[…]Monstrosities cannot be separated by any clear line of distinction from mere variations.
– C. Darwin, Origin of Species, Chapter I.

(When I get around to registering on ResearchBlogging, I will link there as well.)

My contribution to celebrating the 200th anniversary of Darwin’s birth will be to touch on how the study of eye development and the genes involved is one kind of daily reminder that variation and natural selection are constantly underway in humans as in all other living beings. Yes, Darwin was wrong in a number of details that I could discuss here, but there is much truth in his theory as borne out by a myriad of subsequent observations and experiments, and it is still a robust one on which to hang one’s hat.

Most of you reading this blog have eyes. You might be hard-pressed to imagine your life without them. Not everyone is born with eyes, though. Children with congenital anophthalmia have the most severe ocular malformation possible. If you or someone you know underwent an ultrasound during pregnancy and the doctor could not find the foetus’ eyes or only residual bits in the sockets, you would want to know why, how, whether the child would be born not only blind but afflicted with any additional physical or mental handicaps, and if future children or grandchildren are likely to be affected as well. This is where genetic counseling can be helpful¹. The answers, which are not always straightforward to give, go back to that abstract concept, the gene.

Refresher in genetics

How does a gene work in an embryo to influence formation of a complex structure such as the eye? Remember, we all start out as a single cell with an equal part of genetic information from our mother and our father, such that you end up with two copies of each gene blueprint for every protein in your body. (If you only need one copy to get an effect with that protein, this is dominant inheritance, whereas if you need both parental copies of the protein for it to be effective, that is recessive inheritance.)

Before fertilization, each egg and each sperm that could meet from your parents had undergone a major reshuffling of your grandparents’ genes. From your mother, every cell in your body has a salt-and-pepper contribution of gene versions that come either from your grandfather or your grandmother; from your father, a similar salt-and-pepper contribution from his parents. If you could trace the origins of your DNA back further, it would be an even more fragmented kaleidoscope of bits and pieces from your maternal and paternal great-grandparents. Through this process of recombination, as well as infrequent copy errors that get introduced as the cells multiply in our bodies, each of us is perfectly unique over the set of all possible gene blueprints for proteins. Each cell that ever constituted our bodies had the same complement of DNA. And yet, some genes and the proteins they encode are absolutely identical among all humans; when they are not, the changes lead to severe congenital malformations.

Genes that will brook hardly any variation in order to make a functional protein are “conserved”. If they are important in the developmental processes leading to the construction of a vital organ or a body axis, and if there are analogous structures in other animals, genes are not conserved only among the members of a given species, but across species. If genes are conserved across species then they have been conserved over time, consistent with Darwin’s idea that species arise over time through the acquisition and then natural selection of some variations. Spontaneous variations happen at a fairly low rate but still, they happen all the time in all parts of our DNA, thanks to parental exposure to mutagens such as oxygen, radiation, or environmental chemicals or subsequent misrepairs in aging eggs and sperm.

Variations in conserved genes can be hazardous for your health

Changes to conserved genes used in the forming embryo can have such a drastic effect on that particular member of the species that it will often have some disadvantage in survival and consequently, in reproduction. Thus, the conservation of gene sequences between the laboratory model embryos of the Drosophila fruit fly and the mouse is a good indication that those genes, among the others, are vital for the survival of the individual.

All of the genes that have been identified as mutated in congenital anophthalmias to date are very highly conserved². Some of those 30 children in a million births who have congenital anophthalmia can receive a molecular diagnosis and thereby, they and their families can receive some answers to the questions above. Families with multiple cases of anophthalmia are ultra-rare but not unknown, thanks to the possibility for blind people to prosper in some societies. Others can not get the answers that come with molecular diagnosis, which is motivation for people like me to look for additional genes. Developmental biologists know of plenty more genes involved in eye development, because in model organisms, mutations in such genes also lead to major eye defects. These “eye” genes thus become good candidates for human malformations. There are so many genes like this, however, that with current technologies it is not feasible to screen all of them for mutations.

Transcription factor society

Not only is it possible that mutations within a gene itself can affect the protein it was supposed to encode the instructions for making, but mutations on the rest of the DNA between genes can affect how well the instructions are copied and sent off to the cytoplasm for synthesis. In the first case, it is as if pages got shuffled, dropped or smudged in the elaborate instructions for building your lawnmower; in the second case, it’s as if the instructions were either never included in your kit or got packed in the kit for a bookcase, in which case the new owner of the bookcase would put the useless instructions right into the recycling bin. Either way, you get a lot of weeds in your front yard, unless you can borrow a mower or scythe from your neighbor. (One would also need to distinguish between variations that matter and variations that don’t; some typographical errors in those instructions could be tolerated, and a new version with a schematic might actually be far more successful. This lack of discrimination is why large-scale sequencing will not be an immediate panacea for human genetics.)

Transcription factors get those booklets written and printed to begin with. A mutation in the gene encoding a transcription factor may have a similar effect to a mutation in non-coding DNA between genes, to which a transcription factor usually binds. Either way, garbled or no instructions. The second sort of mutation is difficult to tell apart from ordinary variations in DNA sequence that are tolerated and propagated because they do not have any effect at all, since the reasons a transcription factor binds DNA in a particular location are only just being worked out.

As some cells in the embryo become different from others over time, the head and tail, middle and lateral and front and back acquire their fates. Position becomes, to some extent, destiny. Progressive series of distinct reactions to their immediate neighborhood by daughter cells lead to increasingly diverse lineages of cells. The eye is no exception to this procedure. Cells get restricted over time in a process highly analogous to speciation – in the end, a liver cell can not substitute for a retinal cell, although they did once have a common ancestor, and a pluripotent embryonic stem cell has as much potential to integrate into a liver as into an eye. (I could go off on a wonderful tangent here, but will restrain myself.)

Nearly all of the genes involved in anophthalmia are genes that, when actively being used to make protein, make the sort of proteins that instruct the cell to activate other genes. Such proteins are known as transcription factors. Genes making transcription factors in effect lord it over other genes – yes, there is a class system in the cell. (There are even housekeeping³ genes!). There are not only lords, but earls and countesses and princes and empresses. Genes that when mutated cause anophthalmia, when activated normally do much the same as a prince who orders a castle to be built in a particularly strategic spot. He needs to have cleared it with the empress, whose benevolent accord will have been necessary if not sufficient, and he may not know the least thing about brick-laying. But the castle will be built nonetheless, if the material conditions are present. And then you can get hired to mow the lawn out front with your newly assembled mower.

Some genes that when mutated cause anophthalmia, will only affect the eye, but others will also affect other organ systems, leading to malformation syndromes. Getting at the reasons behind such associations of symptoms is why careful nosology, or the appropriate description of disease, is still relevant and a vital component of human genetics. One syndromic anophthalmia gene, STRA6, encodes a protein conduit to help to get vitamin A efficiently into cells⁴. Stra6 was originally described in the mouse⁵, but it is also conserved in the cow, and based on a highly similar sequence, it appears to exist in the chicken as well. Once inside a cell, vitamin A can be converted into a transcription factor that directs the formation of many organ systems, not just the eye. Among these, the heart, the lung and the diaphragm⁶. In areas of the world where vitamin A deficiency can still be a problem, or in cases of vitamin overdose, terrible and sometimes lethal malformations in any or all of these other organ systems can occur, (probably) independent of the STRA6 gene sequence. The syndromic anophthalmia due to STRA6 mutation is a recessive condition⁷. One functional copy of the gene can pick up the slack for the other, until an embryo develops with a mutant copy from each of its two parents, so there is no particular selection for or against carriers based on this one criterion.

Intention or selection?

I recently came across this quote from an essay that originally appeared in 1997, but still present on a creationist website called “Answers in Genesis”:

“The cuttlefish also has eyes which are similar in construction to human eyes, but evolutionists [sic] do not believe it has any direct evolutionary relationship to humans (i.e. there is no possible ancestor to both cuttlefish and humans which could have had such an eye). So this similarity is explained away as ‘convergent evolution’: the eyes of the cuttlefish and other cephalopods ‘evolved independently’ to humans. In other words, it is simply an evolutionary coincidence. However, the similarity in the design of both the cuttlefish and human eye is easily explained—they had the same Designer!”

Science is all about generating and then testing and re-testing hypotheses. Darwin’s theory of natural selection works for me because I can make predictions based on it, and confirm them with experiments which give results I can observe and challenge again. Walter Gehring’s group took a copy of the mouse Pax6 gene, so conserved that it is still extremely similar to the fruit fly’s version of the same gene and engineered it into a fly such that it would be turned on in developing antennae and wings. Extra (compound, or fruit-fly-appropriate) eyes then developed in those places⁸ ! Why? Because certain outer bits of all early Bilaterian embryos have the capacity to respond to the ultra-conserved Pax6 protein – they speak the right language and therefore understand the building orders of the prince, as it were. If that is true, then a similar experiment should work in the frog embryo, too. It does⁹.

We did evolve from a common ancestor with the cuttlefish. This common ancestor used a Pax6 gene to induce a light-sensitive ocular structure in the ectoderm. In this much, the human eye is indeed a homologous structure to that of a cuttlefish or even that of a fly. What differs, and the reason we are unique as individuals and as a species, has everything to do with the complex context I tried to touch upon herein. Even starting with conserved genes, the cellular context will become more and more divergent in the eye of a developing embryo of a fly or cuttlefish relative to that of a human, until we observe today’s result in each species, which will depend in the details in part on genes that have a human-, fly- or cuttlefish-specific function. This evolving understanding continues to develop. Omnia mutantur nos et mutamur in illis.

There is an elegant and more polished review developing similar themes to this blog post in today’s issue of Nature, by Neil Shubin, Cliff Tabin & Sean Carroll. If you don’t have access to it, I can help you out with that.

“Whoever is led to believe that species are mutable will do good service by conscientiously expressing his conviction; for only thus can the load of prejudice by which this subject is overwhelmed be removed."
C. Darwin, Origin of Species, Chapter XIV

-References-

¹ Verma and Fitzpatrick, 2007. Orphanet J Rare Dis. 2:47.

² Nilsson et al. 2004. Current Opinion in Neurobiology 2004, 14:407–414.

³ Eisenberg et al., 2003. Trends in Genetics Vol.19 No.7.

⁴ Kawaguchi et al., 2007, Science 315(5813):820-5.

⁵ Bouillet et al., 1997. Mech. Dev. 63, 173

⁶ Golzio et al., 2007. Am J Hum Genet. 80(6):1179-87.

⁷ Pasutto et al., 2007. Am J Hum Genet. 80(3): 550–560.

⁸ Halder et al., 1995. Science 267 (5205): 1788.

⁹ Onuma et al. 2002. Proc Natl Acad Sci U S A. 99(4): 2020–2025.