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.