Saturday, February 28, 2009

Zombie blog

Mrs. Lemming and I are fixing up the home study this month, which will entail painting, moving everything around, and intermittent computer access. I've queued up some auto posts to keep y'all amused. In the mean time, feel free to talk among yourselves, or answer the poll to the right.

Friday, February 27, 2009

What to do when you review?

ResearchBlogging.orgPeer review is one of those exercises that is vitally important to the promulgation of scientific knowledge. It is also one for which we get absolutely no training. and if that is not bad enough, it is cloaked in unnecessary secrecy and anonymity. The way it works is this:

In between irate meetings, technical emergencies, slipping deadlines, and normal workload, you get an unsolicited email from a total stranger. Assuming it doesn’t go directly to the spam bin, opening it reveals that it is Professor Joe Blogger, associate editor of the Journal of Acceptable Results, and he’d like you to review a paper.

Hopefully the paper is on a topic with which you are actually familiar.

Generally there is a multiple choice card or sheet, in addition to the actual brain-required part of the job- namely writing intelligent and useful commentary on somebody else’s research.

As far as I can tell, there are two basic approaches. These are ideally similar but in practice can be opposite. The first is imitation of reviews that one has received. The second is the golden rule.

For me, the first option would involve some combination of non-specific pleasantries, attacks based on a misunderstanding of the literature or techniques used, or multi-page lists of specific minor points which are not related to each other or the using-whole-sentences part of the review. So when asked to review, I tried the second method, but without any real sense of guidance or idea what I was working towards. My inability to find a type specimen of a quality review is probably due to the lack of transparency that surrounds peer review. So in order to illuminate this mysterious process, here is my reviewing experience.

I reviewed my first paper a bit less than two years ago. The finished paper was finally published last southern winter while I was in the field, so I was unaware that it had come out until this week. My main aims were:

1. Pay close attention to the methods. In this case, the methodology used in the paper included techniques that I used, albeit with technical support and a long time ago. I asked: Are they appropriate? Will they overcome noise and interference problems? Do the authors demonstrate their awareness of what the pitfalls are, and show that they were avoided?

2. Look at the data. If it’s good, proceed. If not, double check it. If it’s better than the described methods is capable of producing, get very suspicious.

3. Is the result important to the study? If so, try to convey this to the editor, who is probably not an expert in both the experimental application AND the topic for which it is being applied. (He may not know much about either). I did not google the handling editor, but in hind sight I probably should have, in order to ascertain my audience.

4. Is it worth publishing? It is possible for a study to be correct, but unimportant. This point generally forms the central thesis of the review. All of the above points are used to justify it.

I generally don’t pay a huge amount of attention to conclusions or interpretations, as long as they are consistent with the results and with previous work. When reading papers professionally, I am generally data-mining or method-hunting, so it is hard to care about part of a paper that I never read. If the introduction is adequate, then the meaning of the results should be self-evident once the data is presented. Also, the way I see it, if a person does the hard yards and produces a good data set, he or she earns the right to arm-wave about it a little bit.

Note that what I paid attention to when evaluating the paper was not the same as what I wrote in the review. In particular, although I spent a long time looking at the methodology, I assumed the editor wasn't interested in knowing what the nitty-gritty details were. I assumed he just wanted to know if they were appropriate. As a result, I put most of my effort into describing why the results they present were significant. Unfortunately, I was not able to incorporate all suggestions into a coherent essay, and reverted to bullet point suggestions towards the end. If anyone has any tips or suggestions as to how to review effectively, please let me know in comments.

In this particular case, I did check the references, but I probably won’t in the future. That doesn’t require specialist knowledge, so anyone can do it.

So what does this all boil down to? Well, here's the final copy. It is posted with the surviving author’s knowledge and permission:

Dear Handling Editor,

The paper “Infrared and Raman spectroscopic observations on Central African carbonado and the implication to its origin” presents new data that constitutes a significant step forward in the study of this material.

While there have been several previous Raman studies of carbonado, none of them have looked at the possibility of annealing caused by polishing the stone, so that part of the paper is important. But the main value of this paper is the FTIR data.

Science has been trying to determine the IR spectra and nitrogen aggregation of carbonado diamond for almost 20 years. There have been numerous studies that have shown the important 1000-1400 cm-1 region is cluttered with interfering inclusions, and Garai et al. (2006) recently claimed to have an answer by simply interpreting what appear to be inclusions as diamond signal.

However this is the first paper to demonstrate the successful removal of interfering silicates, and to show that the remaining diamond spectra are consistent. The determination of N aggregation state for carbonado and the demonstration that fluid inclusions are intrinsic to the diamond are both key developments towards understanding the early history of this type of diamond.

There are a few minor improvements that should be made to the typescript before publication, however.

Firstly, the abstract and introduction should be read and edited by a native English speaker. There are several awkward sentence constructions that make the paper more difficult to read than it ought to be. The Raman conclusions are occasionally hard to understand as well.

The carbonado spectra in figures 4, 5, and 6 should be labeled so that we know which of the samples in table 1 the spectra correspond to. Figures 5 and 6 should show more than one carbonado spectrum, and figures 4 and 5 might be combinable into one figure.

A data table containing the Raman peak positions and widths observed should be included in the paper.

It would be nice if data files for the spectra were included in the supplementary material.

The Walker 1979 reference is not cited.

Overall, it is a good paper, and an important achievement in the field of carbonado study.

Dr. Charles Magee

You can find the whole paper here, access permitting.

Hiroyuki Kagi, Satoshi Fukura (2008). Infrared and Raman spectroscopic observations of Central African carbonado and implications for its origin European Journal of Mineralogy, 20 (3), 387-393 DOI: 10.1127/0935-1221/2008/0020-1817

Tuesday, February 24, 2009

Saturday, February 21, 2009

Climate and bushfires

Professor David Karoly has an excellent post describing the relationship between climate and the recent Victorian bushfires.

Thursday, February 19, 2009

Avoiding barriers to innovation

Like everyone else on the internet, I recently watched the NASA Barriers to innovation and inclusion video produced by astronaut Andrew Thomas. It actually kept me up at night. “Process” is one of the main reasons that I’ve remained a technician/ project scientist ever since graduation- I have neither interest in nor a gift for bureaucratic fluff. I don’t even like verbosity. So one of the things I was thinking about last night was how fortunate I am to have a manager who basically throws himself under the bureaucratic train so that the rest of us scientists in the group can work relatively unhindered. He spent the day talking about process with suits; I changed a turbo pump in the morning and prepared analytical standards in lab all afternoon.

But as I was thinking about it, I realized that my luck wasn’t random chance. In part, it was natural selection.

I have terrible career skills. I’m terse in interviews, my resumé is plain, I don’t meta-analyse or talk in points. As a result, I am simply not hired by process-oriented employers, even when I do apply for such jobs. So the chances of me ending up in a situation like Heather’s are slimmer than they would be if I was an attractive candidate to such organizations.

I do intentionally pursue jobs that involve doing stuff, as opposed to arguing about what the best way to go about it is. But in addition to that I have this unconscious defense mechanism against red tape employment. This is good for me, but I wonder, how does it apply to the less privileged.

Now, I watched this video over at Sciencewomen’s blog. And one of their themes is how to improve the academic system to be more female friendly. But I wonder, could this be counterproductive?

Suppose the following:
1. Women and men are equally talented.
2. We remove systemic, but not personal barriers to women in academia.
3. Environments which favor systemic approaches stifle innovation.

If all three conditions are met, then women will be preferentially selected for jobs with stronger systemic structures, for the same reason that I don’t get those jobs. Assuming that these jobs stifle innovation, then it would be reasonable to expect these equally talented people to be less productive than equivalent folks in less structured environments. And the washed-up emeriti set could then use this productivity gap as evidence for an inherent gender-based lack of ability.

So I guess my point is that without individual change, systemic change is insufficient for producing equality of opportunity.

Tuesday, February 17, 2009

Laser ICPMS imaging

ResearchBlogging.orgOne of the big developments in geology over the past decade or so is to turn everything into a pretty picture. If it isn’t imaged, it’s mapped, and if it ain’t hyperspectral it needs to be saturated in coffee.

In one sense, this is just a continuation of a trend that started around 1800 with the first geologic map; it’s simply the best way to present complex spatial information. What makes the last decade or so different is simply the scale, speed, and breadth with which this has been applied.

For me, the turning point was EPMA element mapping. This is where the geologist goes out on the town, and while he or she is partying all night long, the electron probe maps out the elemental variation of a thin section. In the morning, the hangover is vanquished with a pretty picture showing such crazy things as REE zoning in optically homogenous garnets, or alteration features that render a year’s worth of work pointless.

In order to map things easily and rapidly, a few things are required. First, you need a fast analytical method. If you’re taking tens to hundreds of thousands of data points, you can’t spend all day on each one.

Secondly, you need to know where you are. You can’t make a map on any scale without positional information.

Thirdly, you need a computer to process the data so that all data is somehow normalized to a useful value, and all the bits are put together in the correct places.

Woodhead et al. show how all this can be done using laser ICPMS. The key for 1 is rapid washout time, and for 2 and 3 are computer-controlled stage operation. They did a bit of extra homework, though, and ran several experiments to show that ejecta resampling produced negligible signal contamination on the scale of their measurements. This is important with destructive mapping techniques, because the sample quality can be compromised by annihilating it with laser beams.

As their example experiment, they show some lovely stalactite images, with U-Mg-Sr spectral maps. You’ll have to read the paper- or guess- to learn which element the vertical axis represents.

Jon D. Woodhead, John Hellstrom, Janet M. Hergt, Alan Greig, Roland Maas (2007). Isotopic and Elemental Imaging of Geological Materials by Laser Ablation Inductively Coupled Plasma-Mass Spectrometry Geostandards and Geoanalytical Research, 31 (4), 331-343

Monday, February 16, 2009

Carnival of the Arid

Chris Clarke has put together a wonderful new blog carnival, focusing on those parts of the earth that get less than a foot of rain in a year. I highly recommend a trip to the Carnival of the Arid if you can't get to a real desert at the moment.

Thursday, February 12, 2009

Top ten ways to spend Darwin’s 200th birthday

10. Trying to win the eponymous award.
9. Mining chromite.
8. studying fruit flies.
7. Reading gushy science blogs talking up the occasion.
6. Visiting the grave of his tortoise.
5. Improving your fitness.
4. Celebrating honest Abe’s birthday instead.
3. Trying to increase your number of offspring.
2. Birdwatching in the Galapagos.
1. Investigating Darwin’s theory of coral atoll formation in an extended field-based study.

Happy Birthday Mr. Darwin

I went looking for a video of a sexy chimpanzee dressed in fancy dead animals who could sing for the scientist. Didn't find much. And by then, I was too tired to draw it myself. But don't worry. I suspect every single other science blogger on the planet will have a more interesting Darwin post than I do.

Monday, February 09, 2009

Ill-fitting lab coats

I was gabbing with some of the technical guys at work today, and the subject of lab coats came up. Our lab manager is getting coats for anyone who spends more than a millisecond in the machine room, and he’s even taking the unusual step of making sure that they fit. To me this sounds suspicious.

As a serial lab coat borrower, I am used to them being small, and generally short-sleeved. But evidently there is more to it. I'm told they can be procured in all sorts of shapes and sizes to fit a variety of body types. In fact, I believe that there was only one person in the building who they had trouble fitting with a lab coat. This person is not particularly large, small, or gangly. He just has broad shoulders, a strong upper body, and very good posture.

After an exhaustive search, they finally realized that lab coats simply weren’t made for people built like that. Can’t imagine why not...

Friday, February 06, 2009

Sponges lived on the snowball Earth

ResearchBlogging.orgThe results I briefly mentioned hearing the preliminary talk for in Melbourne 3 years ago have just been published in Nature.

Short version: Sponges evolved before the end of the Marinoan “Snowball Earth” glaciation, and were common from then through the Ediacaran and into the Cambrian.

How they did it:

As anyone who is conscious about healthy food knows, animal fat contains lots of cholesterol, while plant fats don’t. This fact has been used for years by people worried about their cardiovascular health. But it also lets us explain the evolution of animal life.

At the risk of slightly oversimplifying, there are three kinds of cholesterol: Good cholesterol, which is found in fit people. Bad cholesterol, which is found in bacon rinds. And 24-isopropylcholesterol, which is found in the cell membranes of certain kinds of sponges.

When organisms die in anoxic environments, the organic remains can sometimes accumulate and alter to form petroleum. 24-isopropylcholesterol is altered by this process to form a similar chemical called 24-Isopropylcholestane. 24-Isopropylcholestane is not known to form in any other way. So Love et al. extracted oil from a bunch of Cryogenean and Ediacaran sediments, fed it through their fancy mass spectrometer, and identified lots of 24-Isopropylcholestane.

Of course, oil can migrate- the gasoline in your car migrated from its source rock to a reservoir, and then to a well, to a supertanker, and to a refinery, before entering your gas tank via a pump. So the cool thing that these authors did was to use hydropyrolysis to show that the kerogen also contained 24-Isopropylcholestane.

Hydropyrolysis uses hydrogen and heat to break hydrocarbons apart. Kerogen is basically a large, insoluble organic compound of some sort. If a sterane is bonded to that kerogen, it cannot migrate, until broken off in the lab.
Hot hydrogen attacks the bond between the molecule and the kerogen:

to release the molecule:

Love et al. use this to show that the bound hydrocarbon population is similar to the unbound population.

When organisms die, they don’t just leave characteristic bones behind. They also leave molecules. And those molecules can be just as diagnostic as more traditional fossils.

For more details, read the paper. Or see Callan's take.

Gordon D. Love, Emmanuelle Grosjean, Charlotte Stalvies, David A. Fike, John P. Grotzinger, Alexander S. Bradley, Amy E. Kelly, Maya Bhatia, William Meredith, Colin E. Snape, Samuel A. Bowring, Daniel J. Condon, Roger E. Summons (2009). Fossil steroids record the appearance of Demospongiae during the Cryogenian period Nature, 457 (7230), 718-721 DOI: 10.1038/nature07673

Wednesday, February 04, 2009

Local Warming

So we’ve just finished our 10th straight day of 30+ weather (86+ in cuneiform), and I’m hot and crankier than usual. January was warm. In fact, the high was 3 degrees above average. I don't know if that is statistically significant; you'd have to ask a mighty climate math god, but it isn't real comfortable.

I have to admit, though, that working in the outback has definitely improved my ability to cope with heat- at least while I’m out side. I’m riding my bike a few days a week now- 18 km each way- and I made it home without water a couple times without too much difficulty. What I don’t like is the hot stifling house. It was regularly getting up over 30 inside, and with the outside temperature not dropping until near sunset, it wasn’t much fun.

So last weekend I finally caved in and bought shades for the NW facing windows. They are basically shadecloth rolls that come down over the windows, and they prevent the sun from hitting the glass. Since then, the house hasn’t hit 30 yet- I’d say we’ve saved ourselves a couple of degrees just with the shades. And there’s an additional benefit in that Mrs. Lemming no longer has to be embarrassed that the neighbors can see me walking around in my underwear. Everybody wins.

Tuesday, February 03, 2009

Are Mobile phones bad for geochemistry?

ResearchBlogging.orgThe trace elemental analysis of mineralogical materials is of course what all the cool people are doing these days. A subset of this research is the trace elemental composition of biologically precipitated minerals, such as forams, clams, corals, and teeth. In a recent paper, O. Adiguzel et al. show that by rats exposed to mobile phone type radiotransmissions have different Mg and Zn contents in their teeth than rats with conservative, land-line only parents. They do not propose a mechanism, but they do control against other environmental factors by having a control group subjected to the same conditions, but with a transmitter that isn’t plugged in.

Unfortunately, the analytical side of the paper isn’t terribly strong. They don’t actually present their data, and they describe some results as being statistically significant (Mg, Zn) or not (P, Ca) without showing the variance in the populations or the numbers from which their graphs are derived. In addition, their analytical method was not terribly sophisticated, and did not show when or where in the tooth the compositional changes occurred. And of course, a mechanism would be nice.

Still, it makes you wonder. If biomineral deposition is sensitive to radio frequencies, could paleoclimate reconstructions based on foram Mg/Ca ratios show a false el Nino every time the planktons spent all night on the phone? Could changes in the Great Barrier Reef attributed to agricultural run-off be caused by lite FM? More detailed analysis is required.

O. Adiguzel, S. Dasdag, M. Z. Akdag, S. Erdogan, S. Kaya, I. Yavuz, F. A. Kaya (2008). Effect of Mobile Phones on Trace Elements Content in Rat
Teth Biotechnology& Biotechnology Equipment, 22 (4), 998-1001