An example of peer review

Dear Editor Smith,
I return the Doe et al. manuscript number 5623646 with numerous comments. In my opinion, the manuscript will not be fit for publication until all the flaws described below are corrected:

Title

The title of this paper does not reflect the sort of study which I would like to see done on this material. Please instruct the authors to change it, instead of using the title to push their own agendii.

Introduction

While the paper is nominally about solid solution in simple oxides, the narrow focus of the introduction has resulted in a failure to cite the well-known avian migration papers of Lemming et al. (2003), and Lemming and Aardvark (1998), both of which ought to be mentioned for completeness. Without tying mineral solid solution to bird migration (ibid), econometrics (Lemming and Wesson 2002), and mass spectrometry Lemming et al. 2009), the author fails to cite as wide a selection of my papers as he otherwise could. This indicates an inability to place the science in the broader context of society. Without this context, their results are neither novel nor interesting.

Methods

Like the title, the methods of this paper fail to pursue the angle of inquiry which I would have used, had I their skillsets and funding. This is obviously a serious error. Please require the authors to have done something other than the experiments whose results they are reporting. They would do well to cite Lemming et al. (2009) for the analytical procedures I prefer.

Results

In the first experiment, where the precision is twice as bad as Lemming and Stoat (2006), the data is obviously not precise enough to be worthy of presentation. The second experiment, with precision twice as good as Lemming and Stoat (2006), is obviously too good to be true, and must be the result of incorrect error propagation or outright forgery.

Discussion

Once again, the lack of citations to my unrelated papers is a serious flaw. In addition, the authors insist on drawing conclusions based on their data, and not my preconceptions of where the field was 15 years ago. Ignoring the work that they misguidedly performed renders the rest of their study irrelevant. In fact, their constraints and discussion of the experiments they DIDN’T do is practically nonexistent. This is clearly unscientific. There is a problem of nomenclature as well. The proposed mineral name in this paper is completely unacceptable. I require the authors to name their new mineral after my pet hamster instead.


While this paper is not suitable for publication in a top rate journal, it will be perfect for your rag, providing that the above revisions are undertaken.

Sincerely,
Dr. Lemming

How do extinction events kill so effectively?

“I am flying home from Europe in late August with nothing but a notebook and the 2011 Goldschmidt conference Geology giveaway issue to keep me occupied. Using the old-fashioned method of reading and writing on paper, I will blog my way through the compilation of highlighted geochemistry papers as time allows. These will then be posted via time delay to keep the blog moving while preventing paper burnout.”

The dinosaurs are still alive!

This was the conclusion reached by a group of my fellow undergrads way back in the Pliocene when I was in college. As an independent study project, they investigated all the possible effects of a giant meteorite impact (dust, fires, tsunami, etc), and concluded that none of these effects had the reach or duration to cause widespread global extinction.

Indeed, the actual kill mechanism is generally armwaved and/or hyperbolized (no sunlight for months, scorching acid rain, death from the skies!) under the circular reasoning that, “since everything died, these effects must have been lethal.” Understanding how entire niches get wiped out as actually rather tricky.

Enter Kump et al. (2005), who described a possible kill mechanism; poisoning from massive releases of H₂S gas from an oxygen-starved ocean.

In the absence of oxygen, bacteria will happily metabolize sugars by turning sulfate (SO₄^--) into sulphide (S^--), with the oxygen liberated form the sulfate used to burn sugar into CO₂ + H₂O. In the absence of iron or other base metals, this sulphide becomes H₂S in an aqueous system like the ocean. The ocean is full of sulfate; it is the second most common dissolved salt anion, after chloride.
So under oxygen-free conditions, generating significant amounts of H₂S is easy. Once this H₂S mixed with oxygen-rich water, it oxidizes back into salfate. Water with significant H₂S content is called “Euxinic”. While the modern ocean is well oxidized throughout all, but a few closed basins like the Black Sea, in the geologic past some or all of the deep water may have been euxinic.

In their study, Kump et al. (2005) do two things. First, they determine the conditions under which H₂S-bearing waters can upwell to the surface faster than oxygenated near-surface water can break down the H₂S. This is important because oxygen and hydrogen sulphide react easily in water, but if the H₂S exolves into the atmosphere, then it can co-exist metastably with O₂ gas in the air.

The second thing that Kump et al. (2005) do is to chemically model what happens to this H₂S once it gets into the atmosphere, how it is broken down,. and what other changes occur as a result.

Because H₂S and O₂ do not directly react under normal atmospheric conditions, H₂S oxidation in the atmosphere in generally performed by the OH and O radicals, which are in turn generated by the UV or radiological breakdown of H₂O and O₂ molecules. These are the same radicals that breakdown methane (CH₄), carbon monoxide (CO) and many other metastable gasses.

What Kump et al. (2005) find is that if the H₂S flux into the atmosphere exeeds the present flux by about a factor of 1000, then the H₂S accumulates after than the OH and O radicals can break it down. This leads to a step function increase in H₂S atmospheric lifetime and concentration, and a drop in O and OH abundance.

This depletion of O and OH, in turn reduced methane breakdown, so that methane concentrations and mean atmospheric lifetimes also increase. In addition, the lack of O means that ozone production is curtailed, so the ozone layer is reduced. The combination of reduced ozone protection and direct H2S toxicity is touted by Kump et al. as a highly effective kill mechanism, especially for land creatures and sea creatures in the near-surface waters.

Kump et al. then go on to show that there is evidence for anoxic waters reaching the surface during a number of Phanerozoic extinction events, and further hypothesize that the widespread euxinia in the Proterozoic inhibited the development of land life as a sort of “permanent extinction event” condition that persisted for most of Earth’s history, until mysteriously disappearing in the Cryogenean.

The H₂S-based kill mechanism (catchily coined as a “chemocline upward excursion”) is way outta my field of expertise. So I don’t know if there are reasons outside of my knowledge base to reject it out of hand. However, the nice thing about this paper is that it proposes a mechanism with specific, testable effects which we analysts can go looking for. While determining paleo-ozone and methane levels could be a bit tricky, the study of paleoeuxinity is a significant and ongoing field of study. I don’t know if this paper has withstood the test of time, but I suspect that it has inspired a whole slew of clever experiments. What more could we ask of the theoriticians?
Kump, L., Pavlov, A., & Arthur, M. (2005). Massive release of hydrogen sulfide to the surface ocean and atmosphere during intervals of oceanic anoxia Geology, 33 (5) DOI: 10.1130/G21295.1

The National Hurricane Center's Y2K bug

The following is the current forecast discussion for Hurricane Katia. Note the last line:

ZCZC MIATCDAT2 ALL
TTAA00 KNHC DDHHMM

HURRICANE KATIA DISCUSSION NUMBER 45
NWS NATIONAL HURRICANE CENTER MIAMI FL AL122011
500 AM AST FRI SEP 09 2011

THE CLOUD PATTERN CONTINUES WELL ORGANIZED AND IN FACT A DRIFTING
BUOY NEAR THE CENTER OF THE HURRICANE RECENTLY REPORTED A MINIMUM
PRESSURE OF 968 MB. THE INITIAL INTENSITY IS KEPT AT 75 KNOTS.
HOWEVER WEAKENING IS INDICATED SINCE THE HURRICANE IS ALREADY
REACHING COOLER WATERS AND KATIA IS FORECAST TO BECOME
POST-TROPICAL IN ABOUT 36 HOURS.

THE HURICANE IS MOVING TOWARD THE NORTHEAST OR 050 DEGREES AT 21
KNOTS. SINCE THE HURRICANE IS ALREADY EMBEDDED WITHIN THE
MID-LATITUDE WESTERLIES....IT SHOULD CONTINUE ON THIS GENERAL TRACK
WITH AN INCREASE IN FORWARD SPEED FOR THE NEXT FEW DAYS.

NO 96-HOUR POINT IS BEING GIVEN BECAUSE FORECAST POINTS IN THE
EASTERN HEMISPHERE BREAK A LOT OF SOFTWARE.


FORECAST POSITIONS AND MAX WINDS

INIT 09/0900Z 37.6N 67.5W 75 KT 85 MPH
12H 09/1800Z 39.5N 64.5W 75 KT 85 MPH
24H 10/0600Z 42.0N 55.5W 70 KT 80 MPH
36H 10/1800Z 45.5N 43.0W 60 KT 70 MPH...POST-TROP/EXTRATROP
48H 11/0600Z 49.5N 30.5W 65 KT 75 MPH...POST-TROP/EXTRATROP
72H 12/0600Z 56.5N 10.5W 50 KT 60 MPH...POST-TROP/EXTRATROP
96H 13/0600Z...EAST OF ZERO DEGREES LONGITUDE

$$
FORECASTER AVILA

NNNN

One day posters suck

We are talking about conference posters here, not posts on blogs. In general, there are two main types of presentations at scientific conferences; talk, and posters. Talks are generally supposed to appeal to a large number of people, and feature limited feedback between individual audience members and the speaker (aside from the occasional front-row tantrum, of course).

Posters are generally a more personal affair, wit the poster presenter and the one or two people listening engaging back and forth for as long as it takes to settle their differences.

Back in the good old days, when Demetrodon was our most advanced predator and mollusks ruled the seas, posters stayed up for the entire conference. This was great, because speakers could put the nettle gritty details of their methodology on their co-authors posters, and posters that describe methods used in a number of different talk sessions could all be centrally located. When I gave a poster at Goldschmidt in 2006- my last presentation before starting work in exploration, I had one person come by during the dedicated poster presentation time, Monday morning. But as the conference continued, and more and more people discussed interesting science based on what the lab was doing, more and more people started to swing by and discuss things, or ask me to walk them through the poster, and by Friday afternoon we had engineers from different mass spectrometer factories dueling with whiteboard markers of the the details of the ion optics.

Nowadays, this can’t really happen. At all of the major conferences I have been to since then, posters have been a one day affair. They are put up the day of the discussion, and taken down afterwards. And I reckon that this is an inferior system.

Firstly, it makes coordinating posters that related to multiple sessions difficult. Even within a session, if the timing of the talks and posters are not arranged well, you can have a speaker referring people to details in a poster that has already been taken down.

Of course, the flip side to one day posters is that you can halve four times as many of them, with commensurate increases in attendance (and fees?). But is it really necessary to bring more and more people together for less and shallower interaction? I thought that was what the internet was for.

How odd is our solar system?

One of the most basic observations about the planets in our solar system is that there are two basic types. In the inner solar system, we have four rocky planets with radii less than 6500 km. In the outer solar system, there are four gaseous planets, with radii larger than 24,000 km. One long-held implication of this division is that there is some sort of significance in the lack of planets intermediate in diameter between Earth and Neptune.

One of the most striking observations from the list of planet candidates from the Kelper mission is just how unusual the terrestrial planetary size distribution is. The Kepler planetary radius distribution (figure 1) peaks in the middle of this gap; almost 70% of Kepler planet candidates are larger than Earth but smaller than Neptune.

Figure 1. probability distribution of Kepler planet candidate radii

So our solar system is unusual. But how unusual. A back of the envelope calculation will tell us. If we accept the Kepler figures, then only 30.8% of planets are, like ours, either smaller than 6500 km or larger than 24000 km. So the chances of an eight planet system having zero planets in this size range is 0.308^8. This works out as about one in twelve thousand. So for every 8 planet system like ours, there should be 11,999 with at least one intermediate-sized planet.

With a hundred billion stars in the galaxy, there are still bound to be quite a few solar systems like ours. But with only about 1800 known planets and planetary candidates discovered so far, it is unlikely that we will discover a solar system analog any time soon.

Time away

The lemming family has been on holidays. The geomorphologically curious are welcome to guess LLLL's location in the picture above, but the only hint I will give is that everything in the photo aside from the atmosphere is geologically young in the grand scheme of things, having formed in the last few percent of Earth's history. Scientifically meaningful content will return as time permits.

Mass–independent isotopic fractionation

The whole point of geology is to figure out what happened in the past based on the rocks from that time which are still around today. It isn’t actually about the rocks. It’s about the story. The rocks are just the publishing medium. And the craft of geology is learning to read the language of stones.

Similarly, the purpose of geochemistry is to determine the story told by a rock’s chemical composition. The way we do this is somewhat counter-intuitive. We generally search for chemical relationships- that are hard to change. The reason for this is that a ratio that is easy to change doesn’t tell us very much. The potassium/platinum ratio, for example can be changed by just about any process, so measuring it doesn’t tell us what process was occurring.

This is why geochemists like to study systems like noble gasses, rare earth elements, and isotopes. These things are generally changed by only a few processes, so if a change is seen in a rock, there are relatively few processes that could have made the change.

For example, isotopes are nuclei of the same element with different masses. They generally have similar chemical properties- all sulfur isotopes are still sulfur- so only a few processes can change them: evaporation, digestion by bacteria, and diffusion, are some examples. This is the basis of all stable isotope geochemistry; to use the limited number of possible processes to pin down a story by looking at isotopic changes.

In general, when isotopic ratios change, that change is mass dependent. That is, the change is a function of the difference in mass. For sulfur, for example, the change in the ³³S/³²S ratio should be about half of the change in the ³⁴S/³²S ratio. Mass-independent isotopic fractionation refers to a process that fractionates the different isotopes by a ratio that is not strictly mass-dependent. So instead of the ³³SS/³²S change being half the ³⁴SS/³²S change, it might be 0.6. Or 0.3.

The number of causes of mass independent fractionation is exceedingly small- way smaller than the number of effects that cause normal mass dependent fractionation. So if mass independent fractionation is observed, you pretty much know that a particular unique process must have happened.

Most mass independent isotopic work at present is done in sulfur. This is because mass-independent fractionation of sulfur is ubiquitous in rocks from the first half of the Earth’s history, but is rare to nonexistent since that time. So this is a powerful tool that tells us that the Earth’s surface was fundamentally different in Archean time; a process (photolysis of atmospheric SO₂) was occurring from 3800 to 2450 million years ago, and hasn’t happened since. SO₂ is not stable in the presence of oxygen, and photolysis requires UV light that is currently blocked by the ozone layer, so the sulfur isotopic record is the best tool we have for determining just how different the early atmosphere was from the one we breathe today.

If you think this blog is inactive, visit a craton.

One unfortunate side effect of the wireless and handheld internet revolution of the past five years is that it has made internet cafes harder to find. So expect cratonic style inactivity to continue for a web epoch or two.