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.
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.
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.
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.
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!
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.
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.
Image from the NAU geochronology laboratory.
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
Update
What has Pascal been doing? Here's a list:
Each of these topics is fermenting in my head, and will hopefully appear on this blog soonish.
- 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!
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!