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.

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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)

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)

Grace under pressure

The BBC is running an interview with Dame Jocelyn Bell-Burnell, and it’s very good. Bell-Burnell is the woman who discovered pulsars, and until I heard this interview, I hadn’t realized how it was done.

Yeah, there weren’t computers available so the reams of data came out on strip chart – paper chart – and the configuration produced a hundred foot a day and I ran it for six months, which gave me about three miles of paper, which I had to analyse by hand. I would go through the charts and I would log where I saw what I thought were quasars and I also saw that there were chunks of manmade interference – artificial interference. But just occasionally, one time out of five or one time out of 10, when we looked at a particular bit of sky there was this additional signal that didn’t look exactly like a quasar, didn’t look exactly like low level interference, occupied about a quarter inch of the chart.

So…spotting periodic quarter inch blips scattered on 3 miles of paper. I don’t want to hear any of you students complaining about your daily grind any more!

Unfortunately, she was robbed: she discovered pulsars, it was her persistence that got her advisor to take the observations seriously, after initially dismissing the whole idea — and guess who won the Nobel in 1974 for the discovery? Her advisor, and not Jocelyn Bell-Burnell. She does not complain, however; those were the facts of life.

I think at that time science was perceived as being done by men, senior men, maybe with a whole fleet of minions under him who did his bidding and weren’t expected to think. I believe the Nobel Prize committee didn’t even know I existed.

And then the newspapers covered pulsars, and called her the “girl”…

Oh yes and worse than that what were my vital statistics and how tall was I and you know – chest, waist and hip measurements please and all that kind of thing. They did not know what to do with a young female scientist, you were a young female, you were page three, you weren’t a scientist.

Apparently, it was also the custom when she was a student in Glasgow for the men to stamp their feet and wolf-whistle whenever a woman walked into a lecture hall, and she of course was the only woman in the entire physics program at the time.

None of this could possibly have influenced the career decisions of an entire generation of women, I’m sure.

(Also on Sb)

What have my students been thinking about lately?

I gave them an exam, that’s what. That and long boring lecturings at 8am on pattern formation in the nervous system. But otherwise, I’ve had them blogging, so we can take a peek into the brain of a typical college student and see what actually engages them.

I understand these are all the things all college students everywhere are contemplating.

(Also on Sb)

Watts wrote a check he couldn’t cash

That wacky climate change denier and radio weather broadcaster Anthony Watts took a brave step a while back, and I commend him for it. He was enthused about an independent research project, the Berkeley Earth Project, that would measure the planet’s temperature over the last centuries and compare it to the work of NOAA and NASA on earth’s temperature — he apparently expected that it would show that NASA and NOAA had been inflating the data. He was so confident that he went on the record saying:

I’m prepared to accept whatever result they produce, even if it proves my premise wrong.

Excellent! That’s a good scientific attitude.

So the results have been published, and they look like this:

Results from the Berkeley Earth project data fits existing NASA and NOAA temperature records like a glove

You can probably see the NASA/NOAA data wiggling beneath the dark bold line of new data from the Berkeley Earth Project. They’re rather…close. Intimate, even.

What do you think Anthony Watts’ response was?

I consider the paper fatally flawed as it now stands, and thus I recommend it be removed from publication consideration by JGR until such time that it can be reworked.

Yep. Didn’t give the results he wanted. Therefore, the experiment is bad.

(Also on Sb)

How to examine the evolution of proteins

In my previous post, I described the misguided approach Gauger and Axe have taken to criticizing evolution, and one of the peculiarities of their criticism is that they cited another paper by a paper by Carroll, Ortlund, and Thornton which traced (successfully) the evolutionary history of a class of proteins. Big mistake. As I pointed out, one of the failings of the Gauger/Axe approach is that they’re asking how one protein evolved into a cousin protein, without considering the ancestral history …they make the error of trying to argue that an extant protein couldn’t have directly evolved into another extant protein, when no one argues that they did.

The tactical error is that right there in the very first paragraph of their paper, Carroll, Ortlund, and Thornton point out the fallacy of what the creationists were doing.

Direct comparisons among present-day proteins can sometime yield insights into the sequence and structural mechanisms that underlie functional differences. Such “horizontal” comparisons, however, cannot determine which protein features are ancestral and which are derived, so they are not suited to reconstructing the events that produced functional diversity.

They don’t mention Gauger and Axe, of course — this paper was written before the creationists wrote theirs — but a methodological flaw is still spelled out plainly, the creationists reference it so I presume they read it, and they still charged ahead and did their flawed study, and then had the gall to claim their work was superior.

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