Blind Cave Fish

Darwin, Charles.  On the Origin of Species by Means of Natural Selection.  John Murray, London.  1st edition.  1859.  The first edition of Darwin's book on the origin of species by means of natural selection.  The article uses it for two things Darwin wrote about blind cave animals:  that their eyes were lost through disuse, and that the cave animals' likeness to the other animals of Europe and America is hard to explain if each kind was made separately.

1. 1a.

   Page 137:  “It is well known that several animals, belonging to the most different classes, which inhabit the caves of Styria and of Kentucky, are blind.” ↩

2. 1b.

   Page 137:  “As it is difficult to imagine that eyes, though useless, could be in any way injurious to animals living in darkness, I attribute their loss wholly to disuse.” ↩ ↩

3. 1c.

   Page 139:  “It would be most difficult to give any rational explanation of the affinities of the blind cave-animals to the other inhabitants of the two continents on the ordinary view of their independent creation.” ↩

Wieland, Carl.  “Blind fish, island immigrants and hairy babies.”  Creation Ministries International.  Jan 26, 2006.  A web article by Carl Wieland, a reply to Jerry Coyne's review of Niles Eldredge's book The Triumph of Evolution.  It argues that blind cave fish show mutational loss plus natural selection in total darkness, where eyes become a handicap.  The article uses it as the creationist statement of the loss view, and for Wieland's concession that the blind fish descended from sighted ones.

1. 2a.

   Section 1. Sightless eyes:  “Had he bothered to read the mainstream creationist literature, Coyne would have realized that we delight in using blind cave fish as examples of 'downhill' or 'information-losing' mutations causing 'devolution'.” ↩

2. 2b.

   Section 1. Sightless eyes:  “However, Dr Coyne is on safe ground in assuming that blind cave creatures descended from ones that had eyes.  There are cave fish, for instance, often the same species as 'seeing' ones above ground, who start to develop eyes as embryos.  But then the process halts and they end up with scar tissue where their eyes were evidently meant to be (see aside below).” ↩ ↩

3. 2c.

   Section 1. Sightless eyes:  “Eyes are delicate and thus easily injured in darkness, allowing the entry of potentially lethal bacteria.  So, in total darkness, eyes are no longer an asset, but a handicap.” ↩

4. 2d.

   Section 1. Sightless eyes:  “The evidence from blind cave fish continues to give a great illustration of mutational loss and natural selection, i.e. informationally 'downhill' change.” ↩

Jeffery, William R.  “Regressive evolution in Astyanax cavefish.”  Annual Review of Genetics 43:25–47.  2009.  A review article by William R. Jeffery of the University of Maryland on how the cave Astyanax fish lost its eyes and pigment.  It says the mechanisms of this loss are still poorly understood, and it summarises recent work on the cells and molecules involved, the number and identity of the genes, and the evolutionary forces at work.  The article uses it for how the eye is built and then degenerates, and for Jeffery's own statement that the data do not decide between selection and neutral mutation.

1. 3a.

   Figure 5 caption:  “In cavefish, the eye primordium grows for a while, then arrests, degenerates, and is internalized by overgrowth of the body.” ↩

2. 3b.

   Section Developmental basis of eye regression:  “However, the embryonic lens starts to die several days before any other eye tissue, earmarking it for a possible regulatory role (21, 58).” ↩ ↩

3. 3c.

   Section Developmental basis of eye regression:  “The transplants were done on only one side of the embryo, allowing the other side to serve as a control.  Transplanted lenses behave autonomously: The cavefish lens died on schedule in the surface fish host, and the surface fish lens survived and grew in the cavefish host.” ↩

4. 3d.

   Section Evolutionary forces:  “It should be emphasized that the current data does not allow us to conclude unequivocally that either selection or neutral mutation is responsible for regressive evolution.” ↩

5. 3e.

   Section Evolutionary forces:  “First, the genes involved in eye development that have been identified thus far do not appear to have mutated to a degree in which they have lost function.  For example, the restoration of eyes by lens transplantation suggests that genes operating downstream of lens function are present and potentially active in cavefish (23, 66).” ↩

Yamamoto, Yoshiyuki et al.  “Hedgehog signalling controls eye degeneration in blind cavefish.”  Nature 431(7010):844–847.  Oct 14, 2004.  A paper in Nature that tests hedgehog signalling (a chain of signals that controls how embryos grow) in the eye loss of blind cavefish.  Its abstract reports that two hedgehog genes are expressed across a wider stretch of the embryo's front midline in several cave populations, and that this extra signal makes the lens die by apoptosis (programmed cell death) and stops eye growth.  The article uses it to show that the cave eye is built and then taken apart, and that the broader midline signal is what kills the lens.

1. 4a.

   Section Abstract:  “Small eye primordia are formed during cavefish embryogenesis, which later arrest in development, degenerate and sink into the orbits.  Eye degeneration is caused by apoptosis of the embryonic lens, and transplanting a surface fish embryonic lens into a cavefish optic cup can restore a complete eye.” ↩ ↩

2. 4b.

   Section Abstract:  “Here we show that sonic hedgehog (shh) and tiggy-winkle hedgehog (twhh) gene expression is expanded along the anterior embryonic midline in several different cavefish populations.  The expansion of hh signalling results in hyperactivation of downstream genes, lens apoptosis and arrested eye growth and development.” ↩ ↩

Protas, Meredith et al.  “Regressive evolution in the Mexican cave tetra, Astyanax mexicanus.”  Current Biology 17(5):452–454.  Mar 6, 2007.  A short research paper in Current Biology that maps the genes behind smaller eyes and fewer pigment cells in the Mexican cave tetra.  The team crossed a Pachón cave fish with a surface fish, producing 539 second-generation (F2) siblings, and mapped quantitative trait loci (QTL, regions of the genome that shift a measurable trait).  It found twelve eye and lens loci, and every one of them shrank the eye or lens in the cave version, which the authors say fits natural selection better than genetic drift (chance changes in gene frequencies).  The work comes from one cross, so it describes one cave population.  The article uses it as its first genome-wide map of the eye loss.

1. 5a.

   Section Summary:  “Cave alleles at each eye/lens QTL we detected caused size reductions.  This uniform negative polarity is consistent with evolution by natural selection and inconsistent with evolution by drift.  In contrast, QTL polarities for melanophore number were mixed, consistent with evolution by genetic drift or indirect selection through pleiotropy.” ↩ ↩

2. 5b.

   Section Summary:  “Past arguments against a role for selection in regression of cave fish eyes cited the insignificant cost of their development [2, 3], but we argue that the energetic cost of their maintenance is sufficiently high for eyes to be detrimental in the cave environment.”  Their references 2 and 3 are Culver's Cave Life (1982) and Eigenmann's Cave Vertebrates of America (1909). ↩

3. 5c.

   Section Results and Discussion:  “Cave alleles at all 12 eye/lens QTL effect relatively modest, but steady decreases of eye/lens size (Fig. 1a).  In contrast, cave alleles at QTL affecting melanophore number have positive (n = 5), as well as negative slopes (n = 8), and their substitution affects are much larger (Fig. 1b).” ↩ ↩

4. 5d.

   Section Results and Discussion:  “We hybridized Pachón cave and surface fish, creating a mapping progeny of 539 F2 siblings.” ↩

Borowsky, Richard.  “Restoring sight in blind cavefish.”  Current Biology 18(1):R23–R24.  Jan 8, 2008.  A two-page piece in the Magazine section of Current Biology reporting Borowsky's own hybrid crosses between blind cavefish from different caves.  A hybrid is the offspring of two different parent populations, here a first-generation (F1) cross.  Some of the hybrids could see, the share depending on which two caves were crossed, from 1% to 39%.  The crosses use fish from only three caves, Molino, Pachón and Tinaja-Curva, so the result describes those three.  The article uses it to show that different caves lost their eyes through partly different genes.

1. 6a.

   Page R23:  “Eye loss has evolved independently at least three times [4,5] and at least some of the eye loci involved differ between the different cave populations [3].” ↩

2. 6b.

   Page R23:  “Here we demonstrate restoration of vision in cavefish whose immediate ancestors were blind and whose separate lineages may not have been exposed to light for the last one million years.” ↩

3. 6c.

   Page R24:  “This suggests that loss of function at three or four eye loci suffices to abolish vision.” ↩

4. 6d.

   Page R24:  “On average, 39% of Molino/Tinaja, 8% of Pachón/Tinaja, and 1% of Molino/Pachón F1 hybrids could see.” ↩ ↩

5. 6e.

   Page R24:  “Thus, Molino, Pachón, and Tinaja-Curva represent three independent multilocus convergences on eye regression.  This observation underscores the power of a well defined environment to repeatedly direct the evolution of the same end phenotype, regardless of initial genotype.” ↩ ↩

Protas, Meredith E. et al.  “Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism.”  Nature Genetics 38(1):107–111.  Jan 2006.  A genetic study of albinism (loss of pigment) in cave populations of the Mexican tetra, published in 2006.  Its abstract reports that the two cave populations it compares carry different deletions (missing stretches of DNA) in the same gene, oca2, and that both deletions stop the protein from working, so the two populations lost pigment independently through similar mutations.  The article uses it for the claim that albinism rests on different deletions in each cave.

1. 7a.

   Section Abstract:  “We found different deletions in Oca2 in each population and, using a cell-based assay, showed that both cause loss of function of the corresponding protein, OCA2.  Thus, the two cave populations evolved albinism independently, through similar mutational events.” ↩ ↩ ↩

Ma, Li et al.  “A hypomorphic cystathionine ß-synthase gene contributes to cavefish eye loss by disrupting optic vasculature.”  Nature Communications 11:2772.  Jun 2, 2020.  A laboratory study of Mexican tetra embryos that identified cbsa, a gene for an enzyme that turns homocysteine into cystathionine, as one of the genes behind cave eye loss.  Cave embryos make less cbsa because of a change in the DNA that controls the gene itself, which the authors call cis-regulation, and blocking the cbs genes in surface fish causes small eyes, leaking blood vessels and bleeding around the eye.  The article uses it as the named gene that is mutated in several cave populations, and "hypomorphic" in the title means a weaker form of the gene.

1. 8a.

   Page 1, section Abstract:  “Vestigial structures are key indicators of evolutionary descent, but the mechanisms underlying their development are poorly understood.” ↩

2. 8b.

   Page 1, section Abstract:  “Here we identify cystathionine ß-synthase a (cbsa), which encodes the key enzyme of the transsulfuration pathway, as one of the mutated genes responsible for eye degeneration in multiple cavefish populations.” ↩ ↩ ↩

Moran, Damian et al.  “The energetic cost of vision and the evolution of eyeless Mexican cavefish.”  Science Advances 1(8):e1500363.  Sep 11, 2015.  A laboratory study that measured the oxygen used by isolated eyes and brains of 10 Pachón cavefish and 10 surface fish, and used those measurements to model the energy cost of vision.  Oxygen use is a measure of how much energy a tissue burns.  The authors say the result does not by itself settle how eye loss evolved, and the article uses the figure as its energy argument for selection.

1. 9a.

   Page 1, section Abstract:  “However, data on relative brain and eye mass in this species or on any measure of the energetic cost of neural tissue are not available, making it difficult to evaluate the "expensive tissue hypothesis."” ↩

2. 9b.

   Page 1, section Abstract:  “The cost of vision was calculated to be 15% of resting metabolism for a 1-g fish, decreasing to 5% in an 8.5-g fish as relative eye and brain size declined during growth.” ↩ ↩

3. 9c.

   Page 3:  “The energetic cost of eyes in a 1-g surface fish was 8% of resting metabolism, decreasing to 5% in an 8.5-g surface fish”. ↩

4. 9d.

   Page 4:  “The cost of the visual system as a fraction of minimal metabolism in juvenile surface fish (15%) approaches the cost of the human brain (about 20 to 25%) (20).  Vision is therefore likely to be under strong selective pressure to regress in caves, where light is absent and food is limited.” ↩

Yamamoto, Yoshiyuki et al.  “Pleiotropic functions of embryonic sonic hedgehog expression link jaw and taste bud amplification with eye loss during cavefish evolution.”  Developmental Biology 330(1):200–211.  Jun 1, 2009.  A laboratory study of sonic hedgehog, a signalling gene with many jobs in development, in cavefish embryos and in hybrids between surface fish and cavefish that differ in eye size.  It found that the hybrids with smaller eyes had larger jaws and more taste buds, and that hyperactive hedgehog signalling enlarges the jaws and taste buds of cavefish.  The article uses it as the test of whether the eyes were lost as a side effect of selection for jaws and taste buds.

1. 10a.

   Section Abstract:  “Genetic crosses between cavefish and surface fish revealed an inverse relationship between eye size and jaw size/taste bud number, supporing the linkage between oral pharyngeal constructive traits and eye degeneration.”  "supporing" is spelled that way in the printed abstract. ↩

2. 10b.

   Section Abstract:  “The results suggest that hyperactive Shh signaling increases oral and taste bud amplification in cavefish and suggest that selection for constructive oral pharyngeal traits may be responsible for eye loss via pleiotropic function of the Shh signaling pathway.” ↩ ↩

Wilkens, Horst.  “Genes, modules and the evolution of cave fish.”  Heredity 105(5):413–422.  2010.  A review, not a new experiment, that places the classical and molecular genetic studies of cave fish in one framework.  It finds no strong evidence that the structural eye genes have been broken by destructive mutations, and it reports that the regressive and constructive traits are inherited independently, which does not support the idea that the eye was lost as a side effect of improving other traits.  The article cites it for the claim that the eye genes are unbroken, which it counts as support for drift.

1. 11a.

   Page 413:  “Sequence data and the wide range of intermediate sized eyes in hybrids between surface and cave fish suggest that currently there is no strong evidence supporting the notion that structural eye genes have been afflicted by destructive mutations.  The hedgehog genes, which are suggested to reduce the primordial eye cup size in cavefish by expanded expression, are also not mutated.” ↩ ↩ ↩

2. 11b.

   Page 413:  “The constructive and regressive modules are shown to inherit independently from each other, which does not support the view that eye regression is a spin off effect of the improvement of beneficial traits through pleiotropy.” ↩

Krishnan, Jaya, and Nicolas Rohner.  “Cavefish and the basis for eye loss.”  Philosophical Transactions of the Royal Society B 372(1713):20150487.  Feb 5, 2017.  A review of the genetic, developmental and physiological evidence on why cavefish lose their eyes.  It lists three explanations, direct selection against eyes, indirect selection through a linked trait, and no selection at all, and it concludes that none has been fully proved.  The article cites it as one of three reviews from three laboratories that say all three explanations probably contributed and none is proved.

1. 12a.

   Section 1. Introduction:  “The neutral hypothesis (the accumulation of hypomorphic mutations in the absence of selection) was favoured until recently when the results of new genetic, developmental and physiological studies supported the adaptive evolution of eye regression in cave animals (see below).” ↩

2. 12b.

   Section Section on evolutionary forces:  “1) Direct natural selection against eyes to conserve energy or mitigate any other disadvantage of having eyes (entry point for infection, prone to injury, etc.).  2) Indirect selection against eyes by selecting for another trait that is negatively linked to eye development.  3) No selection at all.  Simply due to the accumulation of random mutations after relaxed selection for eyes.” ↩

3. 12c.

   Section Section on evolutionary forces:  “None of these theories have been fully proved, and most probably the final answer will be that all three have contributed to some extent.” ↩ ↩

4. 12d.

   Section Section on eye development:  “This appears to be a waste of resources and energy; however, from a neurodevelopmental point of view, it seems to be unavoidable.” ↩

Fumey, Julien et al.  “Evidence for late Pleistocene origin of Astyanax mexicanus cavefish.”  BMC Evolutionary Biology 18:43.  Apr 18, 2018.  A research paper that dated the cave populations by two methods: a program that estimates split times from published microsatellite DNA markers, and a comparison of new SNP data (single-letter DNA differences) from embryos with computer simulations.  It found the caves under 20,000 years old by microsatellites and probably under 30,000 by SNPs, though its dates depend on the mutation rate it assumed.  The article uses it for the under-20,000-year figure from microsatellites.

1. 13a.

   Page 1:  “Twenty-nine cavefish populations have been discovered so far in limestone caves in the Sierra de El Abra region of northeastern Mexico”. ↩

2. 13b.

   Page 1, section Abstract:  “Using IMa2, a program that allows dating population divergence in addition to demographic parameters, we found that microsatellite polymorphism strongly supports a very recent origin of cave populations (< 20,000 years).” ↩ ↩

3. 13c.

   Page 1, section Abstract:  “If cave populations are indeed only several thousand years old, many phenotypic changes observed in cavefish would thus have mainly involved the fixation of genetic variants present in surface fish populations and within a very short period of time.” ↩

4. 13d.

   Page 3:  “we obtained good evidence of a recent origin of all cavefish populations analyzed, e.g. likely less than 20,000 years ago, notwithstanding their "old" or "young" classification.” ↩

5. 13e.

   Page 8:  “good fits could be found between observed and simulated summary statistics when the effective population size of the cave population was much smaller than the surface effective population size and when the divergence was recent, in most cases around 20,000 years”. ↩

Herman, Adam et al.  “The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra, Astyanax mexicanus.”  Molecular Ecology 27(22):4397–4416.  Nov 2018.  A genome study that sequenced 47 whole genomes of the Mexican tetra from three cave populations, two surface populations and outgroup samples used for comparison.  It found that the cave populations come from at least two separate lineages, which split from their nearest surface population about 161k - 191k generations ago, far more recently than the earlier estimate of 5–7 mya (million years ago).  The article uses it for those dates, and for the authors' suggestion that selection, not disuse and drift, may have driven the cave traits; the authors turn generations into years by assuming one generation a year.

1. 14a.

   Section Abstract:  “In this study, we resequenced 47 whole genomes of the Mexican tetra from three cave populations, two surface populations, and outgroup samples.” ↩

2. 14b.

   Section Abstract:  “We confirmed that cave populations are polyphyletic and two Astyanax mexicanus lineages are present in our dataset.  The two lineages likely diverged much more recently than previous mitochondrial estimates of 5–7mya.  Divergence of cave populations from their phylogenetically closest surface population likely occurred between ~161k - 191k generations ago.” ↩ ↩

3. 14c.

   Section Abstract:  “The recency of these estimated divergence events suggests that selection may drive the evolution of cave-derived traits, as opposed to disuse and drift.” ↩

4. 14d.

   Section Results:  “Assuming the generation interval of one year, the oldest estimate for the old and new split is more than an order of magnitude less than that estimated from the cytochrome b which places the divergence time between lineages between 5.7–7.5 mya (Ornelas-García et al. 2008).” ↩

5. 14e.

   Section Discussion:  “Demographic models estimate split time between the two lineages at approximately 257k generations ago, and estimates of cave-surface population splits are ~161k - 191k generations ago.” ↩

6. 14f.

   Section Discussion:  “This suggests that gene flow between caves may hasten adaptation to the cave environment and suggests that repeated evolution in this system may, in part, rely on standing genetic variation.” ↩ ↩

Policarpo, Maxime et al.  “contrasting gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals.”  Molecular Biology and Evolution 38(2):589–605.  Feb 2021.  A genome study that counted broken copies of genes for vision, the body clock and pigmentation in two Cuban cave fish of the genus Lucifuga, one blind and one small-eyed, and compared them with Astyanax and with Chinese cavefish.  It found that the Astyanax cavefish keeps almost all of its eye genes, which the authors read as a sign of a very recent origin; several of its authors also wrote the 2018 dating study.  The article uses it as a third, gene-based clock that points to the same young age.

1. 15a.

   Page 589, section Abstract:  “The limited extent of gene decay in all these cavefishes and the very small number of loss-of-function mutations per pseudogene suggest that their eye degeneration may not be very ancient, ranging from early to late Pleistocene.  This is in sharp contrast with the identification of several vision genes carrying many loss-of-function mutations in ancient fossorial mammals, further suggesting that blind fishes cannot thrive more than a few million years in cave ecosystems.” ↩

2. 15b.

   Page 590:  “The retention of almost all of the eye-specific genes in this blindfish is a paradox under the hypothesis that it evolved millions of years ago, but would be expected under the hypothesis that all A. mexicanus cave populations are very recent (Fumey et al. 2018).” ↩

3. 15c.

   Page 592:  “In A. mexicanus, 86 and 85 vision genes were retrieved from the surface fish and the Pachón cavefish genome, respectively.  Only one pseudogene was found in the Pachón cavefish genome, which is due to a deletion of 11 bp in pde6b”. ↩ ↩ ↩

4. 15d.

   Page 601, section Conclusion:  “the most recent, the Mexican A. mexicanus, during the late Pleistocene or even later in the Holocene.” ↩ ↩

Littleton, Jeanette.  “Designed to Go Blind.”  Answers magazine.  Jul 1, 2016.  A magazine feature for general readers in the Science in Perspective series, arguing that cave fish were designed to lose their sight.  The magazine issue is July–September 2016, and the article was posted on 1 July 2016.  The article uses it as the creationist claim that the cave fish's eye genes are intact, and sets it against the oca2, cbsa and pde6b lesions that it says contradict that claim.

1. 16a.

   The deck, the line printed under the title, reads:  “Scientists once thought cave fish lost their sight by accident.  Now we know they were designed that way!” ↩

2. 16b.

   “A highly developed visual system can use up to 15% of an animal's energy.” ↩

3. 16c.

   “Remember, the fish aren't blind because of information-destroying mutations—their eye genes are all intact.  But the environment changes which genetic instructions are used to build eyes.” ↩ ↩

4. 16d.

   “And even more intriguing: If the blind cave fish are reintroduced to the water outside the cave, within a generation or so, offspring can again be born with fully functioning eyes.” ↩

Tomkins, Jeffrey P.  “Blind Cavefish Illuminate Divine Engineering.”  Creation Science Update, Institute for Creation Research.  Oct 23, 2017.  A Creation Science Update article by Jeffrey Tomkins, the Institute for Creation Research's Director of Life Sciences, who holds a PhD in genetics from Clemson University.  His source for the claim that no mutations were found is the Gore et al. 2017 bioRxiv preprint on promoter methylation, titled An epigenetic mechanism for cavefish eye degeneration.  The article uses it for the creationist claim that no mutations were found, which it says the oca2, cbsa and pde6b lesions contradict.

1. 17a.

   “However, when scientists determined the DNA sequence of different eye development genes in cavefish and compared them to the DNA of normal surface dwelling fish, no mutations were found.” ↩ ↩

Bradic, Martina et al.  “Gene flow and population structure in the Mexican blind cavefish complex (Astyanax mexicanus).”  BMC Evolutionary Biology 12:9.  Jan 23, 2012.  A genetic survey that typed 568 specimens from 11 cave and 10 surface populations at 26 microsatellite loci, short stretches of DNA that differ between individuals and so work as genetic markers.  It found that the cave populations have at least five separate evolutionary origins and came from two surface stocks.  The article sets it against the older picture drawn from mitochondrial DNA.

1. 18a.

   Page 1, section Results:  “The cave populations we studied span the full range of the cave forms in three separate geographic regions and have at least five separate evolutionary origins.” ↩

2. 18b.

   Page 1, section Conclusions:  “The old stock colonized caves at least three times independently while the new stock colonized caves at least twice independently.” ↩

3. 18c.

   Page 2:  “There are 29 known cave populations of this species dispersed over three geographically distinct areas”.  The same count is given by Borowsky 2008 (p. R23), Jeffery 2009 (Fig. 3), Krishnan and Rohner 2017 and Fumey 2018 (p. 1). ↩

4. 18d.

   Page 2:  “The estimates from mtDNA suggest that these two groups diverged about 6.7 Mya”.  Mya means millions of years ago.  The paper cites earlier mitochondrial DNA work for this estimate. ↩

Coyne, Jerry A.  Why Evolution Is True.  Viking, New York.  2009.  A 2009 book on evolution by Jerry A. Coyne.  The article cites it because Coyne keeps both selection (mutations that help) and drift (chance changes that neither help nor hurt) open as causes of eye loss in the dark, and says that eyes cost energy to build.

1. 19a.

   Page 59:  “Like wings, eyes are a burden when you don't need them.  They take energy to build, and can be easily injured.  So any mutations that favored their loss would clearly be advantageous when it's just too dark to see.  Alternatively, mutations that reduced vision could simply accumulate over time if they neither helped nor hurt the animal.” ↩

2. 19b.

   Page 60:  “These include fish (like the blind cave fish you can buy at pet stores), spiders, salamanders, shrimp, and beetles.” ↩

Behe, Michael J.  Darwin Devolves: The New Science About DNA That Challenges Evolution.  HarperOne, New York.  2019.  A 2019 book by Michael J. Behe, the biochemist who argues for intelligent design.  The article cites it because Behe accepts that cave fish descended from sighted ancestors, and explains their lost eyes by random mutations that destroyed structures no longer needed.

1. 20a.

   Page 73:  “Some creatures that live in total darkness, such as cave fish and mole rats, have eyes that can't see due to damaging mutations in genes for functioning eye structures.  Why would a creator endow species with useless structures?  It's hard to fathom.  Yet if the sightless creatures had descended from sighted ones, but over time random mutations destroyed structures that were no longer needed in a changed environment, then the situation would be understandable.” ↩

Yamamoto, Yoshiyuki, and William R. Jeffery.  “Central role for the lens in cave fish eye degeneration.”  Science 289(5479):631–633.  Jul 28, 2000.  A paper in Science whose title says the embryonic lens plays a central role in the loss of the cave fish eye.  Its abstract reports that the eye starts to form in cave embryos and then stops growing and degenerates, and that a surface-fish lens placed in a cave-fish eye cup restores the tissues the cave fish lost.  The article uses it to show that the cave eye is not simply never built.

1. 21a.

   Section Abstract:  “Eye formation is initiated in cave fish embryos, but the eye subsequently arrests and degenerates.  The surface fish lens stimulates growth and development after transplantation into the cave fish optic cup, restoring optic tissues lost during cave fish evolution.” ↩

Rétaux, Sylvie, and Didier Casane.  “Evolution of eye development in the darkness of caves: adaptation, drift, or both?”  EvoDevo 4:26.  Sep 30, 2013.  A review of how cave animals lose their eyes, drawing on developmental biology and molecular evolution, with Astyanax mexicanus as the cavefish it studies most closely.  Its two authors, both at CNRS in France, conclude that genetic drift and selection both acted, and they note that the favoured hedgehog explanation for eye loss has no genetic correlate yet, meaning no matching genes among the known eye loci.  The article uses it as the fullest statement of the dispute.

1. 22a.

   Page 1, section Abstract:  “We conclude that both genetic drift (neutral hypothesis) and direct and indirect selection (selective hypothesis) occurred together during the loss of eyes in cave animals.” ↩

2. 22b.

   Page 8:  “It should be noted, though, that the "developmental Hedgehog hypothesis" does not have a genetic correlate: the genomic regions encompassing Hedgehog genes are not among those that contain the 12 QTLs (quantitative trait loci) identified for the control of eye and lens size in Pachón cavefish [43].  Other factors, possibly upstream of Hedgehog, must be involved.” ↩ ↩ ↩

3. 22c.

   Page 8:  “why do cavefish first develop eyes, before undergoing a progressive degeneration process?  It looks like an unnecessarily complex and energetically costly developmental pathway.  We think that such a process is the consequence of a strong developmental constraint at early stages of forebrain development in vertebrates.” ↩

Gross, Joshua B., and Horst Wilkens.  “Albinism in phylogenetically and geographically distinct populations of Astyanax cavefish arises through the same loss-of-function Oca2 allele.”  Heredity 111(2):122–130.  2013.  The abstract reports that albinism, the loss of pigment, in captive Micos cavefish is caused by the same loss-of-function allele, a version of the gene that stops it working, as in Pachón cavefish.  The article uses it to show that caves in different lineages can share one gene variant.

1. 23a.

   Section Abstract:  “The appearance of albinism in captive Micos cavefish, caused by the same loss-of-function allele present in Pachón cavefish, implies that geographically and phylogenetically distinct cave populations can evolve the same troglomorphic phenotype from standing genetic variation present in the ancestral taxon.” ↩ ↩

Rohner, Nicolas et al.  “Cryptic variation in morphological evolution: HSP90 as a capacitor for loss of eyes in cavefish.”  Science 342(6164):1372–1375.  Dec 13, 2013.  A laboratory study in which surface fish were given radicicol, a drug that blocks HSP90, a protein that helps other proteins fold and so buffers genetic variation.  The drug exposed hidden variation in eye size, and by breeding for smaller eyes the team got reduced-eyed fish even with HSP90 working normally.  The article uses it to show that some of the cave eye alleles were already present in the surface fish.

1. 24a.

   Section Abstract:  “We provide evidence that HSP90 phenotypically masks standing eye size variation in surface populations of the cavefish Astyanax mexicanus.  This variation is exposed by HSP90 inhibition, and can be selected for, ultimately yielding a reduced-eye phenotype even in the presence of full HSP90 activity.  Raising surface fish under conditions found in caves taxes the HSP90 system, unmasking the same phenotypic variation as direct inhibition of HSP90.” ↩ ↩

Bilandžija, Helena et al.  “Phenotypic plasticity as a mechanism of cave colonization and adaptation.”  eLife 9:e51830.  Apr 21, 2020.  A laboratory experiment that raised surface-dwelling Mexican tetra in complete darkness for up to two years and compared them with fish kept on a normal day and night cycle.  Most of the altered traits mimicked cave fish, and they arise through plasticity rather than new mutations.  The article cites it in its discussion of where the cave traits came from, for the point that some of them can appear with no new mutation at all.

1. 25a.

   Page 1, section Abstract:  “Our results indicate that many cave-related traits can appear within a single generation by phenotypic plasticity.” ↩

Jeffery, William R.  “Adaptive evolution of eye degeneration in the Mexican blind cavefish.”  Journal of Heredity 96(3):185–196.  2005.  A 2005 paper by William R. Jeffery arguing that the cave eye could have been lost by default, as a side effect of selection for useful traits such as feeding structures.  Pleiotropy, where one gene affects several traits at once, is the mechanism it names.  The article uses it as the alternative to the view that selection removed the eye directly.

1. 26a.

   Section Abstract:  “Accordingly, eyes could have been lost by default as a consequence of natural selection for constructive traits, such as feeding structures, which are positively regulated by Hh signaling.  We conclude from these studies that eye degeneration in cavefish may be caused by adaptive evolution and pleiotropy.” ↩

Wieland, Carl.  “Let the blind see … Breeding blind fish with blind fish restores sight.”  Creation Ministries International.  Jan 10, 2008.  A pre-publication version of a short article, later printed in Creation 30(4):54–55, on a 2008 New York University study in which crosses between four blind cave fish populations restored some sight, and in some crosses nearly 40 percent of the offspring could see.  Its science comes from the university's press release of 8 January 2008, not from the paper, which was later formally published in Current Biology.  The article calls it the most careful creationist treatment of the crosses and uses it for Wieland's prediction about how long the fish have been in the dark.

1. 27a.

   “Because the same defect (eye loss) was caused by different genes being damaged in each of the populations, 'when you cross them, the genetic deficiencies in one lineage are compensated for by strengths in the other, and vice-versa.'” ↩

2. 27b.

   “Cave fish have arisen by processes that in fact demonstrate the opposite—deterioration of function, consistent with the 'natural' direction of genetic change in a fallen world.” ↩

3. 27c.

   “If anything, the degree of restoration of even the brain connections suggests that there has not been enough time for significant mutational deterioration to occur in most or all of the genetic instructions needed for eyesight (remember that natural selection is not going to preserve any of the eye-constructing genes).” ↩

4. 27d.

   “It is also because the possibility of such a reconstruction would get progressively less likely, the more time that has elapsed since the fish were originally confined to their underworld existence.” ↩

Thomas, Brian.  “Evolution Made Cavefish Go Blind?”  Creation Science Update, Institute for Creation Research.  Feb 7, 2012.  A short news commentary by Brian Thomas, a science writer at the Institute for Creation Research, on a 2012 study by Martina Bradic and colleagues in BMC Evolutionary Biology.  The study compared DNA from 11 cavefish populations with 10 related populations that can see, and found that the cave populations arose at least five times independently.  The article uses it because Thomas reported the study's five origins accurately and drew the information argument from them.

1. 28a.

   “But obtaining the fish sight system required an input of a massive quantity and quality of information.  And making the fish blind merely required the loss of some of that information.” ↩

Mitchell, Elizabeth.  “How Cavefish Went Blind, and Why It Matters.”  Answers in Genesis, News to Know.  Feb 17, 2014.  A short News to Know commentary by Elizabeth Mitchell of Answers in Genesis, on new research suggesting that a molecular chaperone, HSP90, may mask mutations in cavefish until the stress of the cave exposes them.  She argues that blind fish from different caves produce sighted offspring when crossed, so the fish did not evolve their blindness.  The article uses it as a creationist source that conceded loss: she writes that the lost information for sight was reassembled when the populations were reunited.

1. 29a.

   “Evolutionists believe it took 2 to 3 million years for cavefish to "evolve" their blindness.  Yet blind cavefish from different regions, when crossbred, produce sighted offspring in only one generation.  These fish had not evolved blindness.  They were just blind variants of the same kind of fish.  When populations that had lost their genetic information for sight while isolated were reunited, the genetic information for proper eyes was reassembled like the pieces of a puzzle.” ↩

Thomas, Brian.  “Blind Cavefish Shed Light on Creation.”  Creation Science Update, Institute for Creation Research.  Jan 8, 2014.  A short Creation Science Update article by Brian Thomas of the Institute for Creation Research.  The article uses it for the creationist shift after Rohner's 2013 HSP90 paper in Science, when the tone changed from calling the cave fish's blindness loss to calling it design.

1. 30a.

   “But the sightless Mexican tetra exhibits development of helpful, cave-specific traits—not from harmful mutations but through genetic variability buffered by HSP90.” ↩

Ham, Ken.  “Does Evolution Go Backward? A Look at Blind Cave Fish.”  Answers in Genesis, Ken Ham blog.  Feb 20, 2023.  A blog post by Ken Ham, responding to a news report of a new cave fish species, Sinocyclocheilus, found in a dining table-size pool in a Chinese cave, which the report hailed as regressive evolution.  Ham says the post was "written with the assistance of AiG's research team."  The article cites it for the claim that the genes for eye development are switched off and back on within one generation.

1. 31a.

   “These changes cause the genes for eye development to be "turned off"—and it can happen in just one generation and likewise be "reversed" in just one generation!” ↩