How many genes does it take to make a squid eye?

This is an article about cephalopods and eye evolution, but I have to confess at the beginning that the paper it describes isn’t all that interesting. I don’t want you to have excessive expectations! I wanted to say a few words about it, though, because it addresses a basic question I get all the time, and while I was at it, I thought I’d mention a few results that set the stage for future studies.

I’m often asked to resolve some confusion: the scientific literature claims that eyes evolved multiple times, but I keep saying that eyes show evidence of common origin. Who is right? Why are you lying to me, Myers? And the answer is that we’re both right.

[Read more…]

How many genes does it take to make a squid eye?

This is an article about cephalopods and eye evolution, but I have to confess at the beginning that the paper it describes isn’t all that interesting. I don’t want you to have excessive expectations! I wanted to say a few words about it, though, because it addresses a basic question I get all the time, and while I was at it, I thought I’d mention a few results that set the stage for future studies.

I’m often asked to resolve some confusion: the scientific literature claims that eyes evolved multiple times, but I keep saying that eyes show evidence of common origin. Who is right? Why are you lying to me, Myers? And the answer is that we’re both right.

Eyes evolved independently multiple times: the cephalopod eye evolved about 480 million years ago, and the vertebrate eye is even older (490 to 600 million years), but both evolved long after the last common ancestor of molluscs and chordates, which lived about 750 million years ago. The LCA probably did not have an image-forming eye at all.

And that’s the key point: a true eye is a structure that has an image forming element, a retina, and some kind of morphological organization that allows a distant object to form a pattern of light on that retina. That organization can be something as simple as a cup-shaped depression or pinhole lens, or as elaborate as our camera eye, or an insect’s compound eye, or the mirror eyes of a scallop. An eye is photoreceptors + structure. Eyes have evolved multiple times; they’ve even evolved multiple times within the phylum Mollusca, and different lineages have adopted different strategies for forming images.

i-0f6286e48f36b86c30ae81bdbfc6f415-eye_phylo-thumb-500x210-70144.jpeg
(Click for larger image)

Phylogenetic view of molluscan eye diversification. Camera eyes were independently acquired in the coleoid cephalopod (squids and octopuses) and vertebrate lineages.

The LCA probably didn’t have an eye, but it did have photoreceptors, and the light sensitive cells were localized to patches on the side of the head. It even had two different classes of photoreceptors, ciliary and rhabdomeric. That’s how I can say that eyes demonstrate a pattern of common descent: animals share the same building block for an eye, these photoreceptor cells, but different lineages have assembled those building blocks into different kinds of eyes.

Photoreceptors are fundamental and relatively easy to understand; we’ve worked out the full pathways in photoreceptors that take an incoming photon of light and convert it into a change in the cell’s membrane properties, producing an electrical signal. Making an eye, though, is a whole different matter, involving many kinds of cells organized in very specific ways. The big question is how you evolve an eye from a photoreceptor patch, and that’s going to involve a whole lot of genes. How many?

This is where I turn to the paper by Yoshida and Ogura, which I’ve accused of being a bit boring. It’s an exercise in accounting, trying to identify the number and isolate genes that are associated with building a camera eye in cephalopods. The approach is to take advantage of molluscan phylogeny.

As shown in the diagram above, molluscs are diverse: it’s just the coleoid cephalopods, squid and octopus, that have evolved a camera eye, while other molluscs have mirror, pinhole, or compound eyes. So one immediate way to narrow the range of relevant genes is a homology search: what genes are found in molluscs with camera eyes that are not present in molluscs without such eyes. That narrows the field, stripping out housekeeping genes and generic genes involved in basic cellular processes, even photoreception. Unfortunately, it doesn’t narrow the field very much: they identified 5,707 candidate genes that might be evolved in camera eye evolution.

To filter it further, the authors then looked at just those genes among the 5,707 that were expressed in embryos. Eye formation is a developmental process, after all, so the interesting genes will be expressed in embryos, not adults (a sentiment with which I always concur). Unfortunately, development is a damnably complicated and interesting process, so this doesn’t narrow the field much, either: we’re down to 3,075 candidate genes.

Their final filter does have a dramatic effect, though. They looked at the ratio of non-synonymous to synonymous nucleotide changes in the candidate genes, a common technique for identifying genes that have been the target of selection, and found a grand total of 156 genes that showed a strong signal for selection. That’s 156 total genes that are different between coleoids and other molluscs, are expressed in the embryonic eye, and that show signs of adaptive evolution. That’s manageable and interesting.

They also looked for homologs between cephalopod camera eyes and vertebrate camera eyes, and found 1,571 of them; this analysis would have been more useful if it were also cross-checked against other non-camera-eye molluscs. As it is, that number just tells us some genes are shared, but they could have been genes involved in photoreceptor signalling (among others), which we already expect to be similar. I’d like to know if certain genes have been convergently adopted in both lineages to build a camera eye, and it’s not possible to tell from this preliminary examination.

And that’s where the paper more or less stops (I told you not to get your hopes up too high!) We have a small number of genes identified in cephalopods that are probably important in the evolution of their vision, but we have no idea what they do, precisely, yet. The authors have done some preliminary investigations of a few of the genes, and one important (and with hindsight, rather obvious) observation is that some of the genes are expressed not just in the retina, but in the brain and optic lobes. Building an eye involved not just constructing an image-forming sensor, but expanding central tissues involved in processing visual information.


Fernald RD (2006) Casting a genetic light on the evolution of eyes. Science 313(5795):1914-8.

Yoshida MA, Ogura A (2011) Genetic mechanisms involved in the evolution of the cephalopod camera eye revealed by transcriptomic and developmental studies.. BMC Evol Biol 11:180.

(Also on FtB)

Why I am an atheist – Sophie Davis

Am I an atheist? I guess I am, I have never defined myself and put it in a box, but I guess when an opportunity arises… I am a non believer, that’s to say my thoughts are justified by evidence and theory that, to the best of my knowledge explains the truth. As a child I believed in Santa and the tooth fairy and God. .. Not because of my parents, who are distinctly non-religious. I believed, simply because I thought ‘why not?’ Perhaps I wouldn’t have ever known about God was it not for my Church of England schooling, where prayer and bible studies were a common occurrence. As I grew and with it my curious mind, I began to ask why? And How? And what is the evidence for this? My parents never pressured me to be an atheist but instead encouraged me to question and take nothing for granted. As I questioned the less convinced I became and in the blink of an eye my religious phase was over and in its place a much more long lasting love that has lasted to this day. Science, one great adventure that will take a lifetime to learn.

I will always remember a conversation I had with a Mormon at University, out on one of their recruiting missions. He asked me ‘do you pray?’ I replied ‘no’ to which he said ‘How do you know what God has planned for you? And what the point of your life on earth is?’ I explained to him that I did not long for an inherent purpose to my life and any purpose made would be my own. I told him I was a scientist and that understanding everything in life from the behaviour on animals to the orbit of the planets was my life’s work, and that from each piece of knowledge I gained I found great contentment in life. After a little pause he told me he was happy for me. I felt great sadness, that he would not appreciate the great contentment found in the facts of science and nature and instead would lead a life in fear of God.

I live my life knowing it’s the only one I will have and I live it to the full. I guess that makes me lucky, lucky not to be indoctrinated into a way of life or follow unquestioningly something that is taken on blind faith. I love to live and I live to love. Through great chance this planet has come into existence. Through great chance this planet has evolved to sustain life, through great chance I was one of the millions of possibilities my parent’s genes would mix to make me. Through great chance I was born into a family that does not practice brain washing. By great CHOICE I became an atheist, and that makes me…. one of the lucky ones.

Sophie Davis
United Kingdom

Episode CCLXVI: The Pharyngula bump?

Recently, that goofy guru Deepak Chopra thanked me on Twitter for helping his book, whatever it was, become a NYT bestseller. It would be nice to imagine that I have some fraction of the power of Colbert or Oprah, but I think he was indulging in some wishful thinking. So what else is new?

Anyway, just because I can, here’s a short video of a young woman asking Chopra a straightforward question…which he is unable to answer. His mouth moves, his lips flap, his tongue wiggles, but no sense comes out. Again…so what else is new?

(Episode CCLXV: I like turtles)

I have a bad feeling about this

August Berkshire is debating a local pastor, Martin Bownik, Wednesday night, on the subject of “Why would Jesus need to die for my Sins?” It’s a dorktastic organization and a ridiculous topic that begs the whole question (my answer: there was no Jesus, blood sacrifice by proxy is barbaric and stupid, so it doesn’t even deserve addressing), but August is a calm-tempered fellow who’ll probably let them hang themselves on their own rope. Here’s where you can go to listen:

26 October, 7pm
The Mann Theatre Maple Grove
13644 80th Circle, Maple Grove, MN

It’s being advertised on facebook, and of course the wacky pastor wrote the copy and is busily recruiting his deluded followers to show up.

Come hear an Atheist and a Pastor share their thoughts on the subject of Christs death. You don’t want to miss this special event! Speakers will be August Berkshire and Pastor Martin Bownik. This is event is being sponsored by KKMS radio 980 am and The EDGE Christian Fellowship Church

Reading the comments (sample: “I pray the Atheist will be saved, in Jesus name”), I’m afraid this debate is simply going to be packed with zombie gomers. Any rational atheists want to show up and give August some backup?


Word is that it will also be broadcast on KKMS, the worst, sleaziest, most dishonest radio station in the Twin Cities. This does not reassure me.

Someone tell Santa about good kids’ books

There aren’t enough children’s books telling the story of evolution — every doctor’s office seems to be stocked with some ludicrous children’s book promoting that nonsensical Noah’s ark story, but clean, simple, and true stories about where we came from are scarce. Here’s one, a new children’s book called Bang! How We Came to Be by Michael Rubino. Each page is formatted the same: on the left, a color picture of an organism (or, on the early pages, a cosmological event); on the right, a short paragraph in simple English explaining what it is and when it occurred. The book just marches forward through time, showing us where our species came from. Easy concept, nice execution, and it fills a gap in children’s literature.

It’s short enough to be good bedtime reading, and simple enough for pre-schoolers. The illustrations are thought-provoking enough for older kids, but won’t keep them engaged for too long — they’ll be asking for more books to satisfy their curiosity about these strange creatures that lived billions or hundreds of millions or tens of millions of years ago. Which is exactly what we want to do to our kids, right?

(Also on Sb)

MRAs are almost as hilarious as creationists

I swear, it’s the same oblivious stupidity, just expressed in a different domain, and I deal with enough inanity trying to cope with creationionism — I should probably avoid this stuff lest I suffer an overdose. But Manboobz hurts me again, and I can’t turn my eyes away. This is a real revelation about how these guys think:

[W]hen most men pass the age of 30-35, they begin to awaken from this biochemical “dream” and what do they awaken beside? What do married men look forward to the next 30-50 years of their lives? Sleeping with a living corpse, which continues to torture and destroy them day by day? Looking forward to the time when the woman undergoes the process of metamorphosis, into a completely insane mummy (menopause and post menopause)?

Pussy is indeed way overrated and if younger men could get a shot of “anti-testosterone” for a few weeks, they could see through the eyes of men who are 40+; without the haze of hormones, you cannot believe how much farther you can see! It’s the difference between seeing the horizon through LA style smog and seeing the horizon from a high mountain in the Rockies.

Guys, you’re doing it wrong. I don’t think your wives are the insane ones, it’s you.

If you’re doing it right, the relationship gets stronger and the sex gets better the older you get; while I might well be willing to trade in my sputtering 50+ year old body for a 20 year old model, I would not ever want to exchange the kind of sex I get at 50+ for the kind I got at 20 (which was great, don’t get me wrong, but experience in these matters really does improve everything). People who look at their spouses as hostile occupiers are just weird, sick, and deprived individuals; I simply don’t get it.

I also like my testosterone, thank you very much. If those wackos were serious, there really is an easy fix: a do-it-yourself orchidectomy. Just think, a little knife work, and his vision will be so clear it’ll be like sitting on board the space telescope.

Someone tell Santa about good kids’ books

There aren’t enough children’s books telling the story of evolution — every doctor’s office seems to be stocked with some ludicrous children’s book promoting that nonsensical Noah’s ark story, but clean, simple, and true stories about where we came from are scarce. Here’s one, a new children’s book called Bang! How We Came to Be by Michael Rubino. Each page is formatted the same: on the left, a color picture of an organism (or, on the early pages, a cosmological event); on the right, a short paragraph in simple English explaining what it is and when it occurred. The book just marches forward through time, showing us where our species came from. Easy concept, nice execution, and it fills a gap in children’s literature.

It’s short enough to be good bedtime reading, and simple enough for pre-schoolers. The illustrations are thought-provoking enough for older kids, but won’t keep them engaged for too long — they’ll be asking for more books to satisfy their curiosity about these strange creatures that lived billions or hundreds of millions or tens of millions of years ago. Which is exactly what we want to do to our kids, right?

(Also on FtB)