Science Magazine embraces replication (and gets its nose bloodied)

Science has put its money where its mouth is.  In this week's issue, the editor Jeremy Berg writes about "Replication Challenges".  They have published not one, but three NIH-funded replication studies of an earlier paper.  That is the good news.  The bad news is that a sister journal published a 10-patient human clinical trial, also based on the original paper, in parallel with the 3 replication studies.  Like all 3 replication studies, the human study was not able to reproduce the effect claimed in the original paper.

Can you see why journals may be reluctant to press forward with publishing replication studies?  They can certainly get their noses bloodied.  DTLR commends the editor of Science for restating his commitment to publishing replication studies.

Jerry Gollub, 1944-2019

The first substantive post I wrote for this blog, back in 2013, was a commentary on a paper of Jerry Gollub's, on continuum mechanics in physics education.  I learned recently that sadly, Dr. Gollub lost his life earlier this summer.  An obituary by his renowned collaborator, Harry Swinney, has been posted at Physics Today.  See also this obituary posted at his institution, Haverford College.  I never met or corresponded with Dr. Gollub, but his work has been an influence on mine since I was a junior in college, when I studied from his book with Gregory L. Baker, Chaotic Dynamics:  An Introduction.  In graduate school, the book he edited with Swinney, Hydrodynamic Instabilities and the Transition to Turbulence, was of equal importance to my work.  In my student days, I had these books checked out "long term" from the library, and eventually acquired copies of my own.  DTLR joins the physics and fluid mechanics communities in mourning the loss of this inspiring scientist. 

Since I completed my doctoral thesis in 2001, several other titans I cited in it have passed.  These include V. I. Arnol'd (1937-2010), Robert P. Behringer (1948-2018), Philip G. Drazin (1934-2002), Louis N. Howard (1929-2015), Daniel D. Joseph (1929-2011), Leo P. Kadanoff (1937-2015), E. Lothar Koschmieder (1929-2017), Robert Kraichnan (1928-2008), Olga Ladyzhenskaya (1922-2004), Edward N. Lorenz (1917-2008), John L. Lumley (1930-2015), Steven R. Orszag (1943-2011), William Hill Reid (1926-2016), Philip G. Saffman (1931-2008), James B. Serrin (1926-2012), and Norman J. Zabusky (1929-2018).  There may certainly be others I am not aware of.

References

G. L. Baker and  J. P. Gollub, 1996:  Chaotic Dynamics:  An Introduction.  Second edition.  New York:  Cambridge University Press.  (First edition, 1990.)

H. L. Swinney and J. P. Gollub (eds.), 1985:  Hydrodynamic Instabilities and the Transition to Turbulence.  Second edition.  Topics in Applied Physics, Vol. 45.  Berlin:  Springer.  (First edition, 1981.)

The New Yorker weighs in on statistics

Hannah Fry writes in the New Yorker this month about the benefits and pitfalls of statistics.  Highly recommended.

Reviews of Modern Physics 90th Anniversary

The February issue of Physics Today celebrates the 90th anniversary of Reviews of Modern Physics, the review journal of the American Physical Society (APS) and sibling of the Physical Review series journal DTLR has recently discussed on this blog.

Reviews of Modern Physics (RMP) has occasionally included review papers on fluid mechanics, though in an APS News post, the editor states that he wishes to expand to solicit articles on fluids.  This would be in keeping with the new Physical Review Fluids journal that recently joined the APS stable.  Of course, informed readers will know that the undisputed leading review journal in fluids is the superb Annual Review of Fluid Mechanics, founded 50 years ago (1969) this year.

Physical Review E milestones, concluded; and a look back at the 100th anniversary collection.

With the new year, the list of Physical Review E milestone papers that I previously wrote about appears to have been concluded.  To recap, the editors were posting one paper for each year of the journal's 25 in existence, and I drew attention to those papers with the greatest relation to fluid dynamics.  At the time of my last post, the editors had reached 2011, and now they seem to have concluded with 2017.  The most notable fluid dynamics-related paper in the post-2011 cohort is Settnes & Bruus (2012), "Forces acting on a small particle in an acoustical field in a viscous fluid."

In the meantime, I acquired a massive tome published a quarter century ago, The Physical Review:  The First Hundred Years, A Selection of Seminal Papers and Commentaries, edited by H. Henry Stroke (AIP, 1995).  The book includes a CD-ROM with additional papers not reprinted in the book; this CD-ROM was reissued in 1999 with improved software.  Chapter 6 on Statistical Physics, edited by the late Joel L. Lebowitz, includes work on fluid mechanics.  (Chapter 10 on Plasma Physics, edited by Marshall N. Rosenbluth, has related material.)

Naturally, the 1931 Onsager papers on reciprocal relations in irreversible processes, and Halperin & Nelson (1978) on 2D melting, which I discussed previously, appear here as well.  Also reprinted in the book are Onsager's 1945 famous contribution to turbulence theory, "The distribution of energy in turbulence," one of several independently proposing the famous -5/3 scaling law of Kolmogorov and Obukhov, also claimed by Heisenberg and von Weiszacker.  Furthermore, the classic papers of Ahlers (1974), "Low-temperature studies of the Rayleigh-Benard instability and turbulence", and Gollub & Swinney (1975), "Onset of turbulence in a rotating fluid," are reprinted.  Many of the other papers in this chapter are closely related to fluid dynamics as well, as are many reproduced only on the accompanying CD-ROM.  Of the latter, I will point in particular to Siggia & Zippelius (1982), "Pattern selection in Rayleigh-Benard convection near threshold" and Brandstater, Swift, Swinney, Wolf, Farmer, Jen, & Crutchfield (1983), "Low-dimensional chaos in a hydrodynamic system."

Strangely, the Frisch, Hasslacher, & Pomeau (1986) paper on lattice gas cellular automata, the only fluid dynamics paper noted in the 125th anniversary milestone list that I wrote about earlier, did not appear at all in the earlier 100th anniversary collection.  And of course, none of the landmarks papers from Physical Review E, founded in 1993, and thus too recent to be covered in the 100th anniversary volume, appear there.  In this respect, I find that the 100th anniversary volume, which included literally hundreds of papers overall, provide a somewhat better representation than the far more limited 125th anniversary landmark list.  Still, as I argued in my earlier posts, the history of fluid mechanics research is probably better told through other journals with a specifically elite reputation in fluid mechanics.

Scientific American on "How to Fix Science"

The October 2018 issue of Scientific American features a set of articles under the umbrella, "How to Fix Science."  It begins with a prologue describing "antiscience currents" and arguing that one of the ways to "fight back" is to "tackle its own problems" and "shore up their enterprise from the inside."  The articles in the feature are as follows.

• "Rethink funding" by John. P. A. Ioannidis.
• "Make research reproducible" by Shannon Palus.
• "End harassment" by Clara Moskowitz.
• "Help young scientists" by Rebecca Boyle.
• "Break down silos" by Graham A. J. Worthy and Cherie L. Yestrebsky.

The middle three articles are by science journalists, while the first and last are by academic scientists. Readers of DTLR will recognize that the first two articles discuss topics that have been kicked around on this blog over the years.  DTLR readers will also notice that I have been castigating Dr. Rush Holt, CEO of AAAS, recently, for avoiding these very issues.  Holt believes science is just fine the way it is.  DTLR has previously made a similar argument as the prologue of the Scientific American feature:  we need to clean up our own house before we can, with any good conscience, ask the public to continue financially supporting our endeavors.  Thus, I view the Scientific American piece as a rebuke to the Rush Holt model for responding to the "significant erosion of trust in science over recent years" (a phrase used by Worthy & Yestrebsky).

The leading piece by Ioannidis is a good starting point for this conversation.  Perverse incentives stimulate perverse outcomes.  His piece not only touches on funding issues, but hiring, promotion, and tenure decisions. While I disagree with many of the details in his proposed solutions, I believe the spirit of his piece is absolutely on target.  We need to fix the incentive systems in the scientific enterprise, and this is fundamental infrastructure.  Unfortunately the elites who thrive in the current scientific infrastructure have a vested interest in maintaining the status quo, and would oppose all Ioannidis' proposed reforms.


The article by Palus is a decent introduction to the non-reproducibility issue for the general reader, but lacks the space to delve into the methodological details of good experimental design, experimental quality control, and adequate reporting that are discussed, for instance, in Richard Harris' recent book, Rigor Mortis.

Moskowitz states that sexual harassment is more prevalent in academia than in any other arena except the military.  I am not surprised by this.  Having worked in various sectors of the economy - academia, industry, and government - my personal preference for a setting conducive to scientific research is the private sector, not academia.  In fact, the academic tenure system protects 'assholes' including those who practice harassment.

Boyle's article consists of comments by various young scientists on the following issues:  moving, money, culture, family, industry vs. academia, getting jobs/fellowships/into school, and representation and inequality.  I agree with the writer as well as Ioannidis that the treatment of young scientists in today's science ecosystem is appalling, and needs to be drastically reformed.

Finally, the article on interdisciplinary research is really another reflection of the perverse incentive systems for academic science.

I mentioned that I agreed with the spirit, but not many of the details of Ioannidis' piece.  Readers, what problems do you see in the incentive structure for scientists, and what solutions would you propose?

Physical Review E milestones

Previously I wrote about the Physical Review family journals' landmark papers.  In this month's APS News, one of these journals, Physical Review E:  Statistical, Nonlinear, Biological, and Soft Matter Physics, notes that it is celebrating its 25th year.  They have posted a series of 25th anniversary milestone papers, one for each year since its founding in 1993.  At the time of writing, they're up to 2011, with 6 more years to go.  Moreover, I found that in 2015, they celebrated the publication of their 50,000th paper by posting another list of milestone papers.  Both lists were compiled by the editors (and editorial board) for making important/significant contributions to their field.

I will ask the same question I asked in my earlier post:  how many are papers in fluid dynamics?  After all, PRE's original subtitle was Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics.  Of course, many of the papers in both PRE milestone lists are related, and in some cases closely related, to fluid mechanics, broadly understood.  I won't have the space to talk about all of them here.

The most important fluid dynamics paper seems to be one that appears in both PRE milestone lists:  Shan & Chen (1993), "Lattice Boltzmann model for simulating flows with multiple phases and components," appearing in the first year of the journal's life.  The 2015 milestone list includes a second fluid dynamics paper, also from the first year of the journal's life:  Benzi et al. (1993), "Extended self-similarity in turbulent flows."  Finally, the 2018 milestone list features Baskaran & Marchetti (2008), "Hydrodynamics of self-propelled hard rods," motivated by observations of gliding bacteria.  The latter paper could also be considered part of biological physics.  The 2018 list has not been completed at time of writing, so I may need to post an update when the series is complete.

For reasons discussed in my earlier note, PRE does not seem to be part of the group of the most elite fluid dynamics journals, consisting of the Journal of Fluid Mechanics, Physics of Fluids, and new arrival Physical Review Fluids (PRF).  Indeed, with the arrival of PRF in the Physical Review family, Physical Review E's role in the fluid dynamics community could become diminished, though its mission statement continues to include both complex fluids and fluid dynamics.  I checked PRE's website today, and the editorial board continues to have members covering fluid dynamics.  We'll see in the future whether some kind of equilibrium is reached between the two journals.