Archive | April 2016

Eocene Telephone

Recently, GG concurred in the observation that myths can persist in the scientific community and added his own story of the “ignorant sheepherder” comment supposedly directed by Whitney at Muir.  Some readers might have said so what, these are innocent little pieces of color commentary independent of the march of science.  So for those skeptics, a more significant example.

A lot of recent work has been done on the Auriferous Gravels.  These papers pretty uniformly assign a middle-late Eocene age to these rocks.  For instance, Cassel et al. (2009, Int. Geol Rev.) said “Middle – late Eocene flora from within the upper half of the sequence are the only dateable material in the prevolcanic gravel (MacGinitie 1941).” A later paper gets a bit more precise (Cassel and Graham, 2011, GSA Bull):

The “Chalk Bluffs flora,” from the auriferous gravels at You Bet Diggings (Fig. 1), has been used to estimate the depositional age. Originally described as Capay stage and interpreted as middle Eocene by MacGinitie (1941), the Chalk Bluffs flora is now considered to be early Eocene (48.6–55.8 Ma; Wing and Greenwood, 1993; Wolfe, 1994; Fricke and Wing, 2004), which is consistent with comparable floral assemblages in other recently dated sections (Meyer, 2003; Retallack et al., 2004; Prothero, 2008).

Hren et al. (2010, Geology) similarly date these rocks: “Plant fossils are classified as Chalk Bluffs Flora after their best-preserved occurrence, and are dated at 52–49 Ma by faunal and floral correlation (MacGinitie, 1941; Wing and Greenwood, 1993).” It would seem that these sediments are pretty firmly dated to 49-52 Ma.

Except that in fact there is no firm floral date for these rocks.

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Saved by the Ancient Garden

GG has been working on a book on the history and impact of the Sierra Nevada and its relationship to the geology of the range. (This blog exists in part to exercise GG’s weak writing muscles to help in that endeavor). The book is pretty far along and so of course some things have fallen to the side, distractions insufficiently connected to merit inclusion in the final text.  But some stories deserve not to die an unknown death….

In 1988, GG managed to enlist the help of Steve Rocker from RPI, Tom Fairbanks from Oregon State [well, maybe U of O-its been a while] and then-grad student Scott Phelps from Caltech to deploy six seismometers in the backcountry of Sequoia National Park and adjacent parts of the National Forest. Our effort had met with several setbacks, so it was towards the middle of the third week when Scott and I toiled up the 4000′ climb from Kern Hot Springs over the top of the Chagoopa Plateau area and on to the old CCC cabin in the Big Arroyo, where we expected to find that the packer had dropped one of our seismometers. Steve and Tom were to follow the next day. When Scott and I got to the cabin, no seismometer.

So the next day, when we were supposed to be getting things set up so that Steve and Tom could help finish the job late in the day, we instead were hiking down into the Big Arroyo to get our missing gear. We succeeded but could only bring up about 2/3 of it. We would need an extra day.  Meantime, Scott was heading out of the backcountry.

That next day would take Steve and I down the canyon to get the rest of the gear while Tom started preparations for installing the seismometer.  But we had almost no food left–I had part of a package of freeze-dried spaghetti and a freeze-dried meat patty; Tom and Steve had even less.  While Steve and I schlepped up the missing gear, Tom also did a little foraging and came up with some onions and sage.  [This is NOT an approved activity in a national park.  We were kind of desperate]. While I polished off what little was left of the spaghetti, Tom and Steve had a sort of stew made from the meat patty, onions and sage. It was enough for the three of us to get back to our food stocks the next day.

Just where did the onions come from? That seemed quite fortunate.

Overlooked for a long time has been the horticultural efforts of the native peoples of the Sierra.  Their activities had been noted, leading to the derisive term “Digger Indians”, but whites who witnessed this activity didn’t fully appreciate that this was more than simply digging up roots; the Native Americans in these parts were managing the landscape far more thoroughly than Euro-Americans recognized, encouraging and cultivating many food and medicinal plants while using fire to keep other plants at bay.  Work in the past 30 years or so has greatly clarified the role Native peoples played in creating the tapestry of plants found in the Sierran foothills.

These same peoples would spend their summers in the high country.  At these subalpine heights, even modern researchers tend to think their impacts on the ecology were subdued, some amount of burning at meadow edges being the most likely activity. But wouldn’t they also try to do some planting or encouraging of foodstuffs just as in the foothills?  It seemed likely to GG, so the original text suggested that those onions might have been the feral remains of an old Indian garden.

Well, an editor challenged GG on this, and this is not of course GG’s speciality, and the literature is rather vague at these elevations.  The editor knew one of the experts on Native impacts on Sierran ecosystems and so asked: “How much evidence is there for a discernible impact on the vegetation and flora [in subalpine and alpine zones]? Was the high Sierra landscape anywhere near as cultural and anthropogenic as landscapes much lower in elevation where Indians had permanent villages?” The answer came back: “There was Indian burning in high elevation forests to manage for a tighter snowpack and also high elevation meadows to keep them open for willows and sedges (basketry), food, and other resources… I know the Washoe would gather wild onions under the aspens at very high elevations–leaving the bulbs behind to make more and just cutting back the greens.” With no prompting about onions, GG’s speculation suddenly became more secure.

Now the Washoe were far to the north, but hey, maybe our onions really were the leftovers from an ancient Tubatulabal garden. The area we were in in the Big Arroyo seems a likely place for a summer campsite, though GG has not seem archeological discussion of that particular spot.  It is similar to other places in the parks that have archeological evidence of occupation. Although GG felt justified in this rather exorbitant claim, the text was, as the editor noted, distracting from an already complex line of thought, so the little story of the seismologists saved by the old Indian garden fell out of the book. But it seemed a shame to lose a fable that might even be true, so here it is.

Scientific Telephone

An interesting piece over in FiveThirtyEight that considers how some myths persist in scientific communities (along with pointing out a suggestion that Darwin was late to the natural selection party). Its worth a read.

And so it reminds GG to once again rail against lazy scholarship (yes, this has happened before). So to add to the examples in the FiveThirtyEight piece, there is the story that J.D. Whitney attacked John Muir over his glacial theory for the origin of Yosemite by calling Muir “a mere sheepherder, an ignoramus.” You can google this quote (there are some variations out there); it shows up in many popular publications on the Sierra. This seems to first appear in Francis Farquhar’s History of the Sierra Nevada, where he cites the 1869 Yosemite Guidebook. But unless all the scanned versions of that guidebook online have been edited, that quote doesn’t appear in any of them.

There is good reason that you cannot find such a quote in that 1869 volume.  Muir was indeed herding sheep near Yosemite Valley in the summer of 1869; he had arrived in California in 1868 and seen Yosemite shortly thereafter but had not yet begun to formulate his ideas on the origin of the Valley. Whitney would have had to have been rather prescient to attack the ideas that were brewing in Muir in that summer.

So Farquhar cited a phantom.  Now Whitney most certainly disagreed with Muir, and Muir was certainly attacked for his idea, and it is possible that Whitney did say something that dismissive (it was very much in Whitney’s style).  GG has not turned up the source of the phrase. Muir’s identification of living glaciers in the Sierra was attacked by Whitney’s old field assistant, Clarence King, in his 40th Parallel Survey report:

lt is to be hoped that Mr. Muir’s vagaries will not deceive geologists who are personally unacquainted with California, and that the ambitious amateur himself may divert his evident enthusiastic love of nature into a channel, if there is one, in which his attainments would save him from hopeless floundering.

[If you wonder, Muir was more right here, too].

It would probably be 1870 when Muir’s theories on the glacial origin of Yosemite would have first attracted Whitney’s attention, as it was in that summer that Joseph LeConte met Muir and the two agreed on a glacial role in the origin of the range, with LeConte encouraging Muir to write this up somewhere (this led to Muir’s firs published writings). Yet the Yosemite Guidebook would not change with regard to any theories on the valley or those theories’ advocates.

Whitney did eventually respond in his book, The Climatic Changes of Later Times in 1882, but even here Muir’s name is absent (as would be fair, LeConte also having written in favor of a glacial origin): “It seems surprising that a theory so utterly averse to the facts should have ever gained currency, and it is almost humiliating to be obliged to enter into an argument to prove that the Yosemite Valley was not dug out of the solid granite by ice.”

Interestingly, there were no hard feelings.  The Sierra Club elected 10 honorary members shortly after being formed in 1892.  Among them were Whitney and King; Whitney wrote back thanking them for the honor.

Like many of the scientific rumors mentioned in the FiveThirtyEight piece, this isn’t exactly something that would challenge the core assumptions of science, but it does nicely illustrate the hazards of relying on secondary sources. If it matters, it is worth tracking down the original source.  You might be surprised by what you find.

Is P really ρgz?

The discovery of widespread ultra-high-pressure phases in many metamorphic terranes–most dramatically the presence of metamorphic diamonds–has fueled speculation on the deep subduction of crustal materials and their subsequent return to the near surface environment. The extent and geologic continuity of some of these terranes has challenged how we think materials move in subduction zones. But all of this depends mightily on the assumption that pressure is, essentially, the weight of overburden. That is, the pressure determined from petrologic changes was simply the weight of the material above (∫ρg dz).

Hovering over this is the recognition that stress can be focused deep within the solid earth.  The assumption has been that such stresses would not materially differ from the weight of the overburden.  It has never been clear that this was a great assumption: Byerlee’s Law, for instance, allows that if pore pressures are near zero, horizontal normal stresses could be three times the overburden weight, meaning that with no special pleading that the pressure (which would be the average of the normal stresses) could be more than twice the weight of the overburden.  This extreme case though caused little concern for deep rocks as many of these are deforming by creep and so will be much weaker.

But what if you could focus all the normal stresses? Such focusing occurs in artificial situations all the time (most extreme case might be hydrogen bombs, which are triggered by focused blasts from smaller atomic bombs). This question was explored in a recent Geology paper by Georg Reuber and colleagues in Germany and Switzerland.

This paper runs some numerical simulations to show that the presence of enclaves of anhydrous crustal blocks in a weak lower crust can result in pressures within the enclave more than twice the weight of overburden. What was more, the duration of such super-lithostatic pressures was in the millions to tens of millions of years.  A block that would see pressures usually associated with depths of 90 km or more could have been only 50 km or so deep. Similarly high pressures can be achieved if the entire lower crust is anhydrous.

This suggests that petrologists now need to consider the broader environment of their samples before inferring great depths (or rapid rise) for samples of ultra-high pressure rocks.  The models in this paper are basically permissive, indicating that it would be the presence of stiff, water-free materials that would be the key in promoting such great overpressures. It will be interesting to see in the coming years whether a reexamination of these rocks confirms the great depths presently ascribed to them or reveals that dynamic pressures from tectonic activity can cloud our ability to interpret depth from petrology.

How Ethical is Geoscience?

If you are a regular visitor to RetractionWatch, you see on a daily basis papers that are shown to be falsified or duplicates of earlier work or plagiarized from others’ work.  And as a geoscientist, GG is often relieved to see that geoscience papers are a rare commodity over at RetractionWatch. Is this because we are as a community more pure of heart and mind, or is it that there are aspects of our science that are more capable of hiding misbehavior?

On other points, it isn’t clear that geoscientists are saints. Reading Hope Jahren’s blog, for instance, would cure many of any delusion that sexual harassment and discrimination doesn’t exist in the geosciences. GG looked to see if he could find any summary of campus sexual harassment/discrimination cases by academic discipline and failed (if you know of one, please post a link in the comments). But the nature of geologic fieldwork–long periods out in the field with small numbers of people–has long been a potential minefield for female scientists, and plenty of geoscience departments stayed “boys’ clubs” far longer than could be justified. Some geologists have been banned from supervising female students, for instance, because of inappropriate behavior in the field.

So if geoscientists are not particularly saintly on other scores, is there something about earth science that either hides or precludes academic misconduct?

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Are we ready for “Big Literature”

A lot has been written about Big Data, presenting it as some kind of super challenge and opportunity.  Certainly there is a lot of data kicking around out there, but the thing about Big Data is that it is, well, data–if you know what you want to do with one data point, figuring out an algorithm to extract a lot of data points of interest and process them, while time consuming, isn’t hopeless.  (so, for instance, one could argue that seismologists have for some time been in the Big Data pool, extracting and analyzing parts of the many terabytes of stored data for the pieces of interest).

But what if you have to examine each data point on its own? Such is the case with the scientific literature. And the explosion of that literature may threaten the ability to make progress.  (That explosion will only get worse if peer-review is discarded in favor of open repositories). So, can we deal with “Big Literature”?

In the past, the trend has been to become more and more specialized, which allows one to face a tractable part of the literature. But with an increasing emphasis on interdisciplinary work, building on advances in multiple fields in increasingly desirable. How to deal with these pressures?

Perhaps this is why GG has noticed increasingly poor citation habits, where authors are not citing the papers that are the source of the algorithm, interpretation, or data point they wish to make use of but instead are citing some recent paper that also made use of this object. If so, this is unfortunate in two ways: it deprives the originator of the object the credit he/she/they deserve, and it also runs the risk of turning into a game of telephone where progressive misunderstandings of what was actually done/said/observed propagate through the literature, degrading later attempts to conduct research.  That this kind of degraded citation practice exists with the presence of modern tools allowing quick access to nearly the full literature and its citation history suggests that various pressures are breaking down more traditional behaviors. Certainly some of this is the pressure to publish frequently while generating lots of grant applications, but some is probably reflecting the growth of the literature beyond the capacity of many of us to digest.

How will we deal with this? One way is to simply focus on a subset of the literature–probably the literature that supports the direction your research is going.  Certainly a filter many senior researchers apply before reading a paper is a quick skim of the author list–certain individuals may have consistently produced work worth reading, and so the paper gets read, and others maybe have not. This can lead to the echo chambers we see people falling into politically. Or maybe we skim the latest work, missing out on perhaps relevant observations made in the past, thus risking repeating earlier mistakes, or simply unknowingly repeating earlier work (which is different from trying to reproduce a study). (We had a student once who liked to simply plow ahead, not caring what was in the literature.  GG’s comment at the time was that when you reinvent the wheel, you risk reinventing the flat tire.)

GG isn’t sure where this will go.  Will “Big Literature” produce new tools for metaanalysis of science? Are we doomed to trip over ourselves in our growing ignorance of the state of the whole field? Or will we react by compacting and reclassifying literature in some way to make it digestible to human brains? It might be time to start worrying about it before some future Congress calls scientists and program directors before it to explain how they could have unknowingly done the exact same thing as their predecessors some years before.

Searching for Good Samaritans

There is something of an aside at the end of a recent story in the Denver Post on attempts to clean up the numerous mines leaking acid waste into rivers in southwestern Colorado; the story quotes Governor Hickenlooper as saying: “Lastly, we continue to support efforts by our congressional delegation to reach consensus around ‘Good Samaritan’ legislation, which is one of the most significant tools at our disposal to allow for voluntary cleanups of draining and abandoned mines.”

You might ask, what is this about? In many ways, the story starts with gold mines in the Sierra Nevada long ago before intersecting with environmental protection laws.

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