Monday, November 30, 2009

Interesting word for today: graben

According to the American Geological Institute's Glossary of Geology, 4th edition, the definition of graben is the following:

"graben (n) An elongate trough or basin, bounded on both sides by high-angle normal faults that dip toward the interior of the trough."

Breaking it down a bit:

A fault is a crack in a rock body along which the rock has moved--i.e., the rock on each side of the fault has moved relative to the rock on the other side. Most faults are tilted relative to Earth's surface--they're not perfectly vertical. Therefore, there is a body of rock "above" the fault and a body of rock "below" the fault. The rock "above" the fault is called the hanging wall. The rock "below" the fault is called the footwall:

The hanging wall and the footwall can move in two different ways. In a normal fault, the hanging wall moves down relative to the footwall. In a thrust fault, the hanging wall moves up relative to the footwall:

A graben is a valley bounded by high-angle (i.e., steep) normal faults on both sides:

Sorry about the blurry images. Blogger's thumbnails aren't that great. But you should be able to see the images in all their glory by clicking on them...

Friday, November 6, 2009

An open letter... the leftover Halloween candy lurking throughout my house.

Dear Evil, Yet Strangely Delicious and Compelling Ones,

Please, leave me alone. Seriously. Why can't you bother my husband for a while?



Kate, who wishes to remain cavity- free and to not have to purchase new pants

Thursday, November 5, 2009

Wednesday, November 4, 2009

Uncomfortable research

There are a couple of good posts up at ScienceBlogs (at Bioephemera and Adventures in Ethics and Science) about the double standard applied to drug addiction research, and the ethics thereof.

To sum it up succinctly, BioE points out the apparent double standard of research into how to help people quit smoking tobacco = GOOD! but research into how to help people quit smoking pot or crack = BAD! She also points out the (possibly larger) societal costs associated with illegal drug use and addiction and (validly, in my opinion) questions why spending money to try to avert those costs is considered a waste of money. She also touches on issues involved in funding research on other "uncomfortable" topics, such as HIV transmission in transgendered prostitutes.

Dr. Free-Ride, as is her wont, addresses some of the ethics involved in avoiding research on behaviors considered to be "moral failings." She asks (again, validly, in my opinion) "...are we committed to a one-strike policy with bad choices, with no room for compassion or fresh starts? Is that really who we want to be as a society?"

My answer is a resounding "Hell, no!"

And as both Dr. Free-Ride and BioE have asked for others to post their thoughts, I thought I would.

I'd like to write more on this, but between the two of them they've pretty well hit all the points I would have made.

Go forth, read...and then do something about it!

Sunday, November 1, 2009

This requires a new label category

Between this and the Sesame Street Martians, I think I need a new category: "I wish I'd thought of this!"

h/t to Dr. Isis

Check it out!

Suzanne Coldwell--a friend of mine from high school--and her family have an alpaca farm! How cool is that??

Check out their new website and blog.

Saturday, October 31, 2009

Darn, I wish I'd thought of this...

Although I'm not sure my husband would've gone along, and it just doesn't have the same effect if there's only one.

Kind of reminds me of a time I went to my chemistry professor's Halloween party in college. A group of his students came dressed as letters and numbers--a.k.a., the letters and numbers Sesame Street is "brought to you by". It was brilliant.

h/t Orac at Respectful Insolence

Friday, October 30, 2009

Usage tip: its vs. it's--with bonus visual aid!

So you think you've figured out how to use the apostrophe. The apostrophe is used to indicate possession and to take the place of missing letters in a contraction. No problem! You've got it down.

And then, along comes...its.

English being English, you know there has to be an exception to every rule (and several exceptions to each exception, too, in most cases). Well, its is it.

Use its to indicate that it owns something. Use it's to replace it is.

The dog carried its bone to its den.
It's a nice day for a walk.
It's got a big scar on the back of its head.
It's a zombie! Run!

The bird used newspaper in it's nest.
Its too late to watch TV tonight.
Its carrying its baby in it's mouth.
Its after your brains!

And just when I thought I had finished with The New Yorker ad fail, I get this week's issue and see this:

Friday, October 23, 2009

An open letter... the random folks I passed on my bike ride to class last night.

Dear Rockin-Out D00d:

I totally get that your music is, like, so awesome that you have to listen to it ALL THE TIME, even when you're walking somewhere. And I totally respect you for wearing earbuds so we don't all have to listen to it.

However, if you are walking on a joint walking/biking path, it would probably be a good idea to make sure your music isn't so loud that you can't hear my bell when I ring it. Or, at least, if you're going to use it to block out the pesky noises of Pittsburgh, then dude, don't walk down the middle of the path. Pick a side and stick to it. That way, when I need to pass you, I don't have to hold my breath that I might hit you (since you didn't hear the bell).

And to the loving couple,

It's great that you're taking an afternoon walk together, and the river trail is a beautiful place to do it. But please understand that A) it's a mixed-use trail, which means I as a bicyclist have as much right to the trail as you do; B) it's not a very wide trail, which means I as a bicyclist pretty much take up half of it; C) it's a lot easier for you two to walk single-file or move over than it is for me to shorten my handlebars to avoid hitting you; and D) that bell ringing behind you means "Hello, I'm riding a bicycle, and I'd like to pass you because I'm traveling faster--can you please move to one side for a couple of seconds?"

I'm glad I didn't hit either of you. And I don't begrudge you your space on the trail. But if you're going to walk side-by-side, at least, please, walk on the right instead of in the middle. That will give the rest of us plenty of space to go by you.

And finally, to the buttmunch in the car who honked at me,

Dude, get over it. Bicycles are vehicles too. It's just as illegal for me to ride on the sidewalk as it is for you. (And seriously. Have you seen some of the sidewalks around here? Do you know how much it hurts to go over uneven brick like that on a bicycle seat?!?) I'm riding as far to the right as I can. Deal with it.


On the shoulders of giants...

Thanks to Dr. Isis, my complaint about the Intel ad generated an actual response from Intel. Kelly Feller apologized both here and on Dr. Isis's blog for any offense the ad caused.

I do appreciate the apology. I am sure that the intention was not to offend. And I do respect Intel's "Rock Star" line of ads in principle; I like that they're trying to bring visibility and cachet to science and engineering. I suppose when you put together as many ads as they do, a few are bound to flop. But still--maybe this incident will reduce the chances of this particular type of flop in the future.

At any rate, thank you Dr. Isis for bringing some visibility (and for agreeing with me, even though I wear sneakers for non-running purposes), and thank you Intel for a quick and polite response.

Wednesday, October 21, 2009

Am I the only one...

...who finds this Intel ad (from the inside back cover of this week's The New Yorker magazine) vaguely insulting?

Because apparently the geniuses at Intel are far above such plebian activities as physical exercise. After all, really smart people are all skinny nerd-boys who subsist on junk food and chess. If you're low-brow enough to actually exercise, you wouldn't stand a chance against those "big brains" at Intel.

I know it's just an ad. But to me it propagates a false dichotomy: either you're smart and don't care about your physical wellbeing, or you're a gym rat with a brain the size of a ferret. Never mind the large number of studies that have found correlations between physical exercise and concentration, focus, and stress relief (something I'd imagine the Intel folks would know a lot about).

The ridiculous imbalance in X and Y chromosomes also bothers me. Yes, I realize that there is a big gender imbalance in Yoga classes (mostly XX) and technology R&D (mostly XY). But come on. If you're going to go to big lengths to show racial diversity (you can't tell me the two non-white d00ds are there by accident), at least show a chick in one of the games!

I'm not sure if the person in the white coat in the game on the far left is supposed to be a girl. But even if it is, come on, you couldn't pick someone with identifiable female features? Way to support even MORE smart-people stereotypes! (I.e., smart women don't look like women. We all have short hair, dress like men, and never wear makeup. Okay, that might be true for me. But I think Dr. Isis, among others, might have something to say about it.)

I think the folks who do the advertising for Intel deserve a big "congratulations" for taking great strides in making non-scientists even more likely to think that scientists find them stupid. Way to go, Intel!

Tuesday, September 8, 2009

Final results for Race to Read

Well, I wasn't sure I'd make it to 10, but I did. Eleven, actually. For the record (this is also available on the original post), here are the 11 books I read for the GPLC International Literacy Day fund raiser:

1. The Good That Men Do (Andy Mangels and Michael A. Martin)
2. What Einstein Told His Cook: Kitchen Science Explained (Robert L. Wolke)
3. Kobayashi Maru (Michael A. Martin and Andy Mangels)
4. Proust and the Squid: The Story and Science of the Reading Brain (Maryanne Wolfe)
5. Holy Hullabaloos: A Road Trip to the Battlegrounds of the Church/State Wars (Jay Wexler)
6. Prime Directive (Judith and Garfield Reeves-Stevens)
7. Speaking Up: The Unintended Costs of Free Speech in Public Schools (Anne Proffitt Dupre)
8. Memory Prime (Gar and Judith Reeves-Stevens)
9. A Suitable Vengeance (Elizabeth George)
10. When Gay People Get Married: What Happens When Societies Legalize Same-Sex Marriage (M.V. Lee Badgett)
11. The Kobayashi Maru (Julia Ecklar)

To make your donation, visit my fund raising page.


Wednesday, August 19, 2009

FINAL RESULTS: Race to Read for International Literacy Day

International Literacy Day is September 8. I've decided to participate in the Greater Pittsburgh Literacy Council's fundraising event: Open Up a Book, Open Up a Life.

Here's what I have in mind:

I will read as many books as I can between now and September 8. I'll keep a record of the books I finish here in this post. If you'd like to make a donation, pick an amount to donate per book I read. After September 8, come back here to find out how many books I've read. Do the multiplication to figure out your total donation, then go to my donation page and make a secure online donation. (Or, if you'd prefer to donate through the mail, just let me know.)

(Of course, if you'd prefer to just make a single fixed donation, you can do that through the donation page, too.)

You can donate any time between now and September 30. GPLC's tax ID number is, I believe, 25-1392652, if your company can make matching donations. [h/t to Erin for reminding me to look this up!]

If you're not able to make a monetary contribution, please consider donating some time to GPLC or to your local literacy group. Or, just pass the word along to others.

Thank you!


1. The Good That Men Do (Andy Mangels and Michael A. Martin)
2. What Einstein Told His Cook: Kitchen Science Explained (Robert L. Wolke)
3. Kobayashi Maru (Michael A. Martin and Andy Mangels)
4. Proust and the Squid: The Story and Science of the Reading Brain (Maryanne Wolf)--Recommended!
5. Holy Hullabaloos: A Road Trip to the Battlegrounds of the Church/State Wars (Jay Wexler)--Recommended!
6. Prime Directive (Judith and Garfield Reeves-Stevens)
7. Speaking Up: The Unintended Costs of Free Speech in Public Schools (Anne Proffitt Dupre)
8. Memory Prime (Gar and Judith Reeves-Stevens)
9. A Suitable Vengeance (Elizabeth George)
10. When Gay People Get Married: What Happens When Societies Legalize Same-Sex Marriage (M.V. Lee Badgett)
11. The Kobayashi Maru (Julia Ecklar)

Wednesday, August 5, 2009

Usage tip: everyday vs. every day

This one crops up so often, it's practically an everyday occurrence. (ha, ha, ha...sorry.)

Here's the difference between everyday and every day:

Everyday is an adjective.
Every day is an adverb.

But that doesn't really matter. You want to know how to use them correctly, right? Here's a handy rule of thumb:

If you can replace the term in your sentence with occasional or frequent or any other adjective and have the sentence still make grammatical sense, chances are you should be using everyday. If you can replace the term with Tuesdays or sometimes, you should probably be using every day.

For example:

This shampoo is best for every day use.
Everyday, I walk my dog.
People should try to exercise everyday.
Luckily, loud street arguments are not an every day occurrence in my neighborhood.

You can use this shampoo every day.
Some trainers say you should run every day, but I think that's too much.
He's trying to prove that he's an everyday guy.
Let's try to make laughter an everyday event.

Friday, July 17, 2009

The mystery of the rotating seeds

If you live in a temperate deciduous climate, you probably know what a maple tree is. And if you’ve been in a maple forest during spring or fall—or, really, any time of year—you’ve probably seen maple seeds. They look a bit like badminton birdies, only flattened: a heavy, solid "nut" at the bottom, with a single "wing" above. The wing helps the seed fly relatively long distances (for a plant)—up to a few kilometers in some cases.

A maple seed. From

Watching a maple seed fly is an interesting experience—they flutter and twist very rapidly. Because they twist and spin as they fall, scientists say they autorotate. In fact, they autorotate quite stably—a factor that allows the wind to carry them far from their parent trees.

Maples aren't the only trees with autorotating seeds—hornbeams, for example, have similar winged seeds. In all of these seeds, the autorotation is thought to help create extra lift on the seed, enabling it to travel farther from the parent tree. (Rambling offspring are a benefit for plants, because plant seedlings compete with surrounding plants for soil nutrients, sunlight, and water. If they land too close to the parent tree, they end up competing with their own parents—which benefits neither parent nor offspring, and therefore is detrimental to the survival of the species.)

Maple seeds and other autorotating seeds produce surprisingly large amounts of lift as they fall, considering how small and relatively slow they are. This is similar to the wings of many insects, which can produce a lot of lift from a relatively small surface area. Insect wings create this lift through the production of a leading edge vortex (LEV)—that is, a maelstrom of disrupted air along the edge of the seed that is "cutting through" the air as the seed falls. (Think of a wing—one edge of it is pushing through the air as it moves forward. The other edge trails along behind. The edge cutting through the air is the leading edge.)

In the 12 June issue of Science, Lentink et al report results of an investigation into the motions of maple seeds as they fall. Because the LEVs generated by insect wings help the insects produce significant lift, the researchers reasoned that maple seeds might produce similar LEVs.

Maple seeds are relatively small, and studying them while they fall can be challenging. This is especially true if one is interested in observing the flow of air over and around the seed as it falls. Therefore, as an initial test, Lentink et al built a scale model of a maple seed that was somewhat larger than a real seed. To make studying the movement of the air over the seed easier, they attached the model seed to a large arm inside a tank of mineral oil.

It may not be immediately clear how putting a model seed in mineral oil can be used to study the flow of air around a real seed. It turns out that this works because air and mineral oil are both fluids—substances that can flow in response to stress (pressure). As it happens, all fluids behave pretty much the same way under specific kinds of stress, provided that their differences in viscosity (resistance to flow, or thickness) are taken into account. The main difference viscosity makes is in the force required to move through the fluid—as you know if you've ever tried to walk under water. The more viscous the fluid, the more force is required to push through it, and the more slowly it returns to its original position. This latter property is the reason that many fluid dynamics studies are performed in oil or water, rather than air: the higher viscosity of a liquid makes observing its flow paths much easier. The path the liquid follows around the object is the same as the path that air would follow, so the results of the study are easily transferred to air.

Lentink et al used digital particle image velocimetry (DPIV) to make an image of the fluid flow around the model seed as it "fell" through the oil. DPIV is a technique that uses laser light, high-speed cameras, and computer integration to determine the velocity (speed and direction) of the fluid moving around an object in various locations. In DPIV, tiny particles are suspended in the fluid. During the experiment, as the fluid is moving, rapid flashes of laser light shine on the fluid, making the suspended particles visible for brief instances. A high-speed camera photographs the particles during each flash. The images are fed into a computer, which analyzes the locations of the particles during each instant. Because the computer knows the location of each particle at specific instances in time, it can calculate the velocity of each particle over time. Once the computer has calculated the velocities of the particles, it can create a three-dimensional image of how they move (and, by extension, how the fluid moves).

Using DPIV, Lentink et al identified a very pronounced LEV along the model seed. To confirm that their model seed accurately represents real seeds, they placed real maple seeds in a vertical wind tunnel. They adjusted the wind speed in the tunnel so that it matched the air speed the seeds would experience as they fell. As a result, the seeds hovered in place, but still spun the same way they would if they were actually falling. They recorded the motions of the seeds as they rotated. They were also able to create images of the flow of air around the seeds. The experiments with the real seeds confirmed the results seen in the model studies: maple seeds do, indeed, produce significant LEVs as they fall.

By comparing the maple seeds to other plant seeds, Lentink et al showed that the rotation of the maple seeds, and the resulting development of the LEVs, allows maple seeds to fall more slowly than non-rotating seeds of a similar wing loading (wing loading is the ratio of seed weight to surface area). Therefore, maple trees (or hornbeam trees, or other trees with rotating seeds) can produce heavier seeds (which can contain more food for the embryonic tree), but those seeds can still travel far enough from the parent trees to avoid competition.

Maple and hornbeam trees are not the only organisms to make use of the extra lift provided by LEVs, though. Hovering insects, bats, and possibly some birds also benefit from the production of LEVs along their wing edges. It makes me wonder whether "winged" marine organisms might generate similar vortices along their wings as they "fly" through the water.

Lentink, D., Dickson, W., van Leeuwen, J., & Dickinson, M. (2009). Leading-Edge Vortices Elevate Lift of Autorotating Plant Seeds Science, 324 (5933), 1438-1440 DOI: 10.1126/science.1174196

Tuesday, July 14, 2009

Normally I'm against Twitter, but... this case, I think I'll make an exception:
(see the original at PHD Comics.)

Friday, July 10, 2009

Calling PA residents!

If anyone who reads this blog is a resident of Pennsylvania, please contact your senator and representative today to ask them not to cut state funding for public libraries. Public libraries provide important services to those most in need during tough economic times: students, the elderly, the un- or under-employed, and other underserved populations. Many public libraries provide assistance with education and job searches. They provide free entertainment in the form of books, magazines, music, and videos. Many host tax preparation workshops, educational seminars, and social activities for seniors, children, non-native-English speakers, and the disabled.

Public libraries rely on public dollars to stay in operation. If you live in Pennsylvania and have ever used, might ever use, or know someone who uses, a public library, please write to your state congresspeople today.

If you live in an area served by the Carnegie Libraries of Pittsburgh, please attend one of the town hall sessions they are holding to determine "...the future direction of public library service to the community of Pittsburgh" (quoted from an email I received today):

WHO: Hosted by the leadership of Carnegie Library of Pittsburgh and moderated by representatives from the League of Women Voters of Greater Pittsburgh.

WHAT: A brief program will be presented outlining the financial situation faced by Carnegie Library of Pittsburgh. Individuals are encouraged to comment about Library services.

Thursday, July 16 at 7:00 p.m.
CLP - Main; Lecture Hall, 4400 Forbes Avenue

Saturday, July 18, at 10 a.m.
Carrick High School; Auditorium, 125 Parkfield Street

Tuesday, July 21 at 7:00 p.m.
CCAC-Allegheny Campus; SSC Auditorium, 808 Ridge Avenue

As a library volunteer, I thank you!

Tuesday, June 23, 2009

Good news for paleontologists?
Paleontologists, as most folks know, study fossils (or, more generally, the evidence of past life of any kind). By examining the types and distributions of fossils in rocks of various ages, paleontologists can give us insight into how life on Earth has evolved. Thanks to the study of fossils, we know, for example, that Cambrian oceans were full of trilobites, that the Mesozoic Era was dominated by giant reptiles, and that giant "terror birds" once roamed South America.

Yes, fossils are undoubtedly vital to our understanding of life on Earth. However, although fossils are the only evidence we have for the existence of past life, they have--like all evidence--limitations. Foremost among these is the preservation bias. There's a reason nearly all the fossils you'll see in a museum or private collection are fossils of shells, bones, and teeth: hard parts are much more likely to fossilize than are soft parts.

This means that critters like the sea squirt and the cuttlefish, cute though they may be, are unlikely to appear in the fossil record. Their bodies are entirely (or almost entirely) made of soft tissue, which decays rapidly once they die. About the only way soft tissue can be preserved is through mummification or other direct preservation methods; and they are pretty darned uncommon.

Size and depositional environment also play a role in preservation bias. Larger body parts may be more likely to be preserved and fossilized than are smaller body parts, because it takes large parts longer to break down (thus allowing them more time to be buried and mineralized--although this isn't a hard-and-fast rule). Similarly, critters that die in the water are much more likely to be preserved, because they're more likely to be buried before they decay completely.

Ultimately, preservation bias means that our understandings of life on Earth are inevitably biased toward largeish, ocean-dwelling animals with shells, bones, and/or teeth. This is why we know so much more about trilobites than we do about, say, ancient jellyfish.

Of course, paleontologists acknowledge this problem, and make attempts to compensate for it. One way to try to compensate for preservation bias is to use so-called "live:dead" ratios. For example, suppose in a particular ocean ecosystem 30% of the animals are bivalves, 25% are bony fish, 35% are crustaceans, and 10% are "squishies" such as anemones and jellyfish. That critter composition is known as a "live assemblage" or a "life assemblage" for that ecosystem. (I made up those numbers. They probably bear almost no relation to realistic numbers--and those particular types of critters may not occur together. Just bear with me for the sake of demonstration.) To try to correct for preservation bias, a scientist might count the number of dead critters in each category. (I should note that this type of analysis would be based on numbers of individuals, not numbers of remains--so two clam shells would count as one clam, for example.) This "dead assemblage" or "death assemblage" can then be compared to the life assemblage to figure out relative preservation rates. If, for example, 30% of the living critters are bivalves, but 40% of the remains are bivalve remains, then bivalves would have a higher preservation rate than other critters in the ecosystem.

Potential problems with this method are probably obvious: How do you know which types of modern environments to compare ancient remains to? How do you know that preservation rates in remains are the same as fossilization rates? How do you know preservation rates for different types of critters are the same today as they were then? What happens if the ecosystem changes rapidly--do the death assemblages still accurately reflect the life assemblages?

In the May 22 issue of Science, Western and Behrensmeyer present data that may help to address the last two of these questions. They used a 40-year record from the Amboseli ecosystem in Kenya to study the relative preservation rates for large mammal (15 kg-4000 kg) bones. Previous studies have shown that the life and death assemblages for these mammals are similar at specific points in time; that is, at a given time, the proportions of different species in the life assemblage are similar to those in the death assemblage.

A variety of factors have caused the Amboseli environment to change quite rapidly since the 1960s. Woodlands have shrunk, grasslands have expanded, and swamps have doubled in size. These environmental changes, in addition to direct human actions, have substantially affected the mammal populations in Amboseli during that time. The ratios of different types of organisms--grazers vs. browsers, for example--have changed as a result, and overall species diversity has declined.

Bone and live animal surveys were conducted during two time periods: 1975-1976 and 2002-2004. The bones studied during those times could be separated into subintervals based on how long ago the animal died; this allowed the researchers to divide the samples into four subintervals (1964-1969, 1970-1976, 1993-1998, and 1999-2004). They also used census data to determine the numbers of live animals in various groups during those same time intervals.

For each of the time periods, the researchers compared the proportions of different organisms in the life assemblages with those in the death assemblages. They used these data to determine how well the death assemblages "track" or represent the life assemblages. What they found is pretty interesting:

Statistically significant correlations between live populations and bone counts for the different time intervals indicate that organisms that make up a larger fraction of a living community also make up a proportionally larger fraction of the bone assemblage for that community. In other words, at least for this ecosystem, you can use the death assemblage as a pretty direct proxy for the life assemblage--if 50% of the individuals represented by the death assemblage are medium-sized grazers, then you can infer that about 50% of the organisms in the ecosystem (on average) over the time period you're looking at were medium-sized grazers. You can also use the death assemblages to study how populations in the ecosystem changed over time; the ratios of grazers to browsers in the death assemblages roughly paralleled those in the life assemblages for the same time period. They were able to distinguish changes in population composition over time scales as small as 5 years; they were even able to "predict" ecological structure from the death assemblages (and those predictions were largely confirmed by the life assemblages).

Western & Behrensmeyer's data could be very useful for paleontologists, particularly large-vertebrate paleontologists; the data suggest that bone distributions in death assemblages can be used to infer population and community structures for ancient ecosystems. With some assumptions about ecolosystem properties, bone assemblages can also be used to infer other properties of ancient ecosystems, such as species richness and productivity.

Obviously, these data have limitations; Amboseli is a relatively dry terrestrial ecosystem populated by relatively large mammals, so it's not clear whether the same correlations apply to marine ecosystems, wetter (or drier) terrestrial ecosystems, or to those inhabited primarily by smaller organisms or invertebrates. Additionally, because all of the remains studied were relatively recent (40 years isn't long enough to produce fossilization or even significant burial in most terrestrial ecosystems), it's not clear how the processes of preservation, burial, and fossilization might affect the death assemblages. (Although they do note that partially buried bones--a "pre-fossil" assemblage--seem to show the same correlations as unburied remains.) But studies like these are still very important in determining the error bars (accuracy) of ecosystem studies based on fossil assemblages.

Their data also suggest that studies of death assemblages in modern ecosystems can be of use to scientists studying the effects of human actions and other phenomena, as well as to those wishing to confirm (or obtain) estimates of vertebrate population sizes and compositions.

Western, D., & Behrensmeyer, A. (2009). Bone Assemblages Track Animal Community Structure over 40 Years in an African Savanna Ecosystem Science, 324 (5930), 1061-1064 DOI: 10.1126/science.1171155

Saturday, June 20, 2009

This is possibly one of the coolest shows ever...

So I took today off to be a lazy bum, which means I watched way too much PBS. One of the WQED digital channels, the Create channel (13.2 for those in Pittsburgh with a digital air signal), is doing a marathon of the show Make.

This is the coolest show I've seen in a long time. It's basically half an hour of people talking about and demonstrating how they make a variety of gadgets and gizmos. It's really pretty neat--things one might never think of, like using an old VCR to make an automatic cat feeder, or building kinetic sculptures.

They have a website, and it's got archived videos of their shows. Check it out!

Tuesday, June 16, 2009

What's the signal, and what's the noise?

As anyone who listens to the (non-satellite) radio knows, signal-to-noise ratio is an important consideration when analyzing a data set. If the ratio is too low, all you get is static. But what if that static actually contained its own signal?

The idea of useful information being "hidden" in apparent noise is nothing new--after all, cosmic background radiation was once thought to be just noise (and for many applications it still is). But in the May 22 issue of Science, Peter Bromirski outlines a rather unusual case of noise-becoming-signal: seismological evidence for climate change.

Geologists use seismographs to record the movements of the crust. Most of the time, the crust doesn't move much, aside from a background "hum" that results from Earth's natural oscillations. That hum can actually show up on seismograms; it has a period of 1-8 minutes or so. Occasionally, though, an earthquake--geologists also sometimes call it a "seism"--causes the crust to move much more emphatically.

During an earthquake, the movements of the crust cause the seismograph needle (or the digital analogue) to move in a specific way. The speed, amplitude, and duration of that motion are related to the motion that occurred to cause the earthquake, as well as to the composition and structure of the materials the resulting seismic waves passed through to get to the seismograph. By studying seismographs from around the world, geologists can infer where and when the earthquake occurred, what caused it, and how the waves it produced traveled. The background hum is just noise, and it's generally ignored.

The thing about seismographs is that, for the most part, they're terrifically sensitive. It's not unusual for them to detect trains and traffic. And, as Bromirski points out, under the right conditions they can also detect ocean waves, particularly those produced by big storms.

During a large storm over the ocean, high winds blow over the ocean's surface. The wind transfers energy to the water, which is where the big ocean waves come from. That energy can generate "microseisms" in the ocean crust. (A microseism is exactly what you'd guess from the name: a very low-amplitude vibration in the crust.) The vibrations produced by wave energy travel through Earth, just like those from an earthquake, and they can be detected on seismographs, too. Therefore, hypothetically, one could use seismogram records to determine the average storminess of the oceans over time.

The use of seismograms to study storminess has a few advantages over more common methods. For one thing, there are accurate seismograms that go back to the early 20th century--as far back as 1930, in some areas. These seismograms were all collected using pretty much the same technology and have similar precision, so they're readily comparable. This is unusual in climate science; many of the techniques commonly used to study recent climate change are fairly...well...recent, so the records don't go very far back or, if they do, they're much less precise.

Another advantage to using seismograms is that the global seismograph network (which has become more and more widespread over time) allows for comparisons between signals from different areas. This can allow scientists to infer the approximate paths and durations of storms in a region. In some cases, microseisms can give information about wave frequency and duration along specific coastline regions, data that may be hard to obtain otherwise.

Some studies using these long-term seismic records do suggest that Earth is becoming stormier: the ambient noise on the seismograms has increased over time.

Some researchers are also studying ways to use storm-driven microseisms to study more than storms. An important use of earthquake seismogram data is the study of Earth's interior. It's similar to the use of ultrasound to see inside the body: just as the path of a sound wave through your body depends on the density and structure of the organs below the skin, so the path of a seismic wave depends on the composition, temperature, and structure of the rock within Earth. Typically, seismologists use earthquake-generated seismic waves to study Earth's interior, because they're very high amplitude and generate strong signals. However, earthquakes are relatively rare and unpredictable. "Background" microseisms produced by storms and wave activity may provide a more long-term and consistent energy source for the study of Earth's interior.

Bromirski, Peter D., 2009. "Earth Vibrations." Science 324: 1026-1027. doi: 10.1126/science.1171839.

Using geometry to find a rainbow

Chad Orzel at Uncertain Principles has a neat little post up about rainbows.

And you thought geometry could never come in handy.

I think it's pretty neat that the angle made by two hands is nearly scale-invariant. I wonder what that angle is for chimpanzees or other apes whose arms are longer relative to their bodies than human arms are?

Scientia Pro Publica 6!

Scientia Pro Publica, the best in science/nature/medicine blogging for the general public, is now posted at Mauka to Makai. Yours truly has a post up!

Check it out.

Monday, June 15, 2009

Usage tip: complimentary vs. complementary

For me, the easiest way to remember the difference between these two is to remember the definitions of compliment (something nice you say about someone) and complement (something that completes a set or group).

Something that is complimentary is either a) free or b) flattering. (Maybe another way to remember it is to think "I like things that are complImentary". Or maybe that's just really corny.)

Something that is complementary completes a set, matches a pair, or fills out a group. Angles, base pairs, and wines can be complementary, but statements and newspapers generally aren't.

So, you can sip complimentary coffee while contemplating the complementary angles on the rafters above your head. But if you start encountering complimentary angles, you might want to get your eyes (ears?) checked...

Friday, June 12, 2009

Usage tip: enormity

Enormity does not refer to size. It means "horribleness" or "horrendousness."

If you talk about the enormity of a situation, make sure it's something terrible.

(My trusty Webster does allow the use of enormity to mean "enormous size or extent", but qualifies it by saying that it's considered "a loose use by some." Count me in that "some!")

If the Girl Scouts had badges like these...

I just discovered Science Scouts. I was a Girl Scout for more than 10 years, and earned my share of badges. But none as cool as these!

As far as I can tell, I've earned 13 of them:

The "I've named a child or pet for science" badge (Sandy's real name is Sanidine. She prefers Sandy because it's less pretentious.)
The "Works with acids" badge (Including both HF and aqua regia, plus the standard highly concentrated nastiness.)
The "I've set fire to stuff" (Levels I and II) badge (No self-respecting chemistry major--or Girl Scout!--has NOT earned these two.)
The "Somewhat confused as to what scientific field I belong to" badge (Probably pretty self-explanatory...)
The "Experienced with electrical shock (Level III)" badge (I grabbed an electric fence once. Actually, I think I've had contact with electric fences twice. Comes from growing up in the country...)
The "I know what a tadpole is" badge
The "I've done science with no conceivable practical application" badge (But don't tell the NSF.)
The "Has frozen stuff just to see what happens" (Levels I and III) badge (I haven't had much experience with dry ice.)
The "Arts and crafts" badge (I'm about to start a crocheted DNA molecule...and realized that the one in the sample photo twists the wrong way!)
The "Talking science" badge
The "I blog about science" badge

(h/t Chad Orzel)

Wednesday, June 3, 2009

It's all in your head

I think most of us are pretty willing to accept that the "will" or "urge" to move originates in the brain, and that the nerve stimulus that initiates the movement also originates in the brain.

What you might not know (I didn't) is that those two impulses--wanting to move, and initiating the movement--may actually happen in different parts of the brain.

I suppose it's not really surprising that this should be the case; the brain is, after all, a pretty big place (from a neuron's perspective), and obviously everything doesn't happen all in one spot. But in the May 8 issue of Science, Desmurget et al give pretty good evidence that the area that starts your body moving is distinct from the area that actually generates the urge to move.

The researchers studied seven human patients undergoing brain surgery for tumors. All seven were conscious during the surgery (possible because the brain, although the largest concentration of nervous tissue in the body, has no actual pain receptors on its surface), so they were able to answer questions. (Although it's not made clear in the article, presumably the patients were on several medications to relax them, but they were still conscious.)

In brain surgeries like this, doctors sometimes stimulate areas of the brain near the tumor to identify what parts of the body (or personality) may be affected by the surgery. In this case, the researchers used a similar technique to learn more about how the brain works.

During each surgery, several different regions of the patient's brain were stimulated with a small electrical probe. The shocks varied in intensity and duration. The researchers repeated the stimulations up to four times for each location, to check for reproducibility.

What they found out strikes me as pretty interesting. It turns out that, for several of the patients, when parts of the inferior posterior parietal cortex were stimulated, the patients felt an urge to move one or more body parts (arm, lips, chest, etc). If the stimulation was repeated with a higher intensity, the patients thought that they had actually moved that body part, even though no movement actually occurred. (The researchers report that one patient even said "I moved my mouth, I talked, what did I say?", although no mouth movement or speech was observed.)

Additionally, when portions of the premotor cortex were stimulated, the patients did actually move some of their body parts. When the stimulation was increased, the movement became more pronounced. However, and this was the part that I thought was kind of neat, the patients were completely unaware that they had moved at all. In fact, when they were specifically asked, the patients denied that they had moved, even when the movement was quite significant (e.g., raising an arm, or making a fist).

During the procedures, the researchers monitored the electrical signals in the patients' muscles as well. They saw no evidence of muscle movement when the parietal cortex was stimulated, even when patients were sure they had moved.

As an interesting side note, Desmurget et al report that stimulation of the right inferior parietal cortex caused patients to want to move their left limbs--hands, arms, feet, etc. However, stimulation of the left inferior parietal cortex seemed to prompt a desire to move the lips, or to talk.

Desmurget, M., et al, 2009. "Movement Intention After Parietal Cortex Stimulation in Humans." Science 324: 811-813. doi 10.1126/science.1169896
Haggard, P., 2009. "The Sources of Human Volition." Science 324: 731-733. doi 10.1126/science.1173827

UPDATE: This post appears in the June 15 Scientia Pro Publica at Mauka to Makai.

Friday, May 29, 2009

Plus, they look a lot better on a shelf.

Check out the highly scientific comparison of Kindle vs. books over at Bookgasm.

Personally, I particularly like that the scenarios they chose are so realistic and statistically likely.

(h/t John at Confessions of a Science Librarian)

Thursday, May 28, 2009


Ed Yong at Not Exactly Rocket Science has a post up about the "bacterial zoo" living on your skin.

It's really pretty amazing how many different little critters are hanging around all the time--and what a huge fraction of them are actually perfectly harmless.

It makes me wonder--when you see those articles in magazines etc. talking about all the different kinds of bacteria living on your keyboard, phone, desk, etc, they never actually say how many of them are pathogenic. My guess is that, unless you've recently had a bacterial infection, most of those bacteria the media like to use for scare tactics are actually quite harmless. But I could be wrong. Anyone have any data on that?

UPDATE: Here's a link to the "official" summary of the article from Science.

Monday, May 18, 2009

Canine dimensions

Okay, apparently Sandy isn't as spectacularly cute as I think she is, because no one wanted to look at her long enough to estimate her dimensions.

This makes Sandy sad, but she'll get over it.

But, I did say I would explain the reason for the challenge in a few weeks. Being a woman of my word, I figured I ought to follow through.

All of the people to whom I've sent photos of Sandy who have subsequently met her have remarked on her size. Apparently, people expect her to be quite a bit larger than she actually is. This led my husband and I to wonder how people judge the sizes of objects when they have no reference points. We concluded that Sandy's proportions must be more similar to those of large dogs than to those of small dogs. I was hoping for some independent data to support this hypothesis. Alas, it was not to be.

(end note: Sandy, demonstrating a typical dog attention span, has now recovered from her disappointment.


Primary sources and creationism

Chad at Uncertain Principles has an interesting post up about the difference between the humanities and the sciences with respect to primary sources. I was all set to make a short comment, when it occurred to me that what I was about to comment on actually spawned a more interesting thought:

My comment was going to be that a critical difference between many (most? all?) humanities primary sources and those in science is that, in science, the primary sources (especially old ones, like Principia) are more than likely no longer totally valid. Once Nietzsche wrote down his ideas, they were there--it's not like someone could come along and "disprove" them. That's the whole point; they're subjective. Most humanities primary sources are--the point of them is to present a position and defend it, in one way or another, but the position and the defense are both subjective. They might be more or less well-supported or more or less relevant, but they're still opinions, and therefore can't be disproved.

The same can't be said for many (most? all?) science primary sources. No one who knows any better claims that The Origin of Species is completely in line with modern evolutionary theory, because we've made discoveries since it was written. (I.e., Darwin didn't have all the facts. Neither do we today, which is why biologists in 150 years probably won't be citing papers published today as definitive references.) Not having read Principia (or even Cliff's notes of it), I can't say that's the case for it as well, but I would imagine it would be. Even in my relatively specific field, there are a few "primary" references that a lot of people go back to, but only for certain things--because the rest of the article has since been replaced by something more specific. This constant reexamination, replacement, updating, etc., of the "going thing" is a fundamental part of science, and it's the reason that it's considered questionable in a lot of fields to cite papers that are more than a few years old: we might have learned something since then that totally overthrows the previous paper. (The time scale of "acceptably recent" varies field-to-field, but it's always there.)

This led me to a thought: I'm wondering what fraction of the struggles we have with creationists might be due to a fundamental difference in the perceived importance of primary sources. A lot of creationism "arguments" against evolution are based on Origin, even though any competent biologist (or, really, any intelligent person who's taken high school biology) should be able to tell you that a great deal of the text in Origin is only somewhat correct, if not flat-out wrong. But a lot of the people arguing against evolution come from backgrounds that are, shall we say, not steeped in the fundamental concepts of science. (This isn't to say there aren't scientists who are creationists; there are. But my impression is that the vast majority of creationists are not scientists and have very little scientific training.)

How much of the problem could be attributed to creationists being more familiar with the humanities "method", and therefore reading the "original" texts and interpreting them, without bothering to think about anything that's come after them? It's completely appropriate in, say, philosopy or literature to read a primary source and then draw your own conclusions and opinions about it. And your opinions are just as valid as those of others who have read the same text and drawn different opinions. (Which isnt't to say there aren't "accepted" interpretations of many famous works, or that dissenting with those interpretations won't open you to ridicule or censure.)

How many creationists who think evolution = Darwininsm read Origin, interpret it in light of common knowledge, and then view works based on Origin (i.e., most of modern biology) as simply others' opinions?

I don't think this is the primary problem or stumbling block; I think that's more likely to be a combination of a poor mainstream understanding of the nature of science and the tendency of creationists to be indoctrinated into an absolute belief system. But I think this also might be part of it.

Thursday, April 30, 2009

Usage tip: i.e. vs. e.g.

Short and sweet:

i.e. means "that is" or "in other words". e.g. means "for example".

Vaccine safety and creationist nonsense

Todd W at AntiAntiVax has an excellent post up addressing some of the most common "arguments" against vaccination. Check it out.

(h/t Phil from Bad Astronomy)

I also recently found an excellent source for refutations to creationist "arguments" against evolution. It's quite comprehensive in scope, although each specific anti-argument is a bit brief.

Wednesday, April 29, 2009

Usage tips (double dose!): insure vs. ensure and tenets vs. tenants

The use of insure vs. ensure might seem fairly straightforward, but I've found multiple instances of its misuse even in that bastion of copyediting, fact checking, and solid writing, The New Yorker. So here we go again:

To insure something means to agree to provide payment to the owner of the thing if something happens to it. You insure your house, your car, and your health. Unless you're talking about something an AllState agent would sell you, you shouldn't be using insure.

To ensure something means to guarantee or make sure that it happens. You insure your health in case you get sick, but you try to ensure good health by eating right and exercising.

incorrect: We hope that the investment in science research today will insure advancements in quality of life in the future.
incorrect: You're required to ensure your car in most states.

I've also seen multiple incorrect uses of tenants to mean tenets. A tenant is a resident of a building. A tenet is a fundamental principle. Thus, religions have tenets, but (one would hope) not tenants.

incorrect: The tenants of Buddhism include rejection of dukkha, or desire.
incorrect: The tenets of the building sued the landlord for negligence.

Sunday, April 19, 2009

On the importance of aspect ratio in estimating canine dimensions

I have a challenge for anyone who reads this post (all two of you):

Here is a picture of my dog, Sandy.
Using only this picture for reference, please answer the following questions:

1. How tall is Sandy (floor to top of shoulder)?
2. How long is Sandy (tip of nose to base of tail, assuming her neck is stretched out)?
3. How much does Sandy weigh?

You may give your answers in Imperial or metric units. Estimates are fine. And if you have the urge, feel free to explain where your estimates came from. I'm especially interested to know if you have ever owned a dog, and if so, what kind(s).

If I get enough responses, I'll post an analysis (highly scientific and rigorous, of course). If I get only a few responses, I'll still post an analysis, but it'll be less interesting.

Regardless of the number of responses I get, in a week or two I'll post again explaining the rationale behind this challenge.

Wednesday, February 18, 2009

And it's not just the gammas...

(Sorry for all the insectoid posts; Science just seems to have the most interesting articles on our six-legged friends lately!)

It's not just gamma male beetles that benefit from fake-outs. According to an article by Barbero et al., some species of butterfly also benefit from mimicry--of ants, of all things.

Ant society is very complex; most species include a number of different "genders" and societal roles, all of which are rigidly defined. (Emancipation has not yet come to the ant world.) Certain castes of ants are more valuable, and therefore more highly protected, than others. The extreme of this is, of course, the queen, who receives the most care and attention.

Although most of the communication necessary to keeping such a complex society running is chemical (e.g., pheromones) and physical (i.e., physical contact), apparently some of it is acoustic. Adults in certain ant subfamilies can produce "stridulations" (which I assume sound something like scraping noises, although I could be wrong) to communicate. Within these subfamilies, different castes produce different sounds (and larvae and pupae produce no sounds at all).

A number of ant species are also parasitized by the larvae and pupae of other insects. Barbero et al focused specifically on the butterfly species Maculinea rebeli, which parasitizes the ant species Myrmica schencki. M. rebeli larvae and pupae can infiltrate M. schencki nests and fool the ant workers into taking care of them. A significant characteristic enabling the butterfly caterpillars to survive in the ant nest is their ability to produce chemicals that mimic the chemicals produced by the ant larvae.

However, M. rebeli larvae and pupae apparently show higher "social status" than would be expected simply from the chemical mimicry. For example, M. schencki workers will rescue M. rebeli larvae and pupae instead of "dummies" that have been painted with the same chemical mimics. In addition, M. schencki queens will sometimes treat the butterfly larvae and pupae as rivals; at the same time, the ant workers treat the butterfly larvae like queens. This discrepancy led Barbero et al to guess that perhaps the butterfly larvae and pupae are able to produce acoustic signals that increase their status in the ants' social heirarchy.

As it turns out, they may be right. M. schencki workers and queens do produce distinct stridulations (i.e., they sound different to the other ants), and M. rebeli larvae and pupae produce sounds that are more similar to the queen ant sounds than to the worker ant sounds.

To test their hypothesis, Barbero et al carried out a number of tests. First, they recorded the sounds produced by the ant workers and queens. They played those sounds to "naive" worker ants. (They also exposed control groups to white noise and to silent speakers.) The worker ants showed more interest in the ant noises than the white noise or the silent speakers. In addition, the noises from the queens caused the workers to become more alert and to assume postures that are associated with "serving" the queens. This test confirmed that worker ants do respond to acoustic signals from other ants.

Next, the researchers recorded sounds from butterfly larvae and pupae. They played those sounds to similarly "naive" worker ants. The ants responded to both larval and pupal calls in the same way they responded to the queen ant calls.

Based on their observations, Barbero et al conclude that M. rebeli larvae and pupae are first able to enter an M. schencki nest through chemical mimicry. Once they are inside, however, acoustic mimicry may also play an important role in preventing the ants from rejecting them.

Barbero, Francesca, Jeremy A. Thomas, Simona Bonelli, Emilio Balletto, and Karsten Schönrogge, 2009. "Queen ants make distinctive sounds that are mimicked by a butterfly social parasite." Science 323: 782-785. doi: 10.1126/science.1163583

More insect phenotypic funkiness

Like the male members of many species, male beetles fight over female beetles. And, like male deer and antelope, many male beetles sport formidable (for a beetle, anyway) horns, spines, and mandibles, which they use to intimidate (if not outright harm) other males. In the February 6 issue of Science, Rowland and Emlen report that some male beetles take a different tack: instead of fighting over the ladies, they pull an Achilles and "dress" like them.

Rowland and Emlen conducted statistical analyses of body size and horn, mandible, or spine length for several different species of beetles. Most previous analyses had assumed only two main male phenotypes for each species (e.g., big horns and small horns, with hornless males being classified in the "small horns" phenotype). Rowland and Emlen, however, found that several species of beetles actually show facultative male trimorphism--that is, the males actually demonstrate three distinct phenotypes (alpha, beta, and gamma). Alpha males have large bodies and large horns (or mandibles, or spines). Beta males have smaller bodies and smaller horns (mandibles/spines). Gamma males have the smallest bodies and no horns (you get the idea).

The differences in phenotype are facultative because they don't seem to be related specifically to genotype. Instead, the main factor determining whether a male is alpha, beta, or gamma seems to be his body size at maturity--beetles that get lots of food and good living conditions end up as alpha males (big bodies = big horns), while beetles that get less food and are smaller at maturity end up as betas or gammas.

Alpha, beta, and gamma males also seem to employ somewhat different mating strategies. Alpha males have the typical pissing contests for access to mates--for example, some alpha males will guard the burrows where the ladies are living, and fight off all comers. Beta or gamma males, though, are sneakier: they might dig side tunnels into the burrows and cuckold the alphas without ever having to fight them. In some other species (e.g., cuttlefish), "gamma"-type males actually get in with the ladies by "cross-dressing"--for example, some male cuttlefish can change color to mimic female cuttlefish, thus allowing them to get in close enough to mate with the females while the other males are busy showing off.

According to Rowland and Emlen, previous studies (and phenotypic analysis methods) have assumed that the majority of beetles display male dimorphism, rather than trimorphism. They suggest that alternative analyses may be necessary to detect trimorphisms--apparently, some of the traditional analyses did not detect all three male morphs in the beetles they studied.

I suppose the moral of the story is, if you're an alpha male, you might want to check the skirts of the ladies in your harem!

Rowland, J. Mark, and Douglas J. Emlen, 2009. "Two thresholds, three male forms result in facultative male trimorphism in beetles." Science 323: 773-776. doi 10.1126/science.1167345

Thursday, February 12, 2009

Darwin in Context

I've been trying to figure out what to write about for my Blog for Darwin entry. I've been reading Origin, but I haven't finished it yet (the last few chapters are not nearly as interesting as the first few). Even so, as I've been reading, I haven't really been struck with any brilliant insights or profound thoughts. One thing that has occurred to me a lot, however, is just how much we've learned since Darwin's time. So, I thought that for my BfD contribution, I would outline what was going on in science while Darwin was doing his thing. I'm hoping it might give some insight into what Darwin did and didn't know, and how his ideas may have been influenced by what was going on around him.

Disclaimer: I am not a historian; the summary below is not intended to be exhaustive. I'm mainly going to focus on the big ideas and events; if you're interested in the gory details, there are a plethora of excellent books out there to satisfy you, I'm sure. Also, please note that I've done my best to verify all of the information below, but I'm not an expert in this stuff. Any errors are solely my responsibility. If you find any, please let me know!

By the 1800s, the study of chemistry was becoming modernized. In the 1600s and 1700s, naturalists began to discover general laws that govern natural processes. Both Boyle's law and Charles's law (on the properties of gases) had been discovered by the early 1800s; a number of gaseous elements and compounds (including oxygen, nitrogen, and nitrous oxide) had been isolated and described.

John Dalton proposed his atomic theory in the early 1800s; although his concept of the atom (i.e., hard, solid, indivisible sphere) has since been replaced, his work on the conservation of mass and the law of definite proportions still underlies much of modern chemistry. His law describing the partial pressures of gases in a mixture is still used today.

The early 1800s also saw the publication of Avogadro's hypothesis (i.e., that equal volumes of gases at the same temperature and pressure contain the same number of molecules).

In the mid 1800s, Lord Kelvin proposed the idea of absolute zero and an absolute temperature scale.

What Darwin didn't know: Most elements were not identified or isolated until after the 1860s. Electrons were not discovered until the late 1800s; the concept of the atom as we know it today (i.e., nucleus of protons and neutrons surrounded by electrons) was not developed until the twentieth century. The nature of chemical bonding was also unknown in Darwin's time, as was the periodic table and the notion of periodic properties.

Electricity and magnetism were the order of the day in eighteenth and early nineteenth century physics. Franklin "discovered" electricity in the late 1700s; Ohm's law was proposed in the 1820s; Oersted discovered evidence of a magnetic field around a current-carrying wire in 1820; Faraday discovered electromagnetic induction in the 1830s; Joule and Helmholtz proposed the law of conservation of energy in the 1840s.

Newtonian mechanics were well established by the 1800s.

What Darwin didn't know: Radioactivity, quantum physics, relativity, and nuclear physics were decades to centuries away in Darwin's time.

As Origin does a pretty decent job of summarizing what was going on in evolutionary biology (such as it was) at the time it was written, I won't spend space on that here. In the mid-1800s, the idea that all living things are made of cells was just beginning to take hold; spontaneous generation was beginning to be discredited. Taxonomy was becoming more rigorous. Paleontology was starting to become a well-established field; most naturalists accepted that the majority of the fossils being unearthed around the world represented organisms that no longer exist.

What Darwin didn't know: Genetics and the theories of inheritance had not been discovered when Darwin did his work; a story I've heard (which I have not verified) is that Darwin had Mendel's papers on his desk when he died. Molecular biology, most of microbiology, and, of course, genomics were completely unknown. The germ theory was still a few years off, as was the discovery of many disease-causing microorganisms.

Earth Science
Naturalists were just beginning to come to grips with Earth's immense age during the late 1700s and early 1800s. The best consensus was that Earth was a few hundred million years old at most; these estimates were based on rates of physical processes (such as sedimentation and cooling). Radioactivity was unknown, so both a method for accurate dating and a mechanism for keeping Earth "warm" for long periods of time were lacking.

However, the principle of uniformitarianism was pretty well accepted, having been proposed in the late 1700s. As I mentioned above, paleontology was becoming more rigorous and "scientific," although some of the interpretations of fossils--especially dinosaurs--were rather interesting.

The idea of a global geologic column or time scale was becoming increasingly popular. Indeed, Darwin makes many references to the accepted contemporary time scale (although the time scale of the mid-nineteenth century bears little resemblance to our modern one).

What Darwin didn't know: The theory of plate tectonics was still about a century away. Radiometric dating (and an understanding of how radioactive decay has heated the planet) wouldn't be developed for quite a while, so Earth's true age was unknown to Darwin. In addition, research into the fossils and strata of the planet was generally restricted to Europe and North America, so Darwin's (and everyone else's) ideas about geologic history (and paleontology) were accordingly limited.

Well, there you have it: the two-bit tour of the state of science in the 1860s. I hope this is helpful to someone. If I had time, I'd go into more detail...yet another item to add to my "things to do when I win the lottery" list!

Tuesday, February 10, 2009

If the Egyptians had only known...

According to legend, one of the way the Egyptians were punished in the time of Moses was with a swarm of locusts.

Locusts are insects that look a bit like big grasshoppers. They're a classic example of what's called phenotypic plasticity. An organism's phenotype is basically its observable characteristics--behavior, color, size, etc. (Phenotype is the outward expression of genotype; genotype is the specific group of alleles that an organism has. Most--all? I'm not sure--genes have at least two alleles, or "flavors." The classic example is, of course, Mendel's peas; the gene that controls flower color in pea plants has two alleles, purple and white. A pea plant's flower-color genotype is the particular combination of alleles that it has; its flower-color phenotype is the particular color of flower it produces.)

Organisms such as locusts that demonstrate phenotypic plasticity can undergo significant changes in behavior, appearance, etc due to changes in their surrounding environment. Locusts are a classic case because the change is so dramatic. If you take two locusts and put them in a box, they will pretty much avoid each other--that is, assuming they're demonstrating the "solitarious" phenotype. This is pretty much the default position for locusts; most of the time, they hang out by themselves (not a lot of singles bars in their neighborhoods, I guess).

Now if you had put, say, 20 or 30 solitarious locusts in that box and shut them in for a couple of hours, they would be quite changed when you opened the box. They would be swarming together, and they would have changed in appearance (from kind of boring and green to a rather striking, Steelers-like combination of yellow/tan and black...sorry, couldn't help it). They would be demonstrating the "gregarious" phenotype.

Solitarious (top) and gregarious (bottom) desert locusts. Image from Dr. Tim Matheson, University of Leicester

Locusts in the gregarious phase are the stuff of legend. These are the critters that mow crops down to the roots and blacken the skies. (Presumably, the Egyptians crowded their locusts.)

The cause of the transition from solitarious to gregarious has been known for a while, at least in broad strokes: being in the presence of lots of other locusts makes a locust more gregarious. In a recent article in Science, Anstey et al identify the mechanism that triggers the transformation.

There are two different sets of stimuli that can make a locust more friendly: mechanical and "cephalic." Mechanical stimulation involves being jostled by other locusts; in contrast to most humans, most locusts become more friendly when strangers stroke their legs. Cephalic stimulation involves the sight and smell of other locusts; locusts apparently have really great makeup and cologne. Both types of stimuli cause the locust's central nervous system (CNS) to produce (what else?) serotonin. (Yes, that serotonin.)

Previous researchers established that serotonin levels are higher in locusts undergoing the solitarious-to-gregarious transition. Anstey et al set out to determine the limits of this relationship. They did four main experiments: first, they figured out whether artificial stimulation of the individual sensory pathways could stimulate serotonin production and gregariousness. Then, they tested whether serotonin antagonists (i.e., chemicals that block the action of serotonin) could prevent the onset of gregarious behavior. Third, they determined whether artificially increasing serotonin levels was enough to induce gregariousness. Finally, they determined whether giving the locusts a serotonin precursor (i.e., a chemical that is easily converted to serotonin) increased their sensitivity to environmental stimuli.

In the first experiment, the researchers either stroked the hind legs of solitarious locusts, stimulated the nerve connecting the legs to the CNS directly, or put the locusts in a cage that allowed them to see and smell (but not touch) other locusts. In all cases, the locusts switched from solitarious to gregarious, and serotonin levels increased, suggesting that either type of stimulation is sufficient to induce gregariousness.

Next, they injected some of the locusts with serotonin antagonists (they also, of course, injected others with just saline--this was the control group). After the injections, the treated locusts (the ones that received the antagonist) were significantly less responsive to stimuli than the control locusts; treated locusts did not become gregarious, even when exposed to stimuli that caused the control locusts to boogie down. This relationship showed that inhibiting the action of serotonin prevents the "phase change."

In the third experiment, Anstey et al applied serotonin directly to the locusts' nerves (again, they also used a control group that received just saline). They also injected a third group of locusts with a serotonin agonist (i.e., a chemical that increases the activity of serotonin--the opposite of an antagonist). The treated locusts became much more friendly, but the control locusts remained aloof. In other words, just increasing serotonin levels (without actual stimuli) can make solitarious locusts more gregarious.

In their final experiment, the researchers determined whether increasing the ability of the locusts to produce serotonin would cause them to become more gregarious after only a small amount of stimulation. Typically, a solitarious locust has to hang out with other locusts for a couple of hours before putting on its party shoes. However, when solitarious locusts were injected with a serotonin precursor, 30 minutes of exposure was enough to get them dancing.

There's some hope that these results might lead to new possibilities for locust control. Individually (i.e., in the solitarious phase), locusts aren't too much of a problem--no more so than, say, grasshoppers, really. It's only when they start to swarm that they become economically disastrous. If a way could be found to prevent locusts from become gregarious, even when crowded, then locust swarms could be controlled. (Too late for Rameses, of course.) Such possibilities are still in the future--currently, there is no locust-specific serotonin antagonist that can be applied appropriately--but it does give some hope.

Until then, there is one thing we can definitely conclude: keep the locusts away from the Prozac!

Anstey, Michael L., Stephen M. Rogers, Swidbert R. Ott, Malcolm Burrows, and Stephen J. Simpson, 2009. "Serotonin mediates behavioral gregarization underlying swarm formation in desert locusts." Science 323: 627-630. doi 10.1126/science.1165939

Stevenson, P.A., 2009. "The key to Pandora's box." Science 323: 594-595. doi 10.1126/science.1169280

(Yes, I know this isn't quite 1,000 words. But it's pretty darned close!)

Blogging for Darwin

I joined the Blog for Darwin blog swarm (which means I have to actually finish Origin soon, so I have something to write about). Check it out--it's pretty cool.

I haven't decided yet what to write about; I'm having a hard time coming up with anything super profound. I'll wait and see if any inspiration strikes as I keep reading.

Thanks to Newton's Ocean for the link.

Thursday, February 5, 2009

From opposite ends of the spectrum

Apparently, the downturn in the economy is causing some of us to become a bit too obsessed with language.

On the other hand, some are just giving up in disgust (or despair?).

And some are robbing stores with bat'leths.

(Thanks to Lou for the first link, erv for the second, and Gwynne for the third.)

Friday, January 23, 2009

You would think...

...that in 200 years, the anti-science crowd would have come up with some new objections to evolution. Apparently not: Check out this quote from Origin.

Long before the reader has arrived at this part of my work, a crowd of difficulties will have occurred to him...These difficulties and objections may be classed under the following heads:--First, why, if species have descended from other species by fine gradations, do we not everywhere see innumerable transitional forms?...

Secondly, is it possible that an animal having, for instance, the structure and habits of a bat, could have been formed by the modification of some other animal with widely-different habits and structure? Can we believe that natural selection could produce, on the one hand, an organ of trifling importance, such as the tail of a giraffe...and, on the other hand, an organ so wonderful as the eye?

Thirdly, can instincts be acquired and modified through natural selection? What shall we say to the instinct which leads the bee to make cells, and which has practically anticipated the discoveries of profound mathematicians?

These questions, of course, have many parallels in the standard litany of "problems" with the theory of evolution often spouted by creationists and intelligent design proponents. Is this yet another example of Darwin's apparent prescience? Or is it more accurate to say that Darwin's statements echo those of modern-day denialists because they are building on the "work" of those who came before, who undoubtedly read Darwin? If the latter, it's really a shame they didn't read the whole book. Even if they'd read a few pages further on, they would have come across this beauty:

When it was first said that the sun stood still and the world turned round, the common sense of mankind declared the doctrine false; but the old saying of Vox populi, vox Dei, as every philosopher knows, cannot be trusted in science.

Perhaps it might be better said that Vox populi, vox veritas "cannot be trusted in science." But the sentiment still holds: Just because most people think it's so, doesn't make it so. The fact that so many people argue that we should teach the Bible as science because "most Americans believe in God" speaks to a fundamental lack of understanding of the way science is done. But I'm not the first to make that statement, nor will I be the last.

Friday, January 16, 2009

Self-catalytic RNA enzymes

GumbyTheCat recently posted about a study in which researchers created self-replicated RNA enzymes. There was a bit of discussion in the comments about what those enzymes are all about and whether they are, indeed, "true" enzymes (i.e., proteins).

As I have access to Science magazine online, I was able to read the actual article (Gumby's post was based only on the abstract, I think), and so I can now answer the question of what, exactly, an RNA enzyme is, and how the research group got it to replicate itself.

An RNA enzyme, it turns out, is not a true enzyme. That is, it isn't a protein made up of amino acids. It's actually a strand of RNA. The particular RNA enzymes this group made look kind of like a capital T with one side of the crossbar a lot longer than the other. Like all RNA, they're made up of nucleotides (a nucleotide is a molecule consisting of a sugar molecule--ribose, in the case of RNA--a phosphate group, and a nitrogenous base). (I am forced to conclude that the "RNA" in "RNA enzyme" is an adjectival form, rather than a description of what the enzyme catalyzes.)

To understand how the enzyme works, you first need to know a bit about bonding in nucleic acids (DNA and RNA). What follows is a brief discussion; details can be found in any introductory biology textbook.

A single strand of a nucleic acid is a polymer (a really big molecule made up of a lot of similar, smaller subunits called monomers). As mentioned above, the monomers in nucleic acids are nucleotides. When nucleotides join together to form a nucleic acid, the sugars and phosphates bond together to form a "backbone." The nitrogenous bases stick off one side of the backbone. There are five nitrogenous bases that can form nucleotides: thymine, adenine, uracil, guanine, and cytosine. They are abbreviated T, A, U, G, and C, respectively. A, T, G, and C are found in DNA; RNA contains A, U, G, and C. So, a single strand of RNA looks kind of like half a ladder; the rungs are A, U, C, and G molecules. A double-stranded nucleotide (such as DNA) looks like a full ladder; the base in each "rung" is bonded to another base on a rung on the other side of the ladder. The bonded bases form a full rung. (Of course, a DNA molecule really looks like a twisted ladder, but the physics of why it twists isn't important for our purposes here.)

These bases aren't just any random molecules, though. As it turns out, their molecular structures force them to bond together in specific ways: A can bind only with T or U, and G can bind only with C (and vice versa, in each case). In a double-stranded nucleotide, therefore, each rung is made up of either a C-G pair or an A-T (or A-U if it's RNA) pair. You can probably see the beauty of this arrangement: it means that if you have one half of a double strand of RNA or DNA, you can construct the other half.

As I mentioned before, the RNA enzymes in this study look like lopsided Ts. The stem of the T is actually a double strand of RNA: part of the RNA molecule has bonded to itself. (A similar structure is found in some kinds of RNA that take part in transcription and translation in eukaryotic cells.) The crossbars of the T are single strands of RNA.

Each enzyme forms from two smaller pieces of RNA: a straight piece (called "B") and a piece that looks like a regular (i.e., not lopsided) T (called "A"). The straight piece binds to one of the crossbars of the T-shaped piece to form the lopsided T (which the researchers refer to as "E", for enzyme).

Each enzyme (and each sub-enzyme piece) actually exists in two "mirror-image" forms (i.e., E and E', A and A', and B and B'). The mirror-image forms can bind to each other because of the way the bases pair. However, A doesn't bind to A', or B to B'. Instead, A binds to B', and B bonds to A'. The A-B' combination forms E; the A'-B combination forms E'. [EDIT: the previous sentences should read "Instead, A binds to B, and B' binds to A'. The A-B combination forms E; the A'-B' combination forms E'."] The drawing below shows my lame attempt to summarize.

Essentially, when the researchers put some E into a mixture of A, B, A', and B', the A' and B' pieces bonded to the E to form molecules of E'. Once there was some E' in the mixture, the A and B molecules could bond to it to form new E molecules, and Presto! self-replicating RNA.

Of course, it wasn't really that simple. And actually, the not-simple part is kind of cool: The original E that the researchers used wasn't very efficient at catalyzing its own formation. So, basically, the researchers evolved it. They generated new A and B with mutations--variations in the sequences of bases on the backbone--and selected the ones that formed E that could replicate itself most quickly.

Because they have groovy tools (such as polymerase chain reaction machines) and computer to do the analysis, they were able to try a whole lot of different combinations in order to find the set of A and B that produced the most efficient E.

All in all, a really groovy little study!

Lincoln, Tracey A., and Gerald F. Joyce, 2009. "Self-sustained replication of an RNA enzyme." Sciencexpress. published online 8 January 2009; 10.1126/science.1167856.