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My Wonder List

There are things that puzzle GG and this is a partial list that will be updated from time to time.

  • When did the High Plains become high?
  • Why did the High Plains become high?
  • What exactly did happen in the Mojave Desert c. 75 Ma?
  • Why did the Sierra Nevada arc shut down?
  • Related, why did it shut down from north to south?
  • If the northern Sierra only went up prior to the Eocene, why are modern rivers cutting well below those deposits?
  • If the northern Sierra have gone up significantly since the early Miocene, why do climate proxies disagree?
  • If the northern Sierra only went up prior to the Eocene, then how did one form of support (crustal root?) get replaced by another (buoyant mantle)?
  • What caused the Ancestral Rockies to rise up where they did?
  • Why did the large thrust on the south side of the Uncompahgre Plateau fail to reactivate in the Laramide?
  • How much of the Laramide foreland (basement-cored) uplifts reflect some different source of stress and how much do they reflect stresses from the Sevier belt driving shortening?
  • It seems likely there was serious slip partitioning in the Sevier; where is it?
  • There are some LANFs that seem to have really formed in the brittle crust at low angles. How?

The Coming Publication Apocalypse

To be clear, we are talking scientific publication. And to save some of you time, there isn’t a lot new here, but the trends are looking to collide sooner rather than later.

What does GG mean by a publication apocalypse? Basically the end of any meaningful evaluation of publications; we are heading rather rapidly into a blizzard of material with no vetting or meaningful review. While there are those who think this will be the most democratic way to distribute science, GG would rather point them to how equally unmoderated blizzards of material have led to minor problems in the political sphere like, oh, insurrection based largely on falsehoods.

What are the trends that are facing the whole concept of journals?

  • open access upon publication
  • high levels of publication for tenure, promotion and funding
  • preprint servers
  • junk journals
  • reviewer fatigue
  • expansion of research into more of academia

Several of these interact in poisonous ways. The perception that faculty must publish more and more frequently to satisfy promotion and tenure committees or funding agencies leads to lots of manuscripts circulating around, all of which need to be reviewed, thus leading to reviewer fatigue. Open access demands on journals are probably putting journals fully into the realm of vanity publishers: their only source of income will be what authors pay. This in turn restricts the support journals can provide to editors and reviewers. Researchers who aren’t flush with funds (for instance, many summer intern programs or honors thesis writers or advanced degree recipients who were supported on teaching assistantships) will be forced to either limit their findings to preprint servers lacking any review or junk journals that claim peer review despite lacking it. The increasing pressure on traditional journal publishers will slow the path to publication, making those junk journals more attractive.

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Left holding the bag by Adobe

Some years back many of us saw an opportunity to make electronic publication of science more than just a limitless pile of page images. We could have interactivity: the deeper and richer datasets and models being created and interpreted could be more fully presented to readers who could interrogate the data directly rather than having to, say, download raw tables and replicate a bunch of work before being able to see if looking at the data a bit differently yielded a different interpretation.

And so some of us demonstrated such tricks by embedding interactive material into pdfs of scientific papers. While some of this was the trivial use of layers or embedding a movie, other examples were more sophisticated. These typically relied on Flash.

Well, as you no doubt know, Flash is no more. Adobe, like the rest of the world, has moved on to HTML5 tricks and beyond. But what was stranded–entirely and apparently irrevocably–are animations embedded in pdfs. There is no tool for embedding html5 in pdfs. There is no scaled-down Flash viewer that works with pdfs. Nope, all you get now from those pdfs is a message that Flash is dead and a worthless link to an FAQ online that doesn’t even consider the possibility that you got there from trying to look at a pdf.

GG had hoped that there would be some substitute. The underlying language of Flash is in fact open source. Adobe wouldn’t just utterly kill off a major capability of their software, would they? Well, the answer is now crystal clear: it is “yes”. And what is more, there is no real substitute out there (the closest are epubs, which are not particularly well supported, especially when it comes to real interactivity).

In an online-always world, maybe you shrug and convert over to html 5. Which, realistically, means you only can access a document live as it will depend on a host of other files to fully become a document. And after the misadventures with Adobe and Flash, just how future proof do you think html5 is going to be? So interactive scientific publication is, once more, dead. Yes, you can do a few tricks with layers and (oddly enough) embedded 3-d models still work (an odd thing to carry forward). But anything more than that is dead and gone.

GG has a couple of papers using these tools that are now very difficult to read; one had even won an award.

All this was unnecessary. Macromedia and then Adobe could have knifed off the troublesome hooks that Flash had developed into the operating system and returned it to a local, sandbox-friendly tool. Apple sounded the alarm when they prevented Flash from running on iOS many years ago. But they fell prey to the same fantasy of write-once-deploy-everywhere that has been a goal for many, from Bill Gates’s versions of Basic to the initial promises of Java and on to Flash (frankly, Python is showing signs of the same lack of hubris).

So we raise a proud middle finger to Adobe and its carefree disregard for its users. You showed us a path forward and then took it away. And so many of us now wish the same oblivion for you.

History (Ab)Use?

A big read in The Atlantic about Peter Turchin, an entomologist turned historian. The hook is that Turchin is forecasting societal chaos in the coming decade and had done so about 10 years ago. The article basically lays out Turchin as a rarity, a historian who is using quantitative tools to use history to predict the future. “Turchin believes he has found iron laws that dictate the fates of human societies” is a rather sizable claim.

And this now very grumpy scientist working in a semi-historical science finds the presentation (and probably the “cliodynamics” being profiled) misleading and lacking and is here to tell you why.

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“Go Educate Yourself”

How many Twitter exchanges, comment threads or even over the fence arguments ended with this phrase? There is something essentially American about this; somehow GG suspects that in some other parts of the world the response might be “you need to have a better education.” The difference between those two phrases represents a yawning chasm in understanding, one we need to bridge before we are so entombed in our comfy bubbles that no amount of reality can shake us to better know the world around us. Educating yourself means that you are intrinsically capable of identifying materials suitable for overcoming personal ignorance. Being educated implies the presence of an educator trained in getting people past their ignorance.

Right now, America stands naked to the world as a society utterly incapable of addressing a pandemic. Government officials often seem hellbent on ignoring public health experts. Armed crowds demand the elimination of public health orders even as sickness increases. In fact, it often seems like Americans are dedicated to seeing how rapidly they can spread the coronavirus, joining up by the tens of thousands in Sturgis or having massive house parties in Los Angeles. All while the U.S. has seen cases grow to 10 times that of the more populous European Union. So just where are folks educating themselves?

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So Just How Do You Read a Scientific Paper?

A nice essay in the New York Times is slugged (online) as “How You Should Read Coronavirus Studies, or Any Science Paper.” It details a bit of the history of scientific prose and notes the familiar standard background/methods/results/discussion structure of such papers. But it doesn’t actually tell you how to read such a paper. In fact, about the most specific advice given is to find authorities on social media and have them inform you. Which is fine for really hot button stuff like coronavirus research, but might leave you at sea in most other fields.

So, putting aside the lingo specific to that field, the ineptitude of authors’ prose, the gutting of the paper by dismissal of key parts to supplemental materials…just how do you approach a scientific paper? Well, no worries, here is GG’s guide. And a hint: don’t just read these papers front-to-back…

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Scientist: Task or Profession?

Right now there is more than usual interest in “science.” There is talk that all of science is refocused on COVID-19. Which is of course insane: neither geophysicists nor particle physicists nor most other people who you might call a scientist can actively assist in research related to COVID-19. But anyways, it does bring out this question of, what really is a scientist?

The classic 1950s version is the white-coated balding white dude wandering through a lab full of bubbling beakers or big banks of dials and switches. What are they doing? Well, science. Of course.

Here’s the thing: most of the people you might think are scientists are spending a hell of a lot of time doing other stuff. To the degree now that most practitioners of science are primarily doing other stuff.

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Preprint Misfits

We’ve discussed some of the issues with peer-review and its issues, and one of those has been the idea of the preprint server. The argument goes that more eyeballs will be on the paper when on a preprint server and so the authors will get a lot more feedback.

Well, be careful what you wish for. Authors of a poorly-thought-through Stanford antibody study certainly got an earful when they released their work to a preprint server (go to the comments at the end). [5/16/20: Buzzfeed obtained a whistleblower complaint alleging that the study was influenced by one of its funders]. If that is all that happened, well, having red-faced Stanford researchers does give GG a mild glow of satisfaction.

However, the press leapt on this preprint as these preprint servers are public (remember, that is the goal, right, all science out there for all to see?), getting comments from the authors in several stories. And so it immediately entered the land of social media, where you go to find confirmation of what you want to believe. And as two journalism instructors helpfully documented for the New York Times, this burned through the Twitterverse at light speed. Where, of course, it started to affect the discussion on how to best proceed with this pandemic.

Given this, what do we learn about preprint servers and their role in moving science forward? On one hand, if there is ever an instance where rapid sharing of results within the scientific community is critical, this is probably it. And the rapid focus of dozens of scientists on this study to (as the NY Times op-ed put it) “roast” it is precisely what you want this kind of peer-review-in-the-round to do. So kudos all round, right? (But then there is XKCD’s view of preprints)

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Reality Bites Back

One of the things GG has watched with dismay has been the growth of alternate universes that facts don’t penetrate. The biggest by far in the U.S. is on the political right, and you had to wonder what it would take to pop the bubble. Update 3/16/20: Looks like we found the needle to pop the bubble: a British report indicating 2.2 million deaths in the U.S. without any action (but also without a higher death rate from overwhelmed medical systems) with a peak in early summer–and pretty high death rates and an overwhelmed medical system without a lot of suppression strategies–appears to have revised White House pronouncements while right-wing opinion hosts on Fox are now taking this threat seriously. (Too bad they are two months late to the party).

Now it isn’t like the U.S. media was always a reliable source of information: the yellow press of the late 19th century skewed the news, and papers prior to the Civil War were virtual propaganda pages. What tends to deflate this kind of partisanship is verifiable misfortune.  If Democratic papers in the North claimed defeat and Union soldiers wrote home to describe victory, the misleading news came to be disregarded.  War dead in world wars made silly the claims of those who would pretend otherwise. And so after WWII American media, in part because of the Fairness Doctrine for radio and television, became quite impartial. This ended in the Reagan administration, when the Fairness Doctrine was dropped and cable television boomed. This led to our modern fragmented media landscape.

[Warning: distressing calculations after the jump]

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Can you find “good” journals?

Many have proposed that science would be best served by everything being out there is some kind of mega-preprint site. The idea is that good stuff would rise to the top and bad stuff would just sink out of sight. And perhaps there is real truth to that, but if you’ve ever come across a long-standing idea that you discovered had no real basis in fact, you might suspect that a system like that might take a very long time to purge itself of attractive but poorly supported ideas. And so many others like the idea of being able to use a journal’s editorial capabilities to presort scientific contributions, the idea being that materials in better journals would be vetted more carefully and so might be more reliable to move forward from.  In addition, a well-edited journal will force authors to more fully display the data and analysis techniques used; this will enable subsequent researchers to really verify the conclusions or results of a paper.

So, how would you recognize such journals?

We might all agree that predatory publishers are unlikely to fall in this category. In essence vanity journals, they will publish whatever comes into their inbox.

Let’s look at the other extreme: Science and Nature. These are among the pickiest of journals, rejecting most stuff that comes their way. Surely those are good journals, right? Um…maybe not. Read More…