Tag Archive | scientific communication

How to Write a Scientific Masterpiece

OK, so GG was asked about how to write a scientific paper after suggesting how you might read one. And, well, there are whole books and fully researched articles and stuff like that out there. But you know, that’s entry level scientific writing. Here’s the real advanced stuff!

  • Don’t start writing until all the work is complete! Why waste your time scribbling down things while you are in the midst of career-defining research. Every second counts! Plenty of time to write once you know the outcome; this way you avoid writing something you ditch later on.
  • Don’t keep notes. You don’t want some snooping competitor to find out what you’ve been doing. Best to just know in your heart all those algorithmic choices you’ve made. If you must write stuff down, be sure to use a code that isn’t described anywhere. No, Leonardo’s mirror writing tricks are passé now…
  • Don’t give talks before submitting for publication. Again, no point in tipping your hand. And after all, are those ninnies who always snipe at you really going to give constructive criticism?
  • Rely on the one computer script that rules them all. Sure, every time you want to adjust a parameter in your statistical analysis or simulation or what not, you overwrite that Python script while leaving plots and data files laying about from older versions of the script, but you are keeping track mentally, right?
  • Delete intermediate results. Less clutter the better, so deleting all that intermediate stuff is a great way to retain organization on your computer drive. Also makes it far easier to ignore demands from reviewers down the road (oops! that stuff is gone).
  • Ditch the background stuff. Blah blah blah, yeah, standing on the shoulders of giants. More like standing on the shoulders of gnats, rightly squished under your boot heel. Why waste the space in Nature or Science with drivel just meant to appease friends of old farts?
  • Find the big story. Originally you were learning the age of some speciation event but you realized the data is predicting the next great earthquake, well, forget that trivia you started with, even though you don’t really know much about earthquakes, your speciation dataset will support you through this.
  • Maximize surprises in the text. You’ve held this great work close to the vest so far–so you want the big reveal at the end, just as in all those murder mystery books. So throw in a few red herrings, make sure the abstract is misleading or obtuse so that the reader will be totally blinded by the brilliance at the end of the paper.
  • Minimize figures. I mean who really can’t make their own figure by downloading the binary supplemental information from your website, whose URL somehow got changed after publication. Real scientists read and digest huge data tables for breakfast!
  • The more jargon the better. Just who the hell do these readers think they are? Only true peers who know the particulars of your vocabulary of polysyllabic ultra-germanic mashups are worthy of receiving the wisdom of your work. Let’s keep the riff-raff out!
  • Maximize inferences. Sure, you just studied one rock from some corner of your garage, but that rock–that rock–tells the entire history of the solar system. Your conclusions should take full advantage of these insights.
  • Be a press master. Your college’s PR department loves to have click bait out there to prove that Big State U is really on top of the cutting edge of science. Feed their needs–why yes, this is revolutionary, and yes, it does show that Einstein was wrong and oh, of course this points the way to a cancer cure, too. No point in having this seminal work get overlooked.

And there you are, ready to take on the world. GG suggests having an off-shore bank account and maybe a spare passport just in case your brilliance attracts the attention of some authorities…

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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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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What WILL Change

There’s been a run of “here are the things that coronavirus will change forever” essays, many of which frankly don’t convince GG. For instance, there have been a string of “remote education will now be important” pieces that frankly are flying in the face of widespread disgust at sitting in front of a computer for hours watching what arguably might be some of the most boring material to appear on a screen ever created. If anything, what higher education has thrown out there as distance learning for their regular students has increased the hunger for regular learning.

Does that mean nothing changes? Well, no. There are several things in academia that look very robust and likely to last. One of the striking changes GG has seen has involved thesis presentations. While defenses were usually announced and open to the public, rooms would only hold so many and in any event you had to be able to physically get to campus, park, get in the building and then be in the room. But defenses over the past month have attracted far larger audiences from all across the globe. While in the past there have been occasional remote members of the examining committee (often on the phone), this kind of widespread access to a defense is fairly new and kind of exciting. GG suspects that we will see a Zoom option accompanying physical defenses once we return to “normal”.

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Does COVID Presage Climate Change? (Update 4/11/20)

Note 4/11. Kind of amazing to see, but the response of people to requests for social distancing appears to be highly correlated with acceptance of the scientific consensus on climate change: “In fact, attitudes toward climate change are one of the strongest and most robust predictors of social distancing behavior.” from Vox, 4/11/20. One has to wonder if COVID-19 races through these communities in the coming weeks if there will be any cognitive dissonance setting in that might change thinking on climate change…Also worth pointing out the 3/28 column by Paul Krugman in the New York Times more or less making the same observations as GG made here…

It is amazing to look at what has happened this year and contrast it with the history of climate change.

Coronavirus was initially a distant curiosity that maybe somebody else had to worry about, but not us Americans. Then some called it a threat, but that was easily shrugged off as this was really just a different cold–the stock market has done great, unemployment is low, and that is what matters. In fact we saw an administration figure say this would be good for America–would drive production back into the States. Then it began to kill people in this country, but it was all contained…nothing to see here folks, under control, move along. And then…the dam broke. Stuff most Americans really cared about was suddenly gone.  No March Madness.  No NBA. No NASCAR. No baseball. No golf. No skiing. Maybe even no Tom Hanks. Students suddenly cast out of classes.  Events like SxSW and Coachella cancelled. GG thinks the Girl Scouts even stopped selling cookies…

How do we react? Well, being Americans, we buy damn near everything in the grocery store for no rational reason (“you know, I bet cans of fried onions are going to be really rare! We’re so lucky we got the last 12 cans…”). But you know what, suddenly government action looks useful. Keep us safe!  Tell us what we need to do! (well, ok, so some folks go out and buy guns because…well, that is in like every collapse of civilization movie ever, so it must be wise). Schools close and the outcry is pretty minimal. Large group events banned with nary a whimper. Here in Colorado, the governor just closed all the ski resorts, which is probably as close to blasphemy as we get here, and no torches and pitchforks are in sight.

So what does this have to do with climate change?  Well, initially it was a far off problem that others worried about. Then, though it was increasingly clearly a potential threat that might require some change in behavior, it was ridiculed by legislators bringing snowballs into the halls of Congress: we don’t need to do anything, we’re fine, the economy matters way more. Hell, it would increase crop yields and so be good for America. Now it is king tides that cover roads along the eastern seaboard and coastal villages in the Arctic falling into the sea, it is stronger hurricanes and more intense droughts. It is COVID-19 except in slow motion. If you want to see the end game for global warming, wait a couple of months. Spoiler alert: it ain’t pretty.

If, somehow, we come through this without reproducing Italy’s problems or worse because the government recovers from lapses so egregious that there should be a pile of wrongful death suits pointed at it, will people decide that we should also unleash the government on this other problem that also threatens us all? Maybe there really is a God, one who likes to use biblical crises as parables….Will we take the hint?

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…

Who Are Journals For, Anyways?

On the heels of the dispiriting notion of advocacy journals, GG would like to ask just who is reading these professional journals, anyways? It seems from what funders and some journal owners are doing that they expect Joe Sixpack to be picking up the Journal of Winter Nighttime Reading and perusing its contents.  Does this make any sense?

First off, why does GG think this? Well, several journals are now publishing “plain language” versions of the abstract (that appear to be required). Given that the background for some concepts some papers explore could well take a textbook chapter, this is often mildly amusing. Second, the government is pushing that all federally funded research be made fully accessible to any member of the public when published (yes, GG knows that isn’t the way this is usually phrased, but as members of the public can in fact access paywalled journals by visiting a library with a subscription, its not like this stuff has been locked in a file cabinet somewhere). Why demand this unless you expect people outside the field to read this stuff?

OK, is this a good idea? Let’s try a few analogies and see what we think. A mechanic gets an update from Honda on the proper way to replace a certain engine gasket for cars with a particular kind of fuel injector. Unless you are big on engine repair, do you understand what is different?  Why it matters? Or your system administrator gets an advisory from Microsoft that the .dll file in your Windows server allows unencrypted access to the trusted machines file whenever a superuser command is issued and should be edited, although this might result in the loss of ability to remotely access other servers. Do you have any idea what this means? Is this important? Should you do it?

Look, this isn’t to argue that the science literature should be kept under lock and key, it is to say that it is for people trained to use that literature. I do not want scientific papers to be explaining the assumptions of isostasy every time they use the phrase, or defining a P-wave, or how a seismometer works each and every time any of these are brought up. What’s more, at the cutting edge, a lot of published material is wrong.  An old saw is to go in front of a class with a textbook and a journal and say that 10% of the textbook is wrong, but only 10% of the journal’s science will prove to be right. Assembling that textbook out of the wilderness of the professional literature is a demonstration of skill and knowledge. It is easy, through a combination of misrepresentation and misunderstanding, to claim the professional literature says something it really doesn’t (the young earth/intelligent design literature is full of examples of this). No amount of plain language abstracts and immediate access will improve the situation.

Only a relatively small fraction of the science we do really translates to something the public might find immediately interesting. Press releases are made for those cases, and if skillfully crafted, they work quite well at conveying the science to a broader public. (It used to be you would get an assist from the science reporter at a paper, but that task is now generally completed by a beat reporter with no special skill). For those few who are really into the science and are willing to work, in essence, to train themselves, the language in the abstract isn’t going to be much of a barrier and for most, access to a library is pretty important in getting up to speed anyways.

So who should be the target of the professional literature?  The public at large? No. Those setting policy? No. Professional journals fill a quite specialized niche, as well they should, in communicating amongst professionals. The Journal of Winter Nighttime Reading shouldn’t be a junior Scientific American wannabe.

Is the Purpose of Science to Change Society?

Or more specifically, the purpose of scientific journals. Apparently so, according to the editor-in-chief of The Lancet (As reported in timeshighereducation.com):

“The journal as we’ve known it, I think, is coming to its end,” Dr Horton told the Academic Publishing in Europe conference. “What we now need to do is to reinvent the idea of the scientific journal that needs to be more activist in its engagement with the challenges of society.”

Yeah, this will turn out well.

First and most obviously, having an activist approach means, of course, pushing forward some science while rejecting other science based on what the editor-in-chief thinks is the more important problem facing society. Just who elected the editor-in-chief? Second, whose society? Third, the model presented is the journal assembling groups of scientists to write these society-changing papers.  Presumably for no pay, but to advance the profile of the journal.

Honestly there is no end of evil in this project. It is trivial to imagine liberal and conservative journals (imagine the Journal of Vaccine Truthiness or the Journal of Healthy Tobacco).

There is some irony in this showing up at the same time that it has been pointed out that Nobel winning physics is not usually published in Nature or Science (Nature‘s editor also spoke on behalf of advocacy of journals with the editor of The Lancet). Because, you know, journals that have editor gatekeepers who decide what science is worthy are so good at identifying important science that they reject stuff that later earns scientific prizes.

Frankly, this grumpy geophysicist can’t find a silver lining to this miserable cloud of arrogance and misunderstanding. If the editor-in-chief wants to go off and found a magazine that solicits panels to weigh in on what science should be doing, or what some science means for society, fine, go for it. But to take a journal that is supposedly trying to publish the best science and instead decide to solicit science articles for their social relevance…well, a pox on that house.

GG is reminded of Apple’s approach to building new devices.  A famous quote from Steve Jobs is “It’s really hard to design products by focus groups. A lot of times, people don’t know what they want until you show it to them.” Now maybe medical science (which is the realm of The Lancet) knows what it wants, but the rest of science does not. And so this is the biggest objection to this proposal: it is saying that basic science is now dead. We only need to pursue that which we know today is needed to solve a societal problem we know of today. So, for one instance, the many years of climate research that predated recognition of anthropogenic climate change…that was necessary to recognize climate change…would not be published.

Here’s a better suggestion: get rid of the tabloid journals and their pompous editors-in-chief.



The Open Access Crisis

You’d think “crisis” might be strong, and maybe it is, but we appear to be on the cusp of the put-up-or-walk-away moment. A trigger recently was a letter from a number of groups protesting possible U.S. government plans to demand that federally financed research be publicly available the moment it is published (right now there is a 1 year delay on that requirement). One cosigner was the American Geophysical Union, which has produced a bit of an outcry from members (and a policy decision that apparently was not presented to AGU’s council). The thread on AGU’s community group (connect.agu.org) has a number of statements of dubious validity, but they reveal something of the anxiety associated with this issue. So as it has been awhile since we plumbed these depths, let’s see what the real problems are and their most likely solutions.

First off, what is scientific publication? It is (1) deciding if paper’s subject is appropriate for a journal, (2) getting mail reviews, (3) making an editorial decision, (4) assuming it is accepted, performing some level of editing/page layout/format migration, (5) placing the appropriately formatted version of the paper online (or printing paper copies) and (6) supporting some permanent archiving of the journal. How expensive is this? Most editors and reviewers are not paid, so steps 1-3 are nearly cost free–the main cost is the system to manage submissions and redirect things around, so it isn’t zero. Step 4 is required of all journals (when was the last time you submitted html-ready copy?) and is a significant source of cost. Steps 5 and 6 are unavoidable.

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Forget Utility, Design Is All!

Scientific professional societies are possibly among the world’s most boring entities. They are generally responsible for three or maybe four main things: publishing science, coordinating science meetings, giving awards, and possibly lobbing on behalf of science. So one might expect a relatively simple, functional website.

Yeah, right.  Because the other thing professional societies have is staff and elected officials, which means there is always a temptation for churn. Let’s move the annual meeting! Let’s have new awards! Let’s change the length of a talk! Well, fine, all those are pretty innocent, but one is “Let’s change the website!”

Who visits these websites?  GG doesn’t know, but gosh, maybe the members?  Maybe people who want to be members?  Is the public crashing on the gates, demanding entry to the science equivalent of Skull and Bones, hoping to learn the deep dark secrets of ambient noise tomography or the thermohaline circulation?

Evidently the wizards at the American Geophysical Union felt that the answer must be the public, because they rebuilt their website to look like a travel brochure for elderly folks with 20/200 vision. Read More…