A Fish Eye View

One of the most interesting sections of Darwin’s On the Origin of Species may be his struggles with perceived perfection in nature.  In Chapter 6 Darwin confronts the organ of which William Paley would be most proud - the remarkable eye, and wonders how such a structure could have possibly evolved through his mechanism of natural selection.  Darwin, of course, goes on to provide a perfectly sensible explanation, but little did he know at the time how many evolutionary wonders the eye would hold.  Others have posted on the evolutionary intricacies of eye development.  A vast literature has detailed how photon capturing opsin proteins in the retina become fine-tuned to the visual demands of specific environments.  Perhaps less appreciated is the evolution of the biological lens.  So I thought I would throw a little lens evolution into the Darwin celebratory mix.

Of course you do not need a lens to see.  The nautilus does just fine without one.  But the benefits of a lens are strong enough that they have evolved across the animal phyla, and even occur in at least one protist.  The function of the lens is to provide a dense structure that will refract light on its way to the retina.  A common solution for making a lens is to express proteins at very high concentrations, especially in aquatic eyes that do not get the benefit of refraction from the cornea.  But interestingly, different organisms use different proteins to do the job.  And as Darwin would have predicted, these proteins are not created de novo, but are borrowed from other parts of the body.  While debates rage about whether the developmental mechanisms to make an eye evolved once or multiple times, the lens clearly has multiple origins.  And each time, organisms have drawn from their biochemical toolbox when producing proteins at high concentration in the lens.  These densely packed lens proteins have diverse evolutionary sources, but they are all referred to as lens crystallins.

Where did lens crystallins come from?  Some are basic housekeeping enzymes, others are protective proteins produced by cells when they are stressed and others have more mysterious origins.  But many of the proteins recruited to build lenses maintain their original function in other parts of the body, and are encoded by the same gene.  That means that one DNA blueprint can simultaneously make a metabolic enzyme like lactate dehydrogenase throughout the body, but when this gene is used in the lens of a duck, its protein product becomes a structural material for bending light.  This concept of gene-sharing, where one gene contains the code for making protein with multiple functions, was first proposed to explain the evolution of lens crystallins.

Were these lens crystallins recruited because of their original enzymatic functions, or were they simply convenient building blocks for the dense packing required to make a lens?  For many crystallins the answer is - both.  My lab does research on an abundant lens crystallin family found in the vertebrate lens, the alpha crystallins.  All vertebrates contain at least two closely related alpha crystallins that resulted from a gene duplication event near the beginning of vertebrate evolution.  When the gene sequences for the alpha crystallins were resolved in the late 1980’s it was clear that they were small heat shock proteins.  This family of proteins is produced by cells that are under stress - perhaps because they are too hot, or are encountering dangerously high oxygen levels.  

So why was a stress-induced protective protein being used to make up to 30% of a vertebrate lens?  There are two reasons.  First, it turns out that alpha crystallins make great building blocks.  You can pack them in at very high concentrations and still maintain the necessary protein fluidity needed in the lens.  But second, the same protective function that they serve in other parts of the body comes in very handy in the lens.  The central cells of the lens destroy their own nuclei and other cellular machinery to prevent the scattering of light as it passes through the retina.  No nucleus means no new protein, so our lens cells must make do with the same proteins for their entire life.  Old proteins get shabby, fall apart, and then start sticking to each other.  This sticky mess interferes with the passage of light, and voila - you now have a cataract.  But alpha crystallins use their stress protective function to prevent this aggregation of old, decrepit proteins, preserving lens transparency until they are used up, generally starting at around age 50 for humans.  

At the macroevolutionary scale a wide array of proteins have been co-opted as lens building blocks because of their structural and enzymatic properties.  My lab is currently investigating the microevolutionary story.  How do small changes in alpha-crystallins alter their ability to function at different temperatures, for example?  Darwin perhaps sensed that the eye would yield excellent examples of his two great ideas: descent with modification and natural selection.

I pulled my head out of a grant proposal writing daze long enough this past week to notice a fellow professor having some trouble with their Facebook privacy settings.  Seems that a religion professor at Dartmouth thought it would be funny to point out the verbosity of some of her colleagues.  Even better, she worried aloud:

“I feel like such a fraud,” she wrote on her profile. “Do you think dartmouth parents would be upset about paying $40,000 a year for their children to go here if they knew that certain professors were looking up stuff on Wikipedia and asking for advice from their Facebook friends on the night before the lecture?”

Unfortunately, said professor was not careful enough with her privacy settings and a screenshot of her profile with the above quote wound up on the student newspaper’s blog. She probably joined the Dartmouth network and didn’t realize that everyone on that network could see her page.

The Chronicle article points out that its readers would be scurrying to Facebook to check their privacy settings, which is of course exactly what I did.  I’d like to think that I am way too savvy to make a mistake like this, but then I googled myself, found that my Facebook page was the second hit, and realized that my profile picture is totally public. I’m not having a Phelpsian moment, but it is a particularly goofy shot of me and my 3 1/2 year old daughter, and not what I want to put out there as my professional face.  So I made the picture private and blocked my Facebook page from Google.

One other sticky point in using Facebook as an academic.  Do you friend students?  I came up with some personal rules on the fly as friend requests started to come in.  I decided to only friend students after they graduate (or leave my University for other reasons).  I feel bad ignoring friend requests from people that I like, but decided to set that barrier between my work and home life.  I have accumulated a lot of former students as friends, and hope current students won’t be so offended by the put off that they will not friend me later.  And I don’t send friend requests to former students myself.  I wouldn’t want to hang out at the creepy treehouse either.  However, I have made an exception for former research students, and they have not been too creeped out to accept.

If you are a prof, leave me comments on how you manage your Facebook page.  I know you have one.

My friend Tom Hayden has a great new piece in Smithsonian magazine on how Charles Darwin’s work remains relevant 150 years after the publication of The Origin.  It includes a nice brief history of Darwin’s early years, the development of his thinking on common descent and natural selection, and most interestingly how new findings extend, but do not refute, Darwin’s work from a century and a half ago.  Even when new findings in epigenetic inheritance are redeeming Jean-Baptiste Lamarck.

While biologists are sometimes criticized for turning Darwin into an icon, we do owe our fundamental understanding of life to his (and Alfred Wallace’s) once revolutionary ideas.  Perhaps no one experiences that fact as much as the practicing biologist.     

And Darwin was a nice guy too (from Tom’s article):

As towering historical figures go, Charles Darwin does not provide much by way of posthumous scandals. The liberty-extolling Thomas Jefferson was slave master to his longtime mistress, Sally Hemings; Albert Einstein had his adulterous affairs and shockingly remote parenting style; James Watson and Francis Crick minimized their debt to colleague Rosalind Franklin’s crucial DNA data. But Darwin, who wrote more than a dozen scientific books, an autobiography and thousands of letters, notebooks, logs and other informal writings, seems to have loved his ten children (three of whom did not survive childhood), been faithful to his wife, done his own work and given fair, if not exuberant, credit to his competitors.

In another take on the man, Desmond and Moore’s new book, Darwin’s Sacred Cause, argues that Darwin’s abhorrence of slavery was an important driving factor in his work.  Critics of evolution try to argue that Darwin’s ideas about human origins support the racist view that some “races” are “higher” than others.  But on the contrary, Desmond and Moore argue that Darwin’s view of shared ancestry meant that all human populations are equal tips on the branch of life.  Furthermore, Darwin’s abolitionism helped give him the moral courage to publish what he know would be socially controversial and uncomfortable ideas in Victorian England.

I’ve been reading a number of reports from the recent ScienceOnline 09 science blogging conference in Raleigh, NC.  The Southern Fried Scientist and Anne-Marie from pondering pikaia have some nice write-ups from the sessions they attended.  What caught my attention most was a session titled Teaching College Science: Blogs and Beyond.  I am teaching my department’s senior capstone biology seminar this semester for the first time, and am focusing on science writing as a central theme.  I started this blog, my first, back in September and have become totally absorbed with the science blogging community.  I also have a strong interest in playing with different teaching technologies.  So for this capstone course I decided to merge the two.  My students are starting their own science blogs in groups of three or four to develop skills in communicating science.  I hope that this will also facilitate discussion of what a well-trained biologists should know - another central them of the course.

You can follow along with this experiment at our central course blog.  My students will have their blogs up later this week, so check back to see our progress.

The Southern Fried Scientist is having his Marine Invertebrate Zoology students produce 2 minute videos on scientific journal articles. They are really fantastic, especially one on the effects of reduced predation risk on mollusk evolution.  What a great way to engage students in the literature and get them thinking about how to communicate science.  Enjoy:

When teaching marine biology I warn my students that if they are there to just learn about sharks and dolphins they will be sorely disappointed, because only microscopic plankton have the biomass to really affect the oceans. Being an ichthyologist this always hurt a bit.  A recent paper in Science has restored my faith that all that microscopic stuff is just fish food - fish CAN change the world. Better yet, this story involves some animal comparative physiology.

First a little background on how we are killing our oceans.  The same CO2 that is accumulating in the atmosphere from the combustion of fossil fuels and other sources, leading to global warming, is diffusing into the oceans and changing their pH.  When CO2 reacts chemically with H2O,  H+ ions are released making water more acidic. This declining pH is already adversely affecting marine organisms, which are often adapted to a narrow pH range.  Calcium carbonate, however, can react with CO2 and limit the drop in pH.  The production of calcium carbonate by microscopic organisms like coccolithophores is thought to be the major player in this regulation of ocean pH.

So where do the fish come in?  Research on the toadfish, Opsanus beta, showed that this fish produces little calcium carbonate rocks in its digestive tract.  Subsequent physiological research showed that the production of these “gut rocks” was involved in the absorption of water in the gut.  Marine fish are less salty than the surrounding ocean.  Water, therefore, diffuses out of the fish into their environment leaving them very thirsty. But when they drink they fill their guts with salty water, which would pull fluids from their bodies leaving them even thirstier. It is for a similar reason that you should not drink ocean water when stranded in a life raft (that’s when you drink your own urine instead). But the fish apparently have a trick.  They accrete some of the salts in their urine as carbonate precipitates, lowering the salinity of the water in their gut and facilitating its absorption. And then the fish defecate the rocks.

Radiographic images of a live European flounder accumulating carbonate precipitates in its gut. The fish on top was living in freshwater and lacks "gut rocks". The same fish is shown below after only three hours in seawater. Note the opacities in the gut resulting from the accretion of carbonates (white arrows).

But would this calcium carbonate release affect the Ocean’s pH balance considering the relatively low biomass of fishes compared to plankters like the coccolithophores?  In their paper Wilson et al. also calculate the total biomass of fishes in the Ocean and the amount of calcium carbonate they produce.  While these types of calculations require a good number of assumptions, the authors claim that their conservative estimate is that fishes produce 3-15% of the Ocean’s calcium carbonate.

So next time PETA tries to convince you not to eat fish because they are cute, tell them a better reason is that fish poop could help save the marine ecosystem.

R. W. Wilson, F. J. Millero, J. R. Taylor, P. J. Walsh, V. Christensen, S. Jennings, M. Grosell (2009). Contribution of Fish to the Marine Inorganic Carbon Cycle Science, 323 (5912), 359-362 DOI: 10.1126/science.1157972

Next time you’re reeling in that fish, picture Whiskers or Fluffy hooked through the mouth on the end of your line.  At least that is what PETA would like you to do.  In a new PR campaign the animal rights group is attempting to rebrand “fish” as “sea kitten”.  The rationale:

When your name can also be used as a verb that means driving a hook through your head, it’s time for a serious image makeover. And who could possibly want to put a hook through a sea kitten?

Point well taken.  But I am not sure how I feel about my subject of study (I am an ichthyologist that does research on the fish eye) being renamed.  PETA argues that:

People don’t seem to like fish. They’re slithery and slimy, and they have eyes on either side of their pointy little heads—which is weird, to say the least.

But I love fish, and I know legions of other ichthyologists that love fish too.  And yes, I occasionally meet people, tell them I am an ichthyologist, then explain what that means, find out that they think that is cool, but am then asked:  then you don’t eat fish, do you?  But I also love eating fish, as do most ichthyologists I know.  Is it weird to like eating the group that you study.  I have a mycologist friend (studies fungi) who doesn’t like to eat mushrooms.  But I think that’s an exception.  And yes, many of you study organisms that you probably don’t want to eat.  I am talking to you, entomologists and parasitologists.  But I bet you malacologists out there love your oysters and scallops.  Admit it, you ornithologists eat chicken.

While our love for eating fish, and the need for this important source of protein in the diets of many humans, is leading to the collapse of fisheries and marine ecosystems, making fish seem cute is not the solution.  Ironically, the economic importance of fish and other marine organisms as food will play an important role in turning back the decay of our oceans, if that is possible.  Whether it is restoration of the Chesapeake Bay to bring back the oysters and crabs, research in the Gulf of Mexico to maintain red snapper populations (check out that mahi my ichthyologist friend Will caught) or limits on trawling in the North Atlantic.

But I did have fun making my custom “sea kitten” (see the top of this post).  Although it was labeled a flounder, but clearly has only one eye on the side of its head.  What’s up with that?

The NPR story on the new PETA campaign attracted a money comment:

This story evokes a wonderful memory of a recent trip I had back to my mountain cabin. I had a nice hike and spotted a wonderful Sky Origami (falcon) crushing a Stuart Little (mouse) in its razor sharp talons. When I got back to the cabin I made sure the House Bunny (dog) was in so it wouldn’t get mauled by a Forest Angel (bear) that night.

That is if you find spiders creepy.  And if you do, maybe your fears are well founded.

This shark video is only creepy if you were in the submarine, and the sharks actually posed a threat.  Which they probably didn’t.  But it is still worth checking out.

Changing climates have the potential to wreck havoc on living things, which are often adapted to very specific local temperatures.  These changes can alter the structure and, therefore, the function of the tens of thousands of proteins that keep cells and their owners alive.  Yet, the presence of living things in extreme environments ranging from the freezing waters of Antarctica to the boiling hot springs of Yellowstone attest to the evolutionary adaptability of proteins.  An interesting place to study this adaptive process, and the possible effects of climate change, is the complex intertidal zone along marine coasts.

George Somero of Stanford University has used many types of intertidal organisms as model systems for examining how protein structure and function adapt to environmental temperature.  In his latest paper, just published in the Journal of Experimental Biology, he has compared the enzyme cytosolic malate dehydrogenase (cMDH) in six species of limpets (the genus Lottia) along the coast of California.  These mollusk species (a group of marine snails) live at different latitudes and different zones of the intertidal, meaning that they are covered by water and baked by the sun for different amounts of time each day.  Limpets living in the upper intertidal in lower latitudes would get the most sun - so they experience the warmest body temperatures.

Somero already knew that cMDH adapted to thermal conditions from work he had done in other species.  The ability of this enzyme to run its chemical reactions changed in tune with the body temperature of these species.  Because the three-dimensional structure of cMDH was well known it was also possible to map the location of amino acid variations between species and get an idea of how they produced altered protein function.  Somero hypothesized that the six closely related limpet species differing in physiological temperature would contain variations in cMDH amino acid sequence that would provide insights into how cMDH, and proteins in general, adapt to changing environmental temperature.  He was not dissapointed.

By grinding up the muscular foot from the six species Somero and his co-author Yunwei Dong were able to collect a crude cellular extract that contained cMDH.  They found that the enzymatic activity and thermal stability of cMDH was adapted to the environmental temperature of each species, confirming their hypothesis.  When they cloned and sequenced the cMDH genes from all six species and determined their amino acid sequences, they found 24 variable residues.  What is really interesting is that the amount of variation between any two amino acid sequences did not correlate with differences in protein function or thermal stability.  The amount of structural variation did not predict how different the proteins would behave.

Two species in this study are of particular interest.  The northern and cold adapted L. digitalis and more southerly warm adapted L. austrodigitalis are so closely related that they are often difficult to tell apart from their physical appearance.  But their respective cMDH proteins are the most divergent in function and thermal stability of the six in the study, matching their divergent latitudes.  And here is the kicker - they only differ by one amino acid.  When you map that one residue onto a computer generated 3D structure for cMDH it falls in an important substrate binding site.  

The amino acid variation in the warm adapted L. austrodigitalis provides greater hydrogen bonding and reduced flexibility - this means that this version of the protein can more stably stick to the molecules that it acts on.  A neat trick when it needs to grab another molecule at elevated temperatures.

How does this research relate to global warming?   Between the 1970’s and 1990’s the range of the southerly L. austrodigitalis expanded northward into Monterey Bay at the same time that waters in the Bay increased in temperature.  The southern range of L. digitalis moved northward during this same period.  These species are shifting northward as waters warm since their proteins (cMDH and presumably others) are finely tuned to a relatively narrow range of temperature extremes.  But this paper also suggests that proteins have the potential to adapt to warming environments.  In this case only one amino acid substitution is needed to dramatically change the ability of this protein to function at higher temperatures.

Will the powerful adaptive ability of proteins allow life on Earth to adapt to our warming planet?  Unfortunately that grand experiment is underway.  Perhaps bittersweet for the comparative physiologist.

Y. Dong, G. N. Somero (2009). Temperature adaptation of cytosolic malate dehydrogenases of limpets (genus Lottia): differences in stability and function due to minor changes in sequence correlate with biogeographic and vertical distributions Journal of Experimental Biology, 212 (2), 169-177 DOI: 10.1242/jeb.024505

The long history of sociologists ignoring the role of genetics in human behavior is being challenged.  The Chronicle asks:

If sociologists ignore genes, will other academics — and the wider world — ignore sociology?

Some in the discipline are telling their peers just that. With study after study finding that all sorts of personal characteristics are heritable — along with behaviors shaped by those characteristics — a see-no-gene perspective is obsolete.

A new supplement of the American Journal of Sociology is devoted to the integration of genetics into the field.  With titles like:

• Gene by Social Context Interactions for Number of Sexual Partners among White Male Youths: Genetics-Informed Sociology
• Happiness and Success: Genes, Families, and the Psychological Effects of Socioeconomic Position and Social Support

this supplement should make some great reading (a few of the articles are open access if you do not have a subscription).  Hopefully the integration of genetics and sociology will break through the academic barriers that have made nature/nurture debates unproductive.