Sunday, December 30, 2007

Weekly Video: Science Music Video

I finally got around to updating my 'That's What Slugs are For' music video. This video was inspired by and makes use of Greg Crowther's song. For more of his fantastic songs click here!

Without further ado, here is 'That's What Slugs are For', now with more slugs!

Friday, December 28, 2007

Animalpedia: Brachiopods

This is a brachiopod, commonly known as a lampshell. Although they look like clams, they are actually very different animals. Clams and mussels posses a foot that allows them to bury themselves in the sand. They also posses a siphon that allows them to draw water into their shell, even as they remain buried. Perhaps the most important difference between brachiopods and clams is the filtering apparatus. Clams filter the water using their gills. Brachiopods have a specialized feeding filter called a lophophore (yes, just like the bryozoa!). You can see it outline in the picture as the darkened horseshoe shaped lines within the shell. Brachiopods are attached to the bottom by means of a stalk (although there are stalkless ones as well). They cannot bury themselves, as they lack siphons. Instead they bring water into their shell by leaving it slightly open and creating a current with the cilia on their filtering apparatus.

These guys used to be the ‘bees knees’ as it were. There was once over 4500 different genera existing in all parts of the ocean. Now there are only 350 different species of brachiopods, and they are only found between 100 to 200 meters (330-600 feet) down.

So what happened? Why do we now have clams and such instead of brachiopods? Well there are several hypotheses, but I will share the one that makes the most sense to me. Brachiopods were well established when the clams came along, and were not giving up the prime spots to any newbie filterer. However, the decline of brachiopods coincided with the rise of shell crushing sharks. The clams, which could bury themselves, had a refuge from predation that the brachiopods could not utilize. So, brachiopods got crunched, and the clams and such took over the filtering the ocean gig.

Brachiopods are so abundant as fossils that they are often used to date rocks. (Like, finding a certain species will tell you that the rock is between x and z years old) They can also be bought at any curio or museum shop, as an example of a real fossil along with the ever-present trilobite.

Thursday, December 27, 2007


Sad news out of San Francisco. The female Siberian tiger escaped her enclosure to kill a young man and wounded two others. She was shot and killed by police officers.

I've been trying to find out more about it but the new stories have been remarkably flash-in-the-pan. There was a big glut of stories till it turned out that the men may have been terrorizing the tiger and may have helped it escape by dangling their legs over the edge. Apparently, she jumped up a 12.5 foot wall (although some reports say 18). I don't know for sure how deep it was, but it looked much taller than two man-heights the last time I was there.

What is disturbing to me is 2 things. First the news reports were so full of misinformation, that I don't believe anything they say. This was the same tiger that scratched up her zookeeper in 2006, when the zookeeper stuck her arm in the cage during a feeding demonstration. Some news reports said she (tiger) ripped or chewed the zookeeper's arm off. Other reports said that the three guys who were attacked did not know each other and made it seem like the tiger was just wandering around mauling people. There were only 20 in the whole zoo at the time of the attack, there were no other witnesses around the cat enclosure. The two other men involved in the incident have not given statments to the police yet.

The second is the reaction against it. Yes, there are many people who think that teasing tigers is not a good idea. Yet the other half protest that the zoos are still responsible, no matter what the boys did. The SF zoo is putting up security cameras (which I think is a great thing, then they can fine people teasing the animals!), and are talking about electrified fences. Basically, to keep people from their own stupidity. But most outdoor cat enclosures in zoos are built the same way.

These people also cry shame on the other half, who believe that if the kids teased the tiger, then they are to blame. How can you be so insensitive, they cry. How can you value the tiger's life over the boy's?

She was part of a breeding program. There are less than 500 Siberian tigers left in the wild.

Wednesday, December 26, 2007

Research: Questions for colonial reproduction (corals)

Some of the talks I go to which are most interesting to me, are those which make me wonder what if. These researchers were looking at the reproductive output of corals, to see if there was a difference in egg size among the different sizes of corals (small, medium, and large) or morphology (plate and branching). They also examined how reproductive output changed over time.

They found that there was no difference in egg size due to colony morphology or size, but smaller colonies were less likely to spawn a second or third time. They did find that chlorophyll concentration of the eggs increased with increasing size of the colony. This may have been due to the fact that larger colonies were deeper down, so packaged their eggs with more zooxanthellae than the smaller, shallow water colonies.

They also found that eggs sizes within the bundles varied, which interests me because I work on maternal provisioning in a colonial animal too. I find that larvae released by my bryozoans can have up to a 2-fold difference. I am most curious to know how much those eggs varied, since most researchers ignore within brood variability. They also found that the egg sizes varied among spawning events. Generally there was a decrease in the size of the eggs on subsequent spawning events, but a slight increase in the number.

This raises some interesting questions. It would be interesting to find out if the same amount of energy is expended for each of the broods (that is does the increase in number balance the fact that smaller eggs are made). Are these smaller eggs as fit as larger eggs? Are parent colonies more willing to take a chance by producing smaller eggs, since they are assured some reproductive success with the earlier large egg brood?

Finally, if would be fun to know if this down shift in egg size (energy into eggs) is accompanied by an up shift in sperm production. Since the eggs and sperm are packaged in the same bundle, it may be relatively interesting to quantify the egg/sperm ratio. It would also be interesting to see if that ratio is different among the different sizes of colonies. It's generally easier (energetically) to be a male, so would smaller colonies increase their reproductive success by packaging extra sperm?

Original abstract:

Padilla-Gamino, J.L.*, and R. Gates Hawaii Institute of Marine Biology

Modular organisms such as corals grow by adding polyps (or individual modules). This growth is not indefinite however, and eventually colony size will be limited by extrinsic (i.e. nutrient availability, microenvironment within the colony) or intrinsic (i.e. senescence, changes in physiology) factors. Although individual coral polyps grow to full size, polyps do not start producing gametes until the whole coral colony has reached a particular size. While there have been several studies analyzing the size at which corals become sexually reproductive, very few studies have focused on the reproductive ecology of the larger colony size classes, mostly due to the difficulty in transporting huge colonies to aquaria or collecting of the gametes in the field. To better understand the relationships between size, morphology and reproductive capacity, this study examined the reproductive output (gametes) in situ of the hermaphrodite coral Montipora capitata. As this coral grows, the morphological complexity of the colony also increases. This coral is highly morphological plastic in response to environmental factors. For example in areas with lower light levels, these species acquires a more flat-shape morphology than in areas with more light (branching morphology). Gametes from different environments were collected in situ during most of the reproductive season (June, July & August). Regardless of differences in morphology and environment, colonies spawned simultaneously and had similar offspring characteristics (egg size, # eggs/bundle).

Monday, December 24, 2007

Cool thing: Whale fossils

What better way to celebrate winter solstice than by visiting some great tidepools? We headed out to the tidepools and stopped by the Cabrillo Aquarium to check out the cool fossil finds that had just been discovered.

The week before, one of the directors of the aquarium was visiting the tidepools when he noticed these really cool fossil whale remains.

This is a shot of the rostrum. The two center lines that are close together are the upper jaw, while the bottom line is one half of the lower jaw.

Here's the neat part. This may be a cast of the inside of the brain case. The knob on the back end may be the foramen magnum.

Finally, a close shot of the fossilized bone. You can see the two layers of bone, the lighter compact bone (or cortical bone) and the darker, more porous spongy bone (or cancellous bone).

What a cool tidepool find!

Saturday, December 8, 2007

Weekly Video: Fertilization envelope formation

Furious bouts of writing followed by furious bouts of procrastination (or is it preceded by?). My newest draft of thesis intro is done (I think this is version seven...), and now I am on to rewriting the methods section...tomorrow. Here is a video of a fertilization envelope forming around a sand dollar egg. Next semester, I might re-film it at a higher magnification.

Tuesday, December 4, 2007

The 'eyes' have it

Three reasons why cephalopod eyes are better than human eyes (I am sure there are more):

The joining of the optic nerve bundle to the retina itself in vertebrates causes a blind spot (no photoreceptor are located here). On the other hand, cephalopod optic nerves are attached at different points along the back of the eye (not the inner layer), eliminating the need for a 'bald spot' on the retina.

The photoreceptor in cephalopod eyes actually face towards the light! Vertebrate photoreceptor face away from the light and light must pass through other layer before hitting the photoreceptor.

Another interesting design plus is that squids very rarely get cataracts in the center of their eyes. What they found was that squids, and some other cephalopods (like octopods) have two types of genes responsible for making the proteins for the lenses in their eyes. These genes have an extra insertion, either short or long insertions, (which are basically like extra instructions) that are not found in our eyes. When these extra insertions are translated into the proteins, they give extra stability to the protein so they won’t unfold. Since cataracts are caused by the proteins unfolding (making an opaque part in the lens), squids are less likely to get cataracts.

Now, the long gene produces a more stable form of protein than the short gene. The ‘long gene’ proteins are found in the center of the squid eye, while the ‘short gene’ proteins are found in the edges. This means that the center of the eye is least likely to get a cataract. You may wonder why the squid does not just use all ‘long gene’ proteins. I don’t know, but there may be some energy costs associated with making the larger more stable protein, so that it is more cost effective to use the ‘short gene’ proteins on the edges where they don’t count (hypothesis).

Either way, they are better lenses than what we have.

Another cool thing is, that each group of ‘advanced’ cephalopods has their own special version of the two genes, but they work very similarly. This stuff was very well put together; I can’t wait to read the paper on this. It will probably end up in Science, if it has not been published already!

Here’s the original abstract…


Evolution of High-Acuity Vision in Coleoid Cephalopods

Spherical lenses with a graded refractive index design are required for camera-like vision in aquatic animals. In cephalopods, these lenses are made of a group of closely related proteins collectively called S-crystallins. Our earlier work has shown that an adaptive radiation these S-crystallin genes and positive selection on the electrostatic properties of S-crystallin proteins led to a graded refractive index lens capable of forming high-resolution images in the squid Loligo opalescens. In the L. opalescens lens, S-crystallins with high charge stabilize the optical properties of regions of low refractive index in peripheral layers, and S-crystallins with lower charge are tightly packed in the high refractive index cortex. The mechanistic link between S-crystallin sequence, biochemistry and refractive index allows us to understand in molecular detail the optical evolution of a camera-like eye in cephalopods. To understand the transition from ancestral cephalopod vision to extant camera-like vision in coleoid cephalopods, we used techniques from molecular evolution, biochemistry, molecular dynamics, optical modeling and image analysis. We sequenced 600 S-crystallin genes from most major coleoid taxa, constructed a gene tree from these sequences and analyzed it for patterns of charge evolution. We also measured the optical quality of these lenses by calculating their modulation transfer functions (MTFs). Our gene tree suggests that high-resolution lenses evolved from a low-resolution ancestor multiple times within the coleoid cephalopods. Consistent with our gene tree data, our MTF data show that there is taxonomic variation in lens quality within coleoid cephalopods. We will discuss the correlations between independent adaptive radiations of S-crystallin molecules, high acuity vision in cephalopods and possible evolutionary scenarios in which these changes in visual acuity may have been occurring during the Jurassic radiation of squid.