Shameless self-promotion and self-organizing

I keep losing the link to the Supplementary Information from my Geology paper (summarized as Geosonnet 42), so I'm posting the direct link here, where I hopefully won't lose it.
http://www.geosociety.org/datarepository/2016/2016176.pdf
And before you tell me a better way to keep track of things in the digital age, GET OFF MY LAWN!

Routine science turns clever- laser ICP vs SHRIMP analysis of Archean detrital zircons

So, last year I published a Geology paper. It is summarized in Geosonnet 42; see link therein to the paper itself. As it turns out, the paper deals with Archean uranium mobilization and the sedimentary history of carbonado diamond. But what the paper doesn’t say is that I wasn’t actually trying to do that. More professional researchers than I might know how state in their articles that it was all just a lucky coincidence, but I don’t know how to squeeze that into a short format journal.

What actually happened is that the second author and I realized that we had different pieces of the puzzle which, with the help of some old Japanese data, could be pieced together for a coherent story. So hey, "write it up."  Most of my part of the puzzle was unpublished bits and pieces from my PhD and post doc 15+ years ago, but the SHRIMP data was actually less than a year old, as I had collected it for an entirely different reason.

Back when I was working at ASI, which had just bought the Resolution laser ablation line from Resonetics, a few of us started looking at how the SHRIMP and laser products could best compliment each other. One of the things we experimented with was controlling the SHRIMP with a version of the laser control software. Another thing we wanted to know was whether there was any advantage to using the SHRIMP for detrital zircon provenance studies, so I pulled out my old PhD zircons, remounted them with modern standards, and we programmed a customized version of GEOSTAR to automatically rerun the same zircons (if they hadn’t been blown up) to compare the results. Of course, the laser data was old, and the SHRIMP was trying to make analyses next to laser holes (which distort the extraction field, due to the unfortunate tendency of holes not to be flat), but it generally worked, and the data is tucked away deep in the supplementary section of the paper.

Since there are analytical geochemists who occasionally read this blog, but might not think to look for microbeam comparisons in the appendix of a diamond radiation defect luminescence paper, I thought I’d mention it, and put up some plots that got culled due to space requirements.

The short answer is that fully metamict zircons (like half of the Tombador grains) are open system with either technique, but for zircons that are only a little bit metamict (most of the Jacobina zircons), the smaller ion probe spot and better ²⁰⁴Pb backgrounds improve data quality. Anyone who is interested is welcome to download the Data Repository data (it’s all there) and ask.

Figure 1 (See data repository for full version): Tombador zircon analyses with SHRIMP (red) and laser ICPMS (yellow). The SHRIMP data are, in general, a little more concordant, but there isn’t much in it.

Figure 2 (See data repository for full version): Jacobina zircon analyses with SHRIMP (red) and laser ICPMS (yellow). For this sample, the SHRIMP data are substantially more concordant.

Figure 3:  Probability distribution curves for Tombador zircons analysed by SHRIMP (purple) and laser (Red).

Figure 4:  Probability distribution curves for Jacobina zircons analysed by SHRIMP (tan) and laser (Red). Note that laser peaks are generally broader and offset to younger ages due to Phanerozoic Pb loss.

Mapping while black

Happy Martin Luther King Day.  Dr. King, of course, was a pivotal leader of the civil rights movement, and was crucial in organizing African Americans to claim their rightful places in American society.   And while the civil rights struggle has continued in the decades after his untimely death at age 39, the progress of integration in geological sciences has been slower than in other areas.  So it seems that today is as good a day as any to discuss some of the potential barriers to racial integration in geology.

One little known problem is the issue of Mapping While Black.  Most people know what driving while black is, but a Google search for “Mapping while Black” reveals a bit less information.  However, in many parts of the world, including the US and Australia, rural land owners often have a tendency to be whiter, more racist and better armed than the urban population.  And this can put black field geologists into uncomfortable positions which their white colleagues never even conceive of. 

While I am not black, and did not experience any such events as an undergrad in the USA, my PhD research brought me to Brazil, where I collaborated with predominately African-Brazilian colleagues.    And while the most memorable event we had was not actually mapping, it does serve to illustrate the hairy end of what can happen if one tries to do geology with (or in the company of those with) low albedo skin.

My PhD research focused on an obscure type of diamond called carbonado.  Carbonado is found primarily in East-central Brazil and the Central African Republic, but a month after my PhD started the fall of Robert Mugabe in neighboring Zaire destabilized the CAR, making it off limits to my project.  So Brazil it was, chiefly the poor, black eastern part of Bahia state known as the “Chapada diamantina” (diamond plateau).

One of the elder statesmen of the (small) field of carbonado research suggested to me, at beers in a conference, to drop in on a man called “Oswaldo”, who owned a saloon in the town of Lençios. Oswaldo was a mid-level diamond trader; someone who bought raw stones off of garimpeiros, and then up sold the better material into exporters for cutting, while retaining the weird stuff in his collection.  I was interested in the weird stuff.

So, after three days of field work with and dealing directly with the local garimpeiros, in we went to Oswaldo’s.  Me, the very white foreign guy, a black Brazilian geologist, and our black Brazilian driver.  We sit down at a table.  A waiter comes over.  We say we would like to talk to Oswaldo about diamonds. No Oswaldo appears. Our driver starts looking nervous. “blah blah something something vamos,” says the driver. (I only had about 5 months Portuguese lessons before the field work, and they didn’t include the Bahian dialect or accent). 

My geologist colleague say to me, “we have to go now.” And gesture towards the rest of the room as he gets up.  Three of the four exits to the room are now blocked by tough looking Brazilian roughnecks.  My memory is blurry, but I think one of them has a gun.  The people at the table next to us start to move away.  And then everything was a blur, until I was in the cab of our truck and we were gunning the engine to get the fuck outta there. As we do, there is a yelp.  A dog (Oswaldo’s  we were never properly introduced, so I can’t say) had crawled under the ute to get out of the harsh November sun, and we had clipped its leg tearing up the street.  I feel bad about the dog, but we lived with that, and didn’t stop.  In fact, we didn’t stop until we were over the mountains, and then we hid the truck at a roadhouse where my colleague knew the patrons, and watched for pursuit for 20 minutes, before turning north and heading for Morro do Chapeu, 200 km away.

Years later, I related this story to the guy who recommended Oswaldo to me. He, a gruff, no-nonsense senior professor, was shocked, and appalled. He and his (white) Brazilian colleagues had been treated very generously by Oswaldo.  And it never even occurred to him that anything different would happen to us.

And therein lies the problem.  There isn’t much on the internet about this phenomena.  Many white geologists simply have no idea that you can get a gun pulled on you in the pursuit of knowledge simply by having the wrong skin tint.  If the field of geology wants to integrate at the speed of the rest of our society, we need to think of tactful and effective ways of identifying, discussing, and solving the extra hurdles raised by mapping while black.

Carbonado, the diamond that looks like pizza.

I like to horrify current and recent students by telling them that I spent a month of my PhD figuring out what sort of film to use for best capturing the colors produced by the cathodoluminescence centres in carbonado diamond.  Of course, by the time it came to submit my thesis, I then had to spend days scanning all those slides.  Although, I still have a poster somewhere that is made from big glossy 8x10 prints, all glued to cardboard backing.

Now if you'll excuse me, I need to chase some kids off my psilphytopsid lawn...

Carbonado cathodoluminescence challenges

When I was a PhD student, I published a short paper in the Proceedings of the VIIth International Kimberlite Conference on luminescence from radiation-induced crystallographic defects in carbonado, a type of polycrystalline diamond. Being a proceedings paper, it was short format- 4 pages, and 6 figures. This work found its way into my Thesis, of course. But since the structural and stylistic conventions of a PhD thesis differ from that of a conference proceedings, that version was 49 pages and 34 figures. After graduating, I tried to publish a condensed version of the full work, but I couldn’t get it accepted anywhere- the conclusions were no different than the short version that came out in ’99, so it was considered uninteresting, old news, and beating a dead horse. I gave up submitting it sometime in 2003 or so.

Fast forward to last year. Yokochi et al. (2008) publish a lovely paper of carbonado spectrometry and microtexture. Their photomicrographs are probably the best published to date. They see the same spectrographic peaks and textural features that have been known since Fettke & Sturges (1933). And with the addition of some nice stable isotope and argon work, they find a novel way to put it all together.

Figure 1: Yokochi et al.'s figure 1b, showing euhedral phenocrysts in a bright matrix. I reckon the CL-dark areas in the upper left of the figure are probably from epigenetic radiation damage. Evidently he prefers another explanation.

In the process of interpreting their fabulous images, they say:

These circular textures are analogous to CL images of carbonado from Central Africa in previous studies (Magee & Taylor 1999, Kagi et al. 2007). Although these authors interpreted them as a result of radiation damage, our cathodoluminescence images show no link between the circular texture and the pores in which the radioactive elements might have been resided. Moreover, the size of this circular texture is occasionally larger than the range of a-particle influence (20 µm). An alternative hypothesis for this particular sample may be that this circular texture had first formed as phenocrysts at earlier stage, and the rounded shape and vague boundaries imply either a partial dissolution of the phenocrysts prior to the formation of the flow structure or an annealing that has erased the sharp boundary after a discontinuous growth.

Now, I don’t think their interpretation is correct. In fact, I have a highly detailed case to support our original interpretation- which is that grain-boundary-crossing CL quench features are epigenetic in origin. But it has been sitting in the back of my garage since we bought the house because nobody has ever doubted the short&sweet version before. Hopefully, the emergence of an alternative hypothesis will make the longer argument relevant.

So, if I’m not blogging here, it means that I’m trying to track down co-authors from a dozen years ago in order to get this paper submitted. Or it means my daughter’s sick. Or the garden needs attention. Or I’m wasting time on facebook instead of wasting time blogging.

Just like carbonado cathodoluminescence features, there are not several competing hypotheses for light blogging here at the lounge.

Refs:
Fettke, C.R., and Sturges, F.C., 1933, Structure of carbonado or black diamond: American Mineralogist, v. 18, p. 172-174.

Kagi, H., Sato, S., Akagi, T., and Kanda, H., 2007, Generation history of carbonado inferred from photoluminescence spectra, cathodoluminescence imaging, and carbon-isotopic composition. American Mineralogist, Volume 92, pages 217-224.
Magee, C.W. & Taylor , W.R. (1999): Constraints from luminescence on the history and origin of carbonado. Int. Kimberlite Conf., 529-532.
Magee, C. W. 2001. Geologic, microstructural, and spectroscopic constraints on the origin and history of carbonado diamond. Ph.D. Thesis, Australian National University.
Yokochi, R, Ohnenstetter, D., Sano, Y., 2008, Intragrain variation in d13C and nitrogen concentration associated with textural heterogeneities of carbonado. The Canadian Mineralogist Vol. 46, pp. 1283-1296.

Yokochi, R., Ohnenstetter, D., & Sano, Y. (2008). INTRAGRAIN VARIATION IN 13C AND NITROGEN CONCENTRATION ASSOCIATED WITH TEXTURAL HETEROGENEITIES OF CARBONADO The Canadian Mineralogist, 46 (5), 1283-1296 DOI: 10.3749/canmin.46.5.1283

What to do when you review?

Peer 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.

Sincerely,
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

Rate your own carbonado news story

Nitrogen defects in diamond. a. is type Ib, b. is type IaA, c. is type IaB. We use FTIR to determine nitrogen aggregation state becasue our eyes aren't sharp enough to make out the balls and sticks unaided.

I had someone else come up to me and ask about my opinion of the carbonado news today. Strangely, they didn’t offer to plot any data or fight the Bruker for me (the software for our IR scope runs in the OS/2 operating system, and the most advanced portable media reader on that computer is a 3.5 inch diskette drive). So, for those of you who want to know how reliable the coverage is in your medium of choice, here is a simple formula to rate the coverage:

They simply rephrase the press release to remove any big words: 0
They say that diamond is usually made by compressing coal: -5
They make any other basic geologic error by trying to over simplify: -1
They use, and explain, the term carbonado: 1 (the scientific community doesn’t even have a rigorous definition, so we can’t really complain about the quality of the press’s descriptions)
They interview an author: 1
They interview an independent “expert,” whose comments show that he doesn’t have a clue about the subject matter and is simply trying not to say anything that might make him look silly: 1
They interview an independent expert who can actually contribute meaningfully: 3
They do their own independent reading and explanation: 5
They interview one of the authors of any of the papers referenced by Garai et al.: 5
They interview a referenced author who speaks knowledgably: 10
They get their independent source to talk about experimental design, and pitfalls therein: 15
They get an author and an independent source to debate methods and data, instead of interpretations and models: 20
They get all interviewees to discuss the ramifications of the paper without anyone flapping their arms: 25

So far, the biggest score I’ve seen is about a 5.

The speed of science: relativistic media vs. classical research

As mentioned previously, I will be writing a comment on a paper which failed to impress me. My general complaints are that I think it misrepresents the literature, fails to describe its samples and analyses well enough to allow an objective interpretation, and overstates the quality of the data. But outside the ivory tower, life goes on.

Despite any previous metaphors used in this blog to describe the comment and reply process, it is one of the more standard, classical ways of discussing scientific findings. When done well, it is measured, fair, and provides greater illumination of how different research groups approach problems and weigh various evidence for and against competing hypotheses.

At the other end of the spectrum of scientific discourse is sound-byte and press release science. As it happens, the paper on which we wish to comment is accompanied by two press releases, by the university and by the NSF.

I think it may be interesting to compare the progress of buzz and reportage to the rate of constructing a scientifically sound counter-argument. So here’s a timeline:

Dec 20
The Astrophysical Journal Letters publishes the Garai et al. paper on carbonado diamond, which I think is a poor research publication.

Jan (date unknown, but probably the 2nd)
American Mineralogist publishes a Kagi et al. paper on carbonado, which I think is a contender for the best paper on the subject in the last 5 years.

Jan 8
Media:
NSF press release issued about Garai et al. paper
Articles on Garai et al. ‘06:
http://www.livescience.com/forcesofnature/070108_spacey_diamonds.html
Articles on Kagi et al. ‘07: (none)

Jan 9
Articles on Garai et al. ‘06:
http://www.diamonds.net/news/NewsItem.aspx?ArticleID=16479
http://www.infozine.com/news/stories/op/storiesView/sid/20089/
http://www.webwire.com/ViewPressRel.asp?aId=25971
http://www.shortnews.com/start.cfm?id=59413&rubrik1=Science&rubrik2=Research&rubrik3=All
http://www.physorg.com/news87577799.html
http://www.eurekalert.org/pub_releases/2007-01/nsf-dfo010907.php
http://www.foxnews.com/story/0,2933,242575,00.html
http://www.spaceref.com/news/viewpr.html?pid=21626
http://www.astrobiology.com/news/viewpr.html?pid=21626
Articles on Kagi et al. ‘07: (none)


Jan 10:
Science:
My postdoc adviser emails me the paper.

Articles on Garai et al. ‘06:
http://www.diamondintelligence.com/magazine/magazine.asp?id=4654
http://www.dailyindia.com/show/101783.php/
http://www.huliq.com/5491/origin-of-earths-mysterious-black-diamonds
http://www.sootoday.com/content/news/full_story.asp?StoryNumber=22052
http://www.swnebr.net/newspaper/cgi-bin/articles/articlearchiver.pl?159523
http://presszoom.com/story_122497.html
http://reports.discoverychannel.ca/
http://www.cosmosmagazine.com/node/960
Articles on Kagi et al. ‘07: (none)


Jan 11:
Articles on Garai et al. ‘06:
http://www.allamericanpatriots.com/m-news+article+storyid-17569.html
http://blogs.zdnet.com/emergingtech/?p=459
Articles on Kagi et al. ‘07: (none)

Jan 12:
Articles on Garai et al. ‘06:
http://www.innovations-report.de/html/berichte/geowissenschaften/bericht-76806.html
http://www.photonics.com/content/news/2007/January/12/85986.aspx
http://www.ccnmag.com/news.php?id=4724
Articles on Kagi et al. ‘07: (none)

Jan 13:
Articles on Garai et al. ‘06:
http://www.spaceflightnow.com/news/n0701/12diamonds/
Articles on Kagi et al. ‘07: (none)

Jan 14:
Articles on Garai et al. ‘06:
http://www.spacedaily.com/reports/
http://space.newscientist.com/
Articles on Kagi et al. ‘07: (none)

Jan 15:
Science:
I get back from summer holiday, check my mail, read paper. Scratch head, read again, explode. Scrape self off ceiling, email postdoc advisors and PhD advisor to see if they are interested in co-authoring a comment (My PhD was on carbonado diamond). I start digging back through papers I haven’t looked at for 6 years.
Articles on Garai et al. ‘06:
http://www.theregister.co.uk/2007/01/15/black_dimaonds/
Articles on Kagi et al. ‘07: (none)

Jan 16-19:
Science:
Post doc advisors get on board, I chat with one of them, we map out a general plan, start looking for the software/ archived files we need. I learn that Statview hasn’t been sold since 2002, start thinking up workarounds.
Articles on Garai et al. ‘06:
http://dsc.discovery.com/news/2007/01/18/blackdiamond_spa.html?category=space&guid=20070118103030&dcitc=w19-502-ak-0000
http://talkback.lancasteronline.com/index.php?showtopic=40034
Articles on Kagi et al. ‘07: (none)

Jan 20-21:
Science:
Go through paper (over weekend) with attention to detail, start categorizing things I don’t like by relevance, type of issue, dubiousness of claim, etc.
Articles on Garai et al. ‘06:
http://www.cleveland.com/news/plaindealer/index.ssf
http://abc.net.au/science/news/stories/2007/1831109.htm
Articles on Kagi et al. ‘07: (none)

Jan 22-present
Science:
Finally get some obscure articles from Geoscience Australia (not in our library) to confirm selective referencing, crash IR scope computer trying to remember how the OS/2 operating system works, get PhD supervisor interested, get swamped with work for visiting scientists.
Articles on Garai et al. ‘06:
http://news.nationalgeographic.com/news/2007/01/070122-black-diamonds.html
http://www.inform.kz/showarticle.php?lang=eng&id=147985
Articles on Kagi et al. ‘07: (none)

Draw your own conclusions.

Comment and Reply

The evolution of animal behavior can be a surprisingly conservative process. Even though the habitat, niche, and social organization of a creature may change as it evolves, certain core behaviors are often retained.

One example of this is the fecal throwing habits of monkeys. Bereft of dangerous claws, poison, or hooves, monkeys have been forced to defend themselves by slinging their own poo at perceived enemies. Despite tens of millions of years of evolutionary divergence, the adaptation of culture, and the invention of the scientific method, researchers do exactly the same thing. Only they call it “Comment and reply”.

There are two criteria that must be met before a researcher engages in this undignified activity.

First, he must identify a paper that, despite appearing to be the summation of a scientific research project, is in fact a huge, steaming pile of shit.

Second, he must fee that this paper was either hurled at him directly by a rival team, or else tossed close enough that the smell distracts him from the dispassionate pursuit of knowledge.

When an aggrieved scientist feels that these two criteria have been met, he then squeezes out his own steaming turd, and fires it off at the editor of the offending paper. That editor takes the crap, examines it with the help of a reviewer, and passes it on to the original authors.

Those authors in turn drop a load in response to the comment, called a reply. The comment and reply are then generally published, side by side, in the journal that ran the original paper.

Usually that is all that happens, aside from the odd snide letter to the editor. Rarely, one side or the other will capitulate, and plate the opposing side’s poop with gold. And every now and again, a real shitfight results, with claims and counter arguments splattering against each other for years to come.

I am about to start putting together my first comment. Hopefully the level of discourse will be higher than that in this explanation.