Monday, December 10, 2007

Snail Luvin' update

Succinea cf. ovalis crawling up the side of the tank. The shell is about 1cm long, not quite maximum size for this species. The yellow splotches were from a pigment marker I tried to use to tell individuals apart, but it rubs off too easily.

Last month (11/30), I mentioned that two of my Succineid snails (one very large individual and an intermediate-sized one (as above) were mating. I didn't get any photos of the dirty deed, but here's an update:

•I found a clutch of about 50 eggs in the tank on Dec. 3rd. They were just below the leaf litter in a little pile.

•The larger snail of the mating pair died about 5 days later. The tank they were in was a little dry, but none of the other snails perished. It's now sitting in alcohol, awaiting dissection to confirm it's species (succineids are notoriously difficult to ID to genus, let alone species without soft tissue [i.e. genitalia], so I was hoping to get the chance to get a peek at the snails naughty bits...).

So this brings me to the point of my post, aside from some neat succineid biology: many species of snails are semelparous. That is to say, they only reproduce one in their lifetime. Other snails are iteroparous (multiple reproductive cycles). Most succineids have been reported to be semelparous, and it appears this is the case for this particular species from Duluth. One interesting note, however, is that one individual who took part in mating is (as yet) alive.

I'm guessing that the large egg clutch was produced by the larger snail, and the sperm was provided by the smaller snail. This could have a distinct advantage in snail survival. By providing sperm at least once (more than once, perhaps?), the snail can reproduce at least twice - once as a sperm donor, once as the egg donor. Thus increasing the total number of individuals with the parent's genetic material. I have more to say about itero- versus semelparity, but that will have to wait until after I get some of my PhD data published. Next up: amino acids from fossil succineids!

Friday, November 30, 2007

Snail Luvin'

I got in to work this morning, and two of my succineid snails were mating. How many people can say that?

Thursday, November 29, 2007

D/L, D or L, D & L... what's an organic chemist to do?

I recently updated my blog with some information about amino acid racemization (often called AAR). By looking at the proportion of L-amino acids to D-amino acids, one can use this as a basic "clock" to compare the relative ages of organic material. There are some important caveats, however. I will cover those in more detail later. But Aydin, over at Snail's Tales had an interesting comment about using the D/L ratio of amino acids to search for life on other planets.

To follow up on his two main points:

1. There may be inorganic processes that can concentrate a particular isomer of amino acids. However, most physical processes that we know of that sort various items involve a kinetic process. Sorting of river sediments from coarse to fine grains involves gravity, fluid dynamics, and the differing abilities of particles to be moved. Isotopic fractionation - where heavier isotopes of a particular element are concentrated - also involve sorting by the ability of a system to move them. Size (and mass) play an important role. For amino acids to be sorted by their stereo isomer through some inorganic process, there needs to be something that has a greater (or lesser) effect upon that isomer. Since the two isomers are essentially identical in mass and size (albeit with a different orientation of ), kinetic influences are not likely to concentrate a particular stereo isomer.

However, Aydin has an important point. There could be a process that sorts by isomer we are not aware of. Outer space is a pretty wacky place, and we would be fools to think we've accounted for all potential chemical/physical processes. So, when looking for extraterrestrial organic molecules, we should not take a racemic mixture as reason to think there is no evidence for life out there. Conversely, while finding a non-racemic mixture is interesting and could be a sign of life, we can't take it as incontrovertible evidence for biological processes. But it would be much harder to explain using a non-biological mechanism.

2. It is also entirely possible that (for the most part) only earth-bound organisms exclusively produce L-amino acids, and other "exobiological" processes utilize both. For example, some earth-bound organisms produce D-amino acids (Cone Snails, for example, produce some D-amino acids). Perhaps on some distant planet, all organisms utilize both isomers. Or, production of both isomers is the norm, and single-handed aminos are the exception. Reason again to think carefully about accepting or rejecting an exobiological hypothesis.

For an interesting technical paper, see: Córdova, Armando; Engqvist, Magnus; Ibrahem, Ismail; Casas, Jesús; Sundén, Henrik (2005). "Plausible origins of homochirality in the amino acid catalyzed neogenesis of carbohydrates". Chem. Commun.: 2047–2049."

Consider the hypothesis: "extraterrestrial life will produce amino acids of one stereo isomer." A null hypothesis of this statement could be phrased: "if I find an extraterrestrial sample with a single stereo isomer, I have found evidence of life." Thus, we could easily reject a null hypothesis if we find a racemic mixture on some distant planet; likewise, we would accept our null hypothesis if we find a concentrated mix of one stereo isomer. But what about the two alternatives mentioned above? Perhaps there is a non-biological process that produces a non-racemic mixture. We would, perhaps falsely, accept our null hypothesis. This would be a Type II error.* Conversely, we may have a situation where exobiological systems use both isomers. We would reject our null hypothesis even though (in "reality") it is correct. This would be a Type I error.*

Given the magnitude of unknowns regarding extraterrestrial racemization, we should certainly take into account other lines of evidence before settling on a pronouncement of the existence/non-existence of exobiological activity.

*I use "Null Hypothesis," "Type I," and "Type II" error more loosely than in the true statistical sense, but the analogy applies just the same.

Wednesday, November 28, 2007

The snail that wasn't: Columella

I have been surveying our local woods and found this particular snail:

At first, I thought I had come across Columella columella alticola. It has a narrow penultimate whorl, tall, columnar shape, and prominent transverse striae. I was rather excited, as this species hasn't yet been found in Minnesota yet. Alas, after talking to several people who have seen multiple Columella edentula (=simplex), it is most likely a columnar morph of that species. This is based on the tapered spire (alticola has a more domed top) and the minimally pinched penultimate whorl. All is not lost, however. The columnar morph could be a separate species. But it will take a much larger sample population than just one shell to determine this. Motivation to keep looking.

Now that the ground is frozen and draped with a 3" blanket of powdery snow, further surveys are on hold. I'll be back in the spring to resume the hunt.

Sunday, November 25, 2007

Amino Acids Part the First

Since I had a request for a topic of discussion, I'll start with that. If any of my readers would like to see anything specific, be sure to let me know. One of the results from my current research deals with the breakdown of Amino Acids in the shells of terrestrial gastropods. Before I dive into the nuts and bolts of my work, I figure I'll start with an explanation of how Amino Acids are used in gastropod paleontology in the first place.

What are amino acids?

Most simply, amino acids are the building blocks of proteins. One of the main functions of DNA is as a "recipe," or code for a particular list of amino acids (this is a gross oversimplification, but is sufficient for our discussion). The ribosome reads the "recipe" from mRNA (which in turn is copied from the DNA) and links the required amino acids together in a polypeptide chain. These polypeptides then form the building blocks of our bodies. The proteins in muscle tissue, hair, fingernails - even enzymes and antibodies are built from these polypeptide chains.

Why are aminos helpful for studying fossils?

One of the peculiar aspects of amino acids produced by living organisms is the fact that while amino acids are chiral molecules - that is they have both "left-handed" (sinistral) and "right-handed" (dextral) versions, living organisms only produce the left-handed versions of amino acids. It's this sinistral quality (referred to as "laevo" in organic chemistry) of biologically produced amino acids that makes them useful for study of fossils. An important aside is how we can use this property to search for signs of life on other planets. If we find amino acids (which do exist in comets, and interstellar debris) consisting of only one chiral form, that's a pretty good hint that we're looking at biologically produced amino acids. This of course assumes that alien life forms use amino acids as their building blocks.

Over time, these biologically produced amino acids will change chirality: switch from left-handed to right-handed. This is matched by the right-handed aminos switching to left-handed. Eventually, all this switching evens out and a 50:50 ratio of left- to right-handed amino acids (this is referred to as a "racemic" mixture).

This alteration of aminos from left to right and vise versa is called "racemization." The rate of racemization is time and temperature dependant. For a pile of snail shells that were buried a long time ago, we can use this rate of racemization to estimate age. If we know the rate of racemization and the temperature history for the particular shells in question, we are left with age as the unknown vvariable. It should be apparent, then, that the older shells will have amino acid ratios closer to a 50:50 mix of left- and right- handed forms. We can use these amino acid racemization measurements to extimate the age of particular shells. Conversely, if we know the age and the rate of racemization, we can estimate temperature. For those of us studying the last Ice Age, this can be really important. We will go into this in more detail in future posts.

The amino acid data that I've gotten was processed and analyzed by the team at the Northern Arizona Geochronology lab. I want to thank Darrell Kaufman and Jordan Bright for all their help with my snails so far. Thanks!

Where are they in snail shells?

Snail shell is mostly calcium carbonate in the form of Aragonite. Binding these Aragonite crystals together is a proteinaceous material. The snail shell is also covered by the proteinaceous periostracum. These aminos can then be separated from the shell and analyzed with a spectrometer to measure the relative amounts of left- and right-handed amino acids. And that is where my work comes in, which will be addressed in the next episode.

Thursday, November 15, 2007


What has Pascal been doing? Here's a list:

  • Writing his dissertation outline, assembling necessary figures

  • Teaching sedimentology/stratigraphy

  • A little photography

  • Writing his dissertation chapters

  • Presented a poster at GSA last month based on Amino Acid results from Ice Age snails

  • Studying pterosaur flight and building gliding and rubber band-powered models of Rhamphorhynchus

  • Collecting modern snails from a small park near the University, including finding a live succineid, Succinea aff. ovalis, who should appear on this blog before long.

Each of these topics is fermenting in my head, and will hopefully appear on this blog soonish.

Thursday, November 01, 2007

What has Pascal been up to?

Yet another post in what is still a woefully under-updated blog. But, just a quick shout to interesting happenings at the annual Geological Society of America (GSA) meeting I attended for the last week. Among the interesting items, was a poster on a fascinating set of full-body imprints from the Pennsylvanian of Pennsylvania (go figure). This was presented by Spencer Lucas at the New Mexico Museum of Natural History and David Fillmore and Edward Simpson at Kutztown University, PA. Photo/drawing provided by the researchers press release:

Besides the cool science, a take home message from this press release is that there are plenty of undiscovered treasures lurking in museum collections and that all it takes is an inquisitive student (undergrad or grad) to start asking the right question. So get out and look through those dusty drawers!

Saturday, October 20, 2007

80 Ma without any

I was browsing BBC news and this article caught my attention:

80 Million Years Without Sex

I found it interesting, but even more so because Aydin over at Snail's Tales introduced me to the world of bdellid rotifers a few years ago.

Makes me think I should write about sex (in a paleobiological sense, you naughty viewers...).

Monday, October 08, 2007

Ode to a tweezers

While working on my project (picking snails), I came across a super, time-saving invention. Featherweight forceps. These are tweezers made of super thin spring steel, which allow me to pick up snail shells without crushing them (even the tiny Vertigo shells). In addition, tweezing them takes a fraction of the time the old "moist brush" method would take. Meaning I can get snails counted in less than half the time it used to take me. Highly recommended for the tiny bug-picker in your family.

These are from Bioquip's website, but I've also seen them offered in Fischer Scientific and other places.

Thursday, October 04, 2007

Meme tag

Aydin over at Snail's Tales posted the "Interesting Animal" meme. Considering how long it's been since I updated, I'll entertain the brave souls that occasionally check this site with something to read:

An interesting animal I've had:
For several years, our family had a pet Eastern Tiger Salamander.

His name was "Coco" (my little sister named him) and he lived with us for nearly 8 years. He loved earthworms, crickets, and mealworms. He also liked being stroked on his back (provided you wet your finger first). We assume it was a "he" because of the swellings at the base of his tail every spring. These animals are threatened in much of their range. While not state or federally protected, loss of wetland habitat is a significant threat to these cute little buggers. Ours was a rescue from one of my dad's co-workers at the Wisconsin DNR. Coco had fallen into their swimming pool, along with a few other hatchlings from that year.

An interesting animal I've eaten:
Last year I was at a conference in Philadelphia. I ate frog legs. They tasted like fish and were very greasy. I wouldn't eat them again, but I figure I have to try different things now and again. I can be a picky eater and get stuck in a food rut sometimes.

An interesting animal in a museum:
Where to begin? I worked for several years as a PA in the UW Geology Museum and I've met hundreds of interesting animals. Perhaps the most interesting, however, would have to be our collection of Burgess Shale fossils. My favorites, are probably Marella splendens, Burgessia bella, and Anomalocaris. Being able to actually handle these fossils and then use them for reconstructing the animals (I'll have to post the drawings sometime) was really fun.

An interesting thing I've done with/to an animal:
As PA at the museum, I've had the opportunity to work on several exhibits. Including painting this full-size cast of the skull of "Stan," one of the most complete T.rex skeletons ever found. It was a real treat to put my artistic talents to use to paint this thing. And provided me a unique perspective on the skull of these large predators, too.

Tags: well, I guess if you read this and you haven't done this meme - you're it.

Tuesday, July 10, 2007

8 Things...

Well, The Other 95% and Snail's Tales among others are doing the "8 Random Things" meme. While I have not been posting often enough to warrant tagging others, I figure it'll give anyone stopping by something to chew on while I cook my data in a statistical stew and prepare to share it with the world...

1). I have loved dinosaurs since about age 3. I can say that I have discovered dinosaur bones, and dug them up. When I was in preschool, I drew a picture where I wrote, "I want to be a scientist or a bus driver."

2). I hate driving; I will not be a bus driver.

3). I have painted a full-size cast of a T. rex skull. It took me an entire day to finish.

4). I am extremely accident prone.

5). I prefer dry-erase boards to chalk boards to the point where I put a dry-erase board over the chalkboard in my office.

6). I have two noticeable scars on my head. The first came from running into a chain-link fence (I was running with my eyes closed, by the way) and the second was from sliding headfirst into a door jamb (at about the same age - go figure).

7). I am 6 years older than my sister.

8). I have counted more than 10,000 individual snails and sieved through more than 200 kilograms of mud for my dissertation.

Wednesday, June 06, 2007

What on earth has Pascal been doing?!?

It's been nearly four months since my last post. See what teaching a college course on dinosaurs as well as dissertation research will get you? A whole lot of "time for nothing else." Here's a shot of me in the field - digging for snails:

I've gotten a few comments that deserve a response, especially as it relates to the Driftless Area. But I'm off to Ohio to meet up with some geologists for a few days. I'll try to update sooner, rather than later.