Category Archives: Science

More about Sandy -or- I have data!

I explained in an earlier blog post the significance of the sampling effort that was undertaken to understand the pattern of isotopic values, and how this changed over time, of precipitation coming from Superstorm Sandy as it made its landfall and slowly died over the interior of North America.

I ended my sampling effort on Saturday night after collecting a total of nine samples, one every twelve hours since about the time Sandy made landfall on Monday night, the 19th of October. There was only one span of time – on Halloween – when it did not rain sufficiently for me to collect a sample.

Precipitation samples from Superstorm Sandy collected at my house. Rain water was collected in a bucket (that was strapped down so it wouldn’t blow away!) then poured into vials at approximately twelve-hour intervals. The bucket was dried then set out again.

These nine fine samples are now on their way to the University of Utah where their isotopic values will be measured. But, see, I’m also an isotope geochemist. And I also have a water analyzer in my lab. And I might be just a tad impatient.

So I analyzed the waters before I sent them off.

Our water analyzer, Norm, analyzing the Sandy waters. This is a Los Gatos Liquid Water Isotope Analyzer.

Let’s think back on what I said before, about Rayleigh Distillation. So if a cloud rains, the isotopically heavier water (mass 19 or 20) is more likely to fall (because it’s heavier) than the more common, lighter (mass 18) water. So the rain is isotopically heavier than the cloud. After the rain has fallen, the cloud is isotopically lighter than it was before.

So, what happens when that cloud rains again?

When a big storm (like Sandy) moves inland, the rain causes the cloud to get lighter and lighter. And since the cloud water is getting lighter and lighter, so does the rain coming from the cloud, though it is always heavier than the cloud itself. This leaves a tell-tale pattern of heavier isotopes near the coastlines where the storm first came on land, to lighter and lighter isotopes further inland.

So what pattern would you expect if you did all your sampling in one place and a storm simply passed over? What if a storm parked over your house and rained for days and days? What would that look like?

Think about it. I’ll give you a few minutes. I need a glass of water.

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Keep thinking. I need to check my e-mail.

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Any ideas?

Well, it would stand to reason, that unless – somehow – heavy water vapor was getting back into the cloud, the isotopic values would get lighter and lighter over time.

So, one might predict that the rainwater that I collected would get lighter and lighter over time.

Let’s see:

Isotopic values from precipitation from Superstorm Sandy collected near Rochester. Blue lines and symbols are hydrogen; Red lines and symbols are oxygen. The patterns are very similar, as they should be. Hurricane Sandy makes landfall on the left side of the graph. Water samples are plotted according to when I collected the sample (at the end of the twelve-hour period). In the final analysis, it’ll probably be plotted by the mid-point of the sample interval.

The pattern we expected to see was completely borne out for the first three collections, from when Sandy made landfall, to when the center of the storm was supposed to be over the Rochester area, where the samples were being collected.

But then what happened? The values start to increase again. Any ideas?

Well, for one thing, Sandy was supposed to pass over Rochester on Halloween, but it didn’t. The bulk of the storm passed to the south. In fact, it didn’t rain at all on Halloween (which made trick-or-treating possible!). Superstorm Sandy swung south and then west of Rochester before becoming too diffuse to know where the core of the storm was.

Something happened. Something changed.

Well, maybe some heavier isotopes did make it into the vapor mass. Perhaps it was the arctic front that was swooping down from the north as Sandy struck from the east that brought the isotopically heavier rain. It definitely cooled off. It was snowing occasionally during those last two sampling intervals. I suppose it’s also possible that the storm picked up some moisture from the Great Lakes as well.

Again, this is the beauty of the larger project and sampling effort. With only one sample site, we can’t be sure. But once we have all the data from the 100+ sampling sites, we’ll be able to map in detail what was happening. It will be obvious of secondary vapor masses (clouds, storms) joined up with the remnants of Sandy. We’ll be able to tell where and when that occurred.

It’ll be a while before all those samples are gone through and analyzed. I sent my own samples off to Dr. Bowen, so he can re-analyze them using his own instrument and add the data to his huge database. In the meantime, I have this one tiny subsample of the data and a lot of excitement for what will be discovered when the entire data set is complete!

Stay tuned!

Peer Review

As a scientist I am frequently asked to review other people’s writing. Typically, it’s a scholarly journal article that I need to read. Other times it’s a textbook that needs a review. These things don’t pay (though sometimes they have perks) and take time, sometimes lots of time. So why bother?

Why should I spend hours and hours reading someone else’s paper when I could be working on my own? My job might depend upon me publishing something scholarly every year. Sometimes more than one paper. And the work I might do on reviews isn’t ‘billable,’ so if you have that kind of job, why waste your time?

Well, here’s some reasons why:

1) You get to read the latest in research even before it’s published.

2) You can keep BAD science from getting published.

3) You can learn the difference between a well-written paper and a poorly written paper, thereby improving your own work.

4) You can help someone make a good paper much, much better.

5) You can save a scientist from accidentally publishing something that has a blaring error.

Really, the peer review process is intended to make sure that anything that makes it to publication is grounded in reality. Published scientific papers should report ‘truth,’ or at least as close to truth that is possible given the current state of knowledge. Peer review is a necessary part of the scientific process. If scientists stop reviewing each other’s papers, science stops. If you’re not willing to review someone’s paper, then I’m not sure you’re doing science right.

So I keep reviewing papers whenever I’m asked. I do the best I can. And when I publish something, I’m grateful to the reviewers who looked at it, whether they remained anonymous or not, or even if their entire review is snarky. That’s okay. I learn something anyway.

And with that… I have a book to review. Cheerio!

Frankenstorm and the Isotopes

Earlier this week, Hurricane Sandy (an anomalous late-season hurricane) made landfall in the United States near Atlantic City, NJ (also anomalously far North). Because of the timing of Sandy (near Halloween), and it’s coincidence with another strong system moving across North America from the West, the weather event was given the moniker “Frankenstorm”.

This storm was a big deal, and my heart goes out to everyone adversely affected by its aftermath. My own heart broke with each image the popped up on my Twitter-feed that night. Yet there were some heartwarming stories, and certainly some good will come from this unfortunate event.

Much of the discussion of Sandy revolved around how unusual it was and how it might be related to global warming. I even got a call from a local journalist wondering if I would be willing to comment on that. (I said no, because it’s really outside of my realm of expertise, but hopefully might be contacted later regarding ancient episodes of global warming which really are my specialty.) There are plenty of web resources on the topic, which cover that question better than I can. This is one of my favorites.

This is all interesting, but is not why I was kind of excited about Sandy (in the way only a geochemist can be). For me, Sandy provides an opportunity to verify what we think we can learn about ancient weather patterns using chemical tracers in rocks. That is, Sandy is a natural isotopic experiment. I’m not the only person who thought this. Gabriel Bowen of the University of Utah thought of it first.  I’ll explain below.

Before you get upset about the term ‘isotope,’ remember that all atoms are isotopes and that not all isotopes are radioactive. Most atoms are ‘stable’ meaning that they don’t undergo radioactive decay. It’s just that the term ‘isotope’ makes people think of nuclear reactors and meltdowns (and somehow Homer Simpson).

So then, what do I mean by an isotopic experiment? I’ll save the details of how isotopes work for a later blog post, and just start with a simpler story of just water. Different isotopes have different masses, or weights. Most water molecules have a weight of 16 atomic mass units. Let’s just say most water has a mass of 18. Some water molecules have a mass of 19, where one of the hydrogen atoms is ‘heavy’ (but stable) and some molecules have a mass of 20, where the oxygen atom is ‘heavy’ (but also stable).

When the mass of the molecule is heavier than most (19 or 20 versus 18) the molecule is, well, heavy! That means that if water evaporates, the lighter (mass 18) molecules evaporate first, because they’re lighter, leaving the heavier water (mass 19 and 20) behind in the puddle. This seems very common-sense, and it is. Vapor that evaporates from puddle is lighter than the water that remains in the puddle and, in fact, the remaining water gets heavier. This process is called fractionation.

Now, if we have a bunch of water vapor, like a cloud for example, and the vapor condenses, the heavier water condenses first and falls as rain (because it’s heavier). The rain is heavier than the vapor in the cloud and the cloud’s water gets lighter and lighter as it rains more. Again, this is fractionation.

When we’re talking about isotopes, we use this crazy delta notation. If we want to say something about the oxygen isotopes in water we use δ18O. For hydrogen, we use δD or δ2H. The number we report is really a ratio, but we tack on the permil symbol (‰) to make the numbers easy to talk about (again, this is something to talk about later). What’s important is that if the delta value is more positive, that means that the water is heavier. If the delta value is more negative, the water is lighter. Everything is measured relative to ocean water which has been assigned a delta value of zero for both hydrogen and oxygen. δ18O = 0‰ and δD = 0‰ for ocean water.

A hurricane, like Sandy, gets all its water from the evaporation of the ocean – so the clouds forming over the ocean will have delta values more negative than zero. As long as the storm is over the ocean rain from the hurricane and falls back on the ocean and new water evaporates keeping the isotopic value of the clouds stable. But once the storm moves over land, the addition of new water vapor from the ocean stops, but lots of water is lost as rain.

The result is that as a storm moves across the landscape, the isotopic value of the cloud gets lighter and lighter over time. The precipitation coming from the cloud also gets lighter and lighter over time, though it’s always heavier than the cloud it came from.

This is called Rayleigh Distillation, and is one of the basic concepts in isotope geochemistry. It seems pretty straight forward and reasonable, and has been used as the basis of isotopic interpretation for many years. But it’s been difficult to test… Until now. With electronic messaging and, more importantly, social media, it is now possible to recruit a fleet of people of a broad geographic area with only a few hours notice to collect rain samples that can then be measured for their isotopic values. We can finally ground-truth this important hypothesis!

This was tried for the first time with a storm called “Snowzilla” (now less creatively called the ‘Groundhog Day Storm’) that happened in 2011. Snow fractionates from clouds just like rain does, so would be expected to show a similar isotopic pattern as rain water. When this huge storm that hit much of the eastern United States, and Gabriel Bowen, then at Purdue University, put out a call for people to collect snow samples and send them to him. The results are detailed here.

The pattern of hydrogen isotopes from the Groundhog Day Storm in 2011. Warmer colors represent isotopically heavier water.

Looking at the figure, we see that the isotopic values shift from more positive in the southeast to more negative in the northwest. From this, it’s easy to see that the vapor moved in from the Gulf of Mexico and Atlantic Ocean.

What might we expect to see from Sandy? Well, this time when the call went out, Dr. Bowen asked participants to collect samples over specified time intervals and to record those times, meaning that it will be possible to make an isotope movie and perhaps watch Sandy move across the continent.

So… Why does this matter? Oxygen isotopes from rain can be preserved in rocks. As rain water is exposed to carbon dioxide and percolates through the soil, it forms carbonate (CO32-)which is then bound into carbonate minerals like calcite. This calcite can form little nodules in the soil or a calcrete layer. The oxygen in the carbonate records the oxygen in the water (with a little more fractionation). Later – as in millions of years later – geoscientists like me can analyze the oxygen from the carbonate and get back to the original distribution of oxygen isotopes in the rain water. From there, we can then figure out ancient air-flow patterns around the world.

With this knowledge, we can start answering other questions. How does the uplift of high mountains (like the Himalayas) affect global air flow? What happens to air circulation when climate changes rapidly, whether it be warming or cooling? We can address these questions and more, which might help us understand what the future might bring if projections of warming bear out.

In the meantime, I’m a participant in the project myself and am still collecting waters. Sandy’s not quite dead, though her destructiveness is well past. We’ll see what the data tell when all is said and done!

***UPDATE***

Here they are: the sample set from my house. I’m done sampling, so the analyses can begin!

Nine rain water samples I collected for the isotopic study of Hurricane Sandy.

 

SVP – Scenes written screenplay style

Because I’m weird like that, I decided to write up some bits of the 2012 annual meeting of the Society of Vertebrate Paleontology in a screenplay format.

This would never make a good movie or TV show and here’s why: NO CONFLICT! There’s over 1000 of us there, and we’re all so happy to be there that there is no conflict. Nothing happens! Everyone is happy.

So, it’s a lousy script, but it highlights some of the things that go on at these meetings, in its own special bizarre way…

Some names have been changed to protect the innocent, and things are written mostly how I remember them, which might not be reality. If you think I might be talking about you, well, I might be!

Also, please forgive the formatting errors. They’re there. I couldn’t make it work right. Poo.

By the way, these things really did happen. …mostly.

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#2012SVP: The movie

EXT. MAJOR HOTEL – NIGHT

PENNY HIGGINS, middle-aged paleontologist exits an airport shuttle bus. She gathers her belongings, pays the driver and enters the hotel.

INT. MAJOR HOTEL – CONTINUOUS

Penny passes through sliding glass doors and is met by the din of loud discussion. She looks toward the bar and sees a crowd within, the source of the noise. She smiles and nods. She knows the sounds of paleontologists.

PENNY
(to herself)
Paleontology. How I love thee!

INT. DARKENED CONFERENCE ROOM – DAY

Penny is checking Twitter on her phone. A tweet from the host society shows up “Beware the flatulent chairs. Sit carefully.”

Penny raises slightly from her seat and sits back down hard. The chair toots. Penny eyes the person sitting beside her. He’s looking back, eyes wide.

PENNY
Oops! Excuse me!

The man smiles and returns his attention to the speaker.

Another person enters the room and sits in front of Penny, causing his chair to emit a loud farting noise. Penny struggles to contain her laughter and quickly re-tweets the earlier tweeted warning.

INT. CONVENTION CENTER – POSTERS – DAY

The room is arranged with several rows of posters, presenting scientific results. Between the rows are packed hundreds of paleontologists, discussing the posters among themselves and with the authors. The room is a cacophony of voices. Nearly everyone has a drink.

DAN
So tell me your story here.

PENNY
(points to poster)
Well, our data seem to show that this takes about one year. But I’m told you’ve already done this.

DAN
Yes.
(grins sheepishly)
We got our data ten years ago. We just haven’t published it yet.

PENNY
Well, you need to publish it! Your data sound better than mine. And your results make better sense.

DAN
We’ll get to it.

PENNY
I’m gonna e-mail you every week until it’s published

DAN
Maybe you should.

Dan moves on. One of Penny’s friends approaches.

JUDY
How goes it?

PENNY
Yeah. This work’s been done already.

JUDY
What happened?

PENNY
This is what happens when people don’t publish.

JUDY
That stinks.

PENNY
At least it wasn’t an oral presentation – or worse: a rejection from a journal. We move on.

Judy pats Penny on the shoulder.

JUDY
It happens.

INT. DARKENED CONFERENCE ROOM – DAY

A video is playing of a Hyena eating a big chunk of meat and bone. Penny furiously tweets what she is seeing. Numerous other tweets scroll past, highlighting the same thing, each containing the phrases “bone cracking” “hyena” and “pig neck”. Penny grins, relishing the morbidity of her paleontological colleagues.

Someone sits down near Penny, causing the chair to fart. Restraining laughter, Penny heads out to find coffee.

INT. CONFERENCE ROOM – DAY

A silent auction is being set out. Items are spread out over several tables throughout the room. People are running around sorting items and arranging them in an appealing way.

Penny enters lugging a hefty wooden rocking-dinosaur.

PENNY
Yup. This is it. You’re going to a new home.

Penny looks around and finds who she’s looking for.

PENNY
Brent!
(indicates the dinosaur)
Silent or live?

BRENT
Live.

Penny hoists the dinosaur onto a table in front of the stage, where the live auction will take place later in the day.

INT. MEETING ROOM – EVENING

Six people stand around, four of whom are dressed as characters from the movie and comics “The Avengers.”

Penny walks out of a back room in a white and black pleather body suit.

PENNY
I’m gonna cook in this thing!

BECCA
Now, who are you?

PENNY
Mockingbird. From the comics.

Penny dons her long, platinum blonde wig and adjusts it on her head.

BECCA
Do you have an extra hair tie?

PENNY
(laughs)
I only have long hair when I’m wearing a wig!

BECCA
(laughs)
Oh! Oops!

There’s a knock at the door. Thor and Loki have arrived. Tony Stark leaves to set the stage for the entrance of the Avengers.

Becca’s phone bings.

BECCA
It’s time.

THOR
Let’s go.

INT. HOTEL BAR – NIGHT

The Avengers (paleontologists in costume) enter the bar to hoots and congratulations from the other paleontologists there.

Thor, Loki, and Penny approach the bar to get a drink.

THOR
Whatever you want. My treat.

A woman and her husband are seated nearby and are delighted to see the three costumed paleontologists standing there.

WOMAN
Oh, please! Let us buy! We’re so happy to meet you!

The husband nods and turns away, disinterested. The woman continues to gush.

WOMAN
I’m so glad to have met real paleontologists! Y’know, on our beach I’ve found some really interesting fossils!

Loki and Penny look knowingly at each other. Thor moves off into another conversation.

WOMAN
I’ve seen fossils of a baby bird being born.

Penny and Loki feign interest. There is little doubt in either one of their heads that what the woman has seen is not a bird being born.

LOKI
We’re glad you got to meet us. We’re pretty tired, though. We just did a big auction and we’re winding down.

WOMAN
Oh sure! Oh sure! I understand! I just think it’s great that you’re here. It’s like a sign or something!

LOKI
Well thank you for the drinks!

WOMAN
Sure! I hope we can talk more!

Loki and Penny roll their eyes at each other, then join Thor in his conversation.

INT. DARKENED CONFERENCE ROOM – DAY

Penny looks at her phone, checking the conference twitterfeed. A tweet pops up promising a blooper reel at the end of a talk. Penny is intrigued, and leaves quietly.

INT. DARKENED CONFERENCE ROOM – MOMENTS LATER

Penny takes a seat in another conference room (though it looks identical to the one she just left). She settles in, phone in hand, ready to be wowed.

The presentation begins.

SPEAKER
It’s hard to motivate an alligator to run.

The audience laughs. Soon videos are being shown of alligators and crocodiles running in a Plexiglas chute.

Penny looks at the twitterfeed. Multiple people are tweeting about this presentation. Penny smiles.

SPEAKER
And, as promised, the blooper reel.

On the screen are shown video clips of the alligators and crocodiles escaping from the chute and lunging at the camera. The audience laughs. Tweets fly.

INT. BANQUET ROOM – EVENING

Several hundred paleontolgists are gathered for a catered meal and a short awards ceremony. The meal has been eaten and the few remaining plates have been removed. Attention turns to the President of the Society of Vertebrate Paleontology. She announces several award winners. As the evening continues, the awards become more significant.

PRESIDENT
The Colbert Student poster prize goes to Stephanie Crofts.

People rise to give a standing ovation. As all sit down, a series of toots and tweets are heard.

PRESIDENT
And the Romer Prize for student research goes to Jack Tseng!

The crowd rises again, clapping and shouting. With sitting, the chorus of toots and farting noises is louder. There is audible chuckling. Penny looks at her twitterfeed. A new hashtag has arisen: #squeakyseat

PRESIDENT
And the Romer-Simpson Medal goes to Philip Gingerich!

The crowd rises once more, delighted for their long-time colleague. The tooting and farting sounds as people sit are very loud this time. Clearly people are intentionally sitting hard to make the noise louder. Penny is laughing so hard, tears are coming from her eyes.

INT. HOTEL LOBBY – MORNING

Penny walks away from the front desk. She pauses, looking back.

PENNY
(to no one)
Next year. L.A. See you soon.

Society of Vertebrate Paleontology annual meeting wrap-up

Ah! The annual meeting of the Society of Vertebrate Paleontology (SVP)! My favorite thing in the world! Four days of paleontological bliss, where I don’t have to define terms or defend your chosen profession. Where you can escape from the forced isolation of being the only paleontologist in your department, or worse, in your city. Where evolution is accepted and assumed rather than danced about using clever euphemisms. And where you can trot out your *really* bad science puns and everyone laughs.

Overall, this year seemed no different than other years, but some things really stood out to me. Because I chose to live-tweet sessions, I felt more connected to the happenings at the meeting than I ever have before (and got to make some new friends, to boot!) And, incredibly, there was not a single talk that I went to that I felt was poorly executed. Usually, there’s one or two a day that are agony to sit through, for whatever reason, but this year it didn’t happen. Every talk was not only enjoyable, but offered something worth tweeting about. A good chunk of the meeting was Storify-ed by Jon Tennant (@protohedgehog on Twitter), so you can see what we were doing.

The venue was splendid. I enjoyed the convenience of all the sessions being side-by-side, and the posters were less than 3 minutes walk from the oral session. Even better, the hotel (if one chose to stay there) was less than 5 minutes from any of the sessions. And (after a little nudging), there was even free wi-fi! Perhaps the best (or worst) part of the venue was the seats that apparently had whoopie-cushions built in. There was a lot of accidental tooting, which was finally recorded here.

Highlights of presentations included video of a hyena eating a pig neck in about 30 seconds (noting the bone breaking capabilities of hyenas) and several videos of crocodiles and alligators running (including a blooper reel!).

For me, one of the biggest parts of SVP is the annual auction. I’ve helped with the auction ever since I started graduate school and finally became a member of the auction committee sometime soon after getting my Ph.D. At first, it was always just a matter of helping with the set-up, but over the last 10 years, we’ve started dressing in costume with a theme for the live auction each year. Those of us on the committee put a great deal of time and effort (and sometimes money) into constructing our costumes. The theme is usually established sometime during the summer prior to the meeting, and we rush to create our costumes while simultaneously preparing our professional presentations for the meeting as well. This year, the theme was the Avengers. I chose to dress as Mockingbird, who did not appear in the movie, but has been in a few of the comics. I liked the look of her costume, which is why I chose her. She also has a Ph.D., so how can I go wrong?

Auction, Avengers-style.

This year, I brought back an item I bought back in 2004: a big wooden rocking dinosaur. My son was an infant then. Now, at eight, he’s not so into the dinosaur. Hopefully, it’s off to make some other kid really happy and the auction winner will bring it back when his child has out-grown it.

The ol’ dino-rocker is off to a new home!

The auction raises money for various programs at SVP that support students. I’m glad to be able to help the society in this way. This year the auction made $22,700!

Dino-Thor?

As usual, I was able to drum up some new work for the lab while I was there, and perhaps start some new collaborations. I’m suddenly thinking an awful lot about microwear on teeth. I found out that what I presented was actually old news — only that the folks who had already done the same project kinda hadn’t bothered to publish it yet. (grumble) All told, this was one of the most productive meetings I have ever had. And somehow, I didn’t get sick during the whole event. I’m still healthy, two days after getting home. How’d that happen?

Well, while the iron’s hot, it’s time for me to attack some old research projects. There’s a short paper burning in me about the problems with the taxa Phenacodus and Tetraclaenodon. Then there’s that huge dataset that I tabulated as a postdoc that still hasn’t seen the light of publication. Yeah, I should get on that. I love this feeling of frantic motivation. I hope it lasts!

If you’re not satisfied with what I have to say about the meeting, then check out what others have said, (below). I’ll be updating this as I hear about other people’s posts.

What do Vertebrate Paleontologists Talk About, by Bora Zivkovic (@BoraZ on Twitter; Scientific American Blogs)

SVP, you’re so silly, Tarchia (Pseudoplocephalus Blog)

 

Society of Vertebrate Paleontology invades Raleigh!

This post was written a while ago, but my blog (for whatever reason) was down. It’s fixed now, so I’m publishing it – after the fact. My musings on the meeting will come later..

—–

I’m currently in Raleigh, North Carolina, sitting in my hotel room, winding down after a crazy-awesome day-and-a-half. I’m here for the annual meeting of the Society of Vertebrate Paleontology, which is, hands down, my favorite meeting. Every year I go to this meeting no matter what the cost. (I’ve been going to this meeting since 1994, and only skipped a few when I was a poor, starving graduate student.) The Society of Vertebrate Paleontology is the one professional organization that I likely will never allow myself to not be a member of.

This year, the meeting is proceeding as it always does for me: Interacting with colleagues; learning about new methods; developing collaborations; making new friends. I brought some research (as I always do) and will be presenting it this afternoon in a poster session. Tomorrow will be busy as the Friday of the meeting always is, because of the annual auction and that I’m an auction committee member.

What’s different about this year over the others is that I’ve decided to join the ranks of those who use social media to disperse what is being discussed in sessions to the wide world. I’ve been ‘live-tweeting’ sessions: commenting on speakers using the hash tag #2012SVP so that other interested parties can know what’s happening if they couldn’t come to the meeting or if they’re just in the room next door listening to someone else. I don’t say much, only commenting on things that really grab my attention and I think others out there would be interested to know.

This experience has been great so far. Over the past year I’ve begun to think that social media and science outreach was a better fit for my interests and passions than hard-core research (even though I do plenty of research and have new results to present every year). The interactions (face-to-face and electronic) I’ve had during this meeting have been amazing and now, more than ever, I’m realizing that my suspicions are true. Research is great. Sharing it with others is even better.

There are two and a half more days to the meeting. I expect my feelings will grow stronger as this time goes on. I like where I am right now. I like where things are going. Stay tuned!

What is this “Mass Spectrometer”?

What is a mass spectrometer? I was just asked this question. It gave me pause.

You know, most of us forget that what is completely familiar to us in our daily lives might be utterly foreign to 99% of the world. For example, I’m a vertebrate paleontologist and know many, many paleontologists. Sometimes, I think the whole world is teeming with paleontologists. But when I think about it, there’s maybe 5-10 thousand people in the world that can call themselves a vertebrate paleontologist. Still a big number, but when compared to the world’s population of ~7 billion, or the population of New York City at ~8 million, it’s quite possible that I may be the only paleontologist that many of my non-paleontology friends know and may ever meet.

I suspect that there are more mass spectrometer technicians in the world than paleontologists, just because there are so many different kinds of mass spectrometers and zillions of applications for mass spectrometry. Nevertheless, most people’s exposure to mass spectrometry comes from watching episodes of CSI, where (naturally) the television show gets it mostly wrong. (Seriously, you don’t just turn on a mass spectrometer in the morning and expect to get results in a few hours. I switched ours on yesterday and I’m extremely hopeful that I can start running analyses tomorrow!)

So, then, what’s a mass spectrometer? Breaking down the name itself is a good start.

Mass: This is the science kind of mass, not a religious ceremony. Mass is generally equated with ‘weight’ or ‘size.’ ‘Mass’ in science-ese is actually more specific than that, but this works. We’re basically considering something in terms of its size or weight.

Spectrometer: Well, the ‘spectro-’ part is the same as spectrum – a range. Just like a spectrum of colors: red, orange, yellow, green, blue, violet. The ‘meter’ part just says that a measurement is being made. We’re measuring a range of something.

Since it’s a MASS spectrometer, we’re measuring a range of sizes or weights.

OK, but measuring weights of what?

Now here’s the fun part, and why I say there are so many kinds of mass spectrometers. We’re usually looking at the weights of components of some material. It may be an unknown material, and we want to know what it is. Or it may be a known material, but we want to look for impurities or (potentially) for its origin.

Some mass spectrometers are set up to look for heavy elements like strontium or uranium and measure their abundance. Others look at organic compounds like fats or waxes to determine, for example, how much unsaturated fat versus saturated fat there is. The one I work with is highly sensitive and can only be used with ‘light’ elements like carbon, oxygen, and nitrogen (and occasionally hydrogen – but I hate hydrogen… we won’t go there!)

All mass spectrometers have the same general components: A means to get the sample into the instrument (an inlet system or peripheral device), a means to separate the masses, and a means to measure the different masses.

A common instrument you might see on a TV show like CSI is a gas-chromatograph mass spectrometer (or GC-MS, seriously, that’s a mouthful!). The inlet system is a combustion chamber (a furnace) where the samples are burned, causing the original molecules to break down into smaller molecules that are now gaseous (rather than a solid). These molecules are separated, by mass, using a chromatographic column, which is essentially just a really, really long narrow tube. The smaller molecules flow faster down this tube than the bigger ones. At the end of the tube is a collector of sorts, which basically counts how many molecules of each size pass through the tube and we get a spectrum of the different sizes of molecular fragments that came from our original sample. The pattern of molecule sizes and amounts is characteristic of a particular material.

Another common mass spectrometer is a quadrupole mass spectrometer. This is used for the heavy elements, and makes measurements atom by atom (not whole or fragmentary molecules). We had one running here at the University of Rochester for a while. The inlet system on it was experimental, but fun. A laser was shot at the sample, forming a fine dust which was then carried into the inlet system in Argon gas. There it went into a plasma torch and was burned up and the gas went into the mass spectrometer. This system has the fancy name of Laser Ablation Inductively Coupled Plasma Mass Spectrometry, or LA ICP-MS. Changing voltages on the four metal rods for which the quadrupole instrument gets its name is how the different masses are selected. A collector is at the end of these rods, which measures how many of our specified atoms got through.

The instrument that I manage is called an isotope ratio mass spectrometer (IRMS). There are several different peripheral devices attached to ours, one of which has a furnace like on the GC-MS, and another that has a series of vials with a moving needle. The peripheral devices are where the solid samples are converted to gas. In the first, samples are burned up and converted only to carbon dioxide and nitrogen gasses. In the other, the solid samples placed in the vials are reacted with phosphoric acid to make carbon dioxide gas, which is what we measure. (And I inject that acid drop-by-drop, vial-by-vial. So when you see me say that I’m dropping acid, that’s what I’m doing!). These gasses go into the mass spectrometer and are ionized by an electron beam (3000 Volts!!) after which they fly away from the electron beam toward the collectors. The different masses are separated by a strong magnet and a voltage is measured by the collector cups.

Speckminster Fuller, or Specky for short. The mass spectrometer I take care of every day.

What’s different about what I do is that I’m only looking at one molecule at a time, usually carbon dioxide. But I’m looking at isotopes. Not radioactive isotopes, but stable ones. Isotopes are atoms of the same element, but with different masses (or weights).  Every atom is an isotope. Some are just unstable.

Carbon dioxide has carbon and oxygen. Carbon has two stable isotopes: Carbon-12 and Carbon-13 (and one unstable, radioactive isotope, Carbon-14). Oxygen has two important isotopes: Oxygen-16 and Oxygen-18.

Some math: carbon dioxide = one carbon plus two oxygens. Most carbon dioxide is composed only of carbon-12 and oxygen-16. Take those numbers and add them up: 12 (the carbon) plus 16 (one oxygen) plus 16 (the other oxygen) equals 44 – the total mass of ‘light’ carbon dioxide.

Let’s say the carbon is the ‘heavy’ isotope instead (Carbon-13). Math again: 13 (the ‘heavy’ carbon) plus 16 (one oxygen) plus 16 (the other oxygen) equals 45 – the mass of carbon dioxide with heavy carbon.

What if one of the oxygens are heavy? 12 (the carbon) plus 16 (one oxygen) plus 18 (the ‘heavy’ oxygen) equals 46 – the mass of carbon dioxide with one heavy oxygen.

Obviously, there are other combinations possible, but these are rare and we don’t worry about them. What’s important is that carbon dioxide comes in three masses: 44, 45, and 46. An IRMS can separate these out and we can measure them.

Subtle differences between the relative amounts of heavy and light isotopes of oxygen and carbon (and nitrogen and hydrogen) can tell us a lot about the origins and history of the sample that we’re analyzing. For some examples from my own research, look in my blog under “stable isotopes”

Rodents of Unusual Size

As I was driving home from work yesterday, I was pondering what the next great bit of science would be that I should publish. I started thinking about this project that has been back-burnered for a while.

Projects in the sciences get back-burnered for many reasons. This particular one has been set aside as I wait for results from other colleagues from other institutions. This happens, and is a common occurrence in the sciences. But as I was driving, I realized that part of the project is complete and can be its own paper in the absence of the contributions from the others for the greater project.

Co-authors, get ready. There’s a manuscript coming together by ME!

So, what’s it about? And why is the title of this post “Rodents of Unusual Size”? ROUSes don’t exist anyway, so what am I worried about?

Well, there are some big rodents out there. The largest modern rodent is the Capypara (or Carpincho), which roam around in South America. These rodents average about 50 kg (110 pounds), so they are fairly large. But in the ancient past, South America hosted even larger species of rodents, including Arazamys, Isostylomys, and Josephoartigasia. The latter, is thought to have potentially weighed 1000kg (2200 pounds)! Now that’s a rodent of unusual size!!

Capybara Grazing (by FinlayCox143)

A common research question that I answer with my type of research is “what did the animal eat?” I can get at this using geochemical analysis of tooth enamel. The larger project that my colleagues and I are working on seeks to answer the question, “What did these giant fossil rodents eat?”

The obvious answer, of course is, “Anything it wants!” But we want to be a bit more specific. So how do we do this? By studying the isotope geochemistry of tooth enamel.

Diet recorded in tooth enamel

We joke in isotope geochemistry that “You are what you eat, plus a few permil.” When I’m analyzing samples, I’m comparing the amount of Carbon-13 (’heavy’ carbon, but not the radioactive stuff, Carbon-14) relative to the amount of Carbon-12 (the common carbon in the world). Slightly less than 99% of all carbon atoms in the universe are Carbon-12. Around 1% of all carbon atoms are Carbon-13. (And whatever is left is the radioactive Carbon-14). A mass spectrometer can measure the relative amounts of Carbon-12 to Carbon-13 and gives us a number, called a ‘delta value’ in units of ‘permil’ (‰).

We write this like: δ13C = -14‰ (said “delta 13-C equals minus fourteen permil”)

Depending upon what you’ve just measured the isotopes from, this delta value can be interpreted in a number of ways. For diet and tooth enamel, it goes like this:

Plants, in general, use one of two types of photosynthesis. These two types are called C3 and C4. C3 plants are typically trees and bushes (or occasionally grasses) that live in cooler moist environments. C4 plants are typically plants especially grasses that live in arid environments. (This is an over-generalization, of course, but is usually our first assumption.)

Luckily for us, C3 and C4 plants have different δ13C values. C3 plants are usually about -27‰; C4 plants usually around -13‰.

Now, let’s say an animal comes along and eats these plants. You are what you eat, they say. Plus a few permil… In the case of mammal tooth enamel and plants, it’s plus 14‰. So a bison grazing on C4 grasses has a tooth enamel  δ13C of about 1‰. A horse that prefers to eat the bushes with have a tooth enamel  δ13C of about -13‰.

The difference in  δ13C in tooth enamel reflects a difference in diet. In general, we assume that animals that show a C4 diet (tooth enamel  δ13C around 1‰) probably were grazing (grass-eaters) and those that show a C3 diet (tooth enamel  δ13C around -13‰) were probably browsing (leaf-eaters). Of course, there are animals that do some browsing and some grazing (horses in particular). We can tease out the relative amounts of grazing and browsing in a single animal too.

So the plan is to look at the tooth enamel of the giant rodents Arazamys, Isostylomys, and Josephoartigasia and figure out if they were browsing or grazing. We might assume that they were grazing, since some of the largest land mammals are also grazers (like elephants), but they might also be browsing, just to eat enough food to fuel such a giant body!

Capybara diets

It’s always a good idea to ground-truth your assumptions whenever you have the opportunity. There are lots of assumptions that go into inferring that an animal is either a browser or a grazer when there is only isotopic data to look at. We decided it would be worthwhile to examine the isotopes in modern giant rodents to see if our predictions and assumptions are borne out. Since capybaras are the largest modern rodents, we decided to study them.

Capybaras are known to be grazers. We can sit and watch them graze on grass in an environment where there is lots of C4 grass to be eaten. We also know that there are some C3 grasses in the places where capybaras live, but we might assume that since the majority of grasses are C4, then the majority of the capybara’s diet is C4 as well. Thus we predict that the tooth enamel  δ13C from a capybara would be around 1‰.

Well, guess what?

Capybaras selectively eat the C3 grasses. Their tooth enamel only reflects a C3 diet! But we didn’t know this until we ran the isotopes! We ran a couple hundred samples, so we know it’s not an error. This was completely unexpected. Seems like we have a problem, right?

Well, really, it’s not the end of the world. It is what it is. This is how science works. We know that capybaras are grazers, but if all we had to go on was tooth enamel, we’d get it wrong.

But we have other things. We have the shape of the teeth themselves. Long and rootless teeth are common in animals that eat an abrasive diet – and is a common characteristic among grazing animals. Have you ever looked at a horse tooth? Most rodents, including the capybara, have these long and rootless teeth.

We can also look at microwear on the surface of the tooth. An abrasive diet (actually, any diet) will scratch and wear the tooth surface, leaving tell-tale marks that we can observe using microscopes. Specific types of marks are associated with different diets: grazing, browsing, fruit-eating, etc. This is the realm of my colleagues. They are looking at the microwear on the teeth of the giant fossil rodents. Hopefully, they’ll get on that soon. I ought to start bugging them.

What does an ROUS eat?

The isotopic analyses from the fossil giant rodents are done. But in the light of what we learned from the capybaras, the interpretation is sketchy. I can’t say more than that right now. Until we have the microwear data, all we can say is “Huh.”

In the meantime, though, the conclusions of the capybara study are important and need to be published, since they kind of shake up some of our basic assumptions for interpreting diets from carbon in tooth enamel. Now all I gotta do is decide which journal. Hmm.

Why I do what I do: Education, one victory at a time.

I had a great experience the other day – the kind of experience that all educators want. I converted someone.

I didn’t know if they needed or wanted conversion, but they were skeptical of what I was presenting. And I – entirely unwittingly – provided that bit of information that converted them from ‘skeptic’ to ‘believer.’

A fair question to ask at this point is, “What didn’t they believe in?” We’ll get there.

I had been invited to give a talk/presentation on the nebulous topic of ‘dinosaurs.’ The group that invited me had recently had a lively discussion about dinosaurs, but found that they still had questions for which no Google search provided adequate answers. So there I was.

I was a little trepidatious, because, despite the fact that I am a ‘vertebrate paleontologist,’ I really don’t know a whole lot about dinosaurs. There are thousands of 9-year-olds who know more about dinosaurs than I do. Mammals are my thing. But they sent me a list of questions, and I realized that I could address most of them easily. Most had less to do with dinosaurs than they did about the science of paleontology.

As it happened, the group was a delight. We had a fabulous time talking about how the turkey you eat at Thanksgiving really is a dinosaur. We talked about how bones and teeth were made of minerals (essentially rocks) and that’s why they don’t rot (and why they’re preserved as fossils). We talked about what was wrong with Jurassic Park. We talked a bit on how we name, and how we recognize, new species, and about some of the ‘mistakes’ paleontologists have made along the way. We talked about tracks and pseudofossils. Really, there were few topics in paleontology that we didn’t cover, and it was only an hour-and-a-half presentation.

With about 15 minutes to go, the skeptic was revealed (paraphrased):

‘If humans and dinosaurs never co-existed – so humans never saw dinosaurs – how do we know that dinosaurs are real? How do we know that they ever really existed?’

From how the question was asked, I could tell that our skeptic was genuinely curious – not intent on discrediting me or the science, but honestly confused. And as I listened, I was frankly boggled by where the confusion was.

You see, I’ve been at this so long that the reasons why we know that dinosaurs existed seem so self-evident, I don’t understand how people don’t see them. However, one thing I have learned in recent years while teaching introductory geology courses: It is impossible to remember what you didn’t know before you started your studies. That is to say, I don’t remember not knowing how we determine relative ages of rocks. I don’t remember not knowing that rocks exposed on the surface are of all different ages. I finally realized that our skeptic didn’t know these things any more than I did 20+ years ago. I also realized that the answer our skeptic wanted didn’t come from paleontology, but from geology. No wonder Google wasn’t being helpful.

So I stepped back and described Hutton’s original observation of the unconformities in Scotland and how this helps us understand of the depth of geological time. Then I explained how some basic principles (original horizontality, superposition, cross-cutting relationships) can help us put rocks in the correct chronological order. Then I drew a stack of rocks and showed that humans were at the top of the stack and dinosaurs were at the bottom.

And the skeptic’s eyes opened wide. ‘I get it! There were dinosaurs!’

Others in the room were delighted. They’d been trying to ‘prove’ the existence of dinosaurs to the skeptic for a while, and here I had done it with two drawings in five minutes.

I was never my intention to go in there and ‘convert’ anyone. (In fact, I hesitate to use the term ‘convert,’ only that the term was being tossed around by everyone in the room when the presentation was done, including by the skeptic.) I was simply there to answer people’s questions about dinosaurs. I don’t care what they believe about evolution or the age of the earth or anything. I was there to be a better database than the world wide web. I think they got the answers that they wanted, and then some.

And I got that fantastic satisfaction that we all yearn for as educators: Somebody learned something – something that may well alter their world view – and thanked me for it.

Oh, yeaaaaah!

How do you measure body temperature of an extinct giant sloth?

Modern sloths are curious beasts. Generally fairly small, tree-dwelling critters, they’re notorious for their slowness. But they come from a grand tradition of great size. Until the big extinction of large mammals that occurred about 10,000 years ago, there roamed across the land giant ground sloths that would have made most people run in terror.

Megatherium americanum

These giant sloths coexisted with great beasts like mammoths and woolly rhinos and saber-toothed tigers. They didn’t live in the trees; they were far too big. Instead, they moved about on the ground, using their huge claws to rake leaves from trees to eat.

All this is romantic, but seriously, if giant sloths were as slow as their modern cohorts, wouldn’t they have just been gobbled up by the saber-tooth tigers and the dire wolves?

Well, that’s a good question. How can it be answered?

Modern sloths are slow because they have low metabolic rates. Their diets consist of foods of poor nutritive value, so they balance this by sticking high in the trees and taking their time to get around. The low metabolic rate is reflected by having a low body temperature. Most mammals (like us, or horses and cattle) keep their bodies at 37-39°C. Modern sloths (and other low-metabolic-rate mammals) keep theirs at around 32°C.

So all we need to do is measure the body temperature of a giant sloth! Oh, wait. They’re extinct. Dang.

Geochemistry to the rescue!

Almost all of my research revolves around the geochemical analysis of fossilized teeth in mammals, to make inferences about their biology, and the environments in which they lived. To do this, I measure the relative amounts of stable isotopes (not the radioactive ones!) of carbon and oxygen from tooth enamel. The methods I use are (relatively) straightforward, and have been used actively for decades. The relative amounts of the different isotopes of oxygen and carbon can be related to temperature – and here’s our foot in the door to get at body temperature.

It can be complicated though, especially for oxygen, and until recently we couldn’t easily distinguish temperature changes from things like changes in the amount of precipitation. We also could only look at changes in environmental temperature, rather than body temperature.  (Sigh.)

That changed a few years back with the development of a new method of temperature determination called “clumped isotope” paleothermometry or just delta-47 (Δ47). As it happens, the heavy isotopes of carbon and oxygen can exist together (clump) in a single molecule of carbon dioxide, CO2 (which is what we measure with the mass spectrometer). This carbon dioxide comes from carbonate (CO3) which comes from the tooth enamel. How often the heavy carbon and heavy oxygen clump in a molecule is directly related to the temperature at which the molecule formed. In the case of mammals, this is the temperature of the mammal’s body.

So all we have to do is count how many carbon dioxide molecules have both the heavy carbon and the heavy oxygen (= clumped isotopes) and we can measure body temperature!

It sounds simple, it’s really not, but only because there aren’t that many molecules with the clumps, so we need a lot of material and tons of analytical time to get it done. This makes it expensive and it’s hard to get materials because you basically have to destroy most of a tooth. Museums don’t like to lend you specimens that you’re going to destroy. I don’t blame them, really.

We’ve been fortunate, however. One museum has recognized the importance of this study: We really do need to know the metabolic rates of giant sloths if we want to understand their biology and behavior. We were lent teeth from two species of giant sloth, as well as teeth from a horse and a bison from the same cave locality that the sloths came from. We know body temperature in horses and bison, so we can use those results for comparison.

We’re also lucky that the clumped isotope method is so new, that the few labs that are capable of running these analyses are eager to try different things. Right now, we’re not having to pay for the analyses, though we do plan to see if we can get funding to pay for more analyses later.

Cool! Let’s do it!

But wait. There’s another problem. You see, sloths don’t have tooth enamel.

We use enamel from fossil teeth because it’s really hard and resistant to alteration during the process of fossilization. If the material we want to measure the isotopes from has been altered, we may be measuring something besides the body temperature signal – and that could be anything!

Sloth teeth are made entirely of dentine (which we have in our teeth, too, underneath the enamel). Sloths have two layers of dentine, a harder outer layer equivalent to enamel and a softer inner layer like our dentine. We’ve decided to measure the clumped isotopes from both the inner and outer dentine layers (assuming that the outer one is less likely to be altered, because it is much harder). We’re also measuring the clumped isotopes from the enamel and dentine of the horse and bison. This is how we’re going to determine if there is any alteration of the dentine in the sloth. If the sloth outer dentine gives the same temperature as the dentine in horse and bison, we have to be suspicious that it represents some alteration value and not really body temperature (and then all this work is for naught!).

Where we are.

Well, the preliminary data are in. They weren’t what I expected, but I’m not a sloth expert, so I’ll wait for my colleagues to chime in.

In the meantime, it’s time to start writing an abstract on the subject for the Society of Vertebrate Paleontology Annual Meeting, which this year will be in Raleigh, North Carolina. I think it’s gonna be pretty exciting!!!