more about the genetic processes involved in eye formation and evolution than creationists think. The requisite genes, as I’ve already established above, are found right across a hole brace of animal phyla from flatworms to mammals, including you and I.
One question I’ve never seen creationists answer with a substantive answer (as opposed to vacuous apologetics) is this: why has their magic man chose to produce cave fishes that have all the genetic and molecular machinery for eye formation, which initiates normal eye development to begin with but then goes into reverse, and moreover exhibit different mutations for this in different populations? If their magic man knew that these fishes were going to end up in caves, why bother giving them the genetic and molecular machinery for eyes in the first place? Bit of a cock up there, creating these fishes in such a manner as to provide evidence for evolution.
Also, I’m reminded of the following video clip (with bonus appearance by Stephen Jay Gould):