Category: science publishing

Should scientific journals strive for “diversity” of reviewers and authors?

November 17, 2020 • 12:00 pm

The New York Times recently had a piece by their new and woke science reporter, Katherine J. Wu, which is basically an indictment of science journals for not keeping track of the “diversity” of authors and reviewers of the papers they publish or reject. The implicit message is that science journals are racist, discriminating against papers by minoritized authors.

Click on the screenshot to read the article:

Wu’s implicit assumption is twofold. First, that a paucity of diversity—which of course means ethnic diversity, but minus Asians since they are surely overrepresented among authors—reflects racism on the part of scientific journals and reviewers.  There is no consideration of whether a lack of diversity may represent simply a paucity of minority authors and reviewers. That itself may reflect racism, past or present, that narrows the opportunities of would-be scientists, but the article implies that it’s racism acting on Ph.D. authors trying to submit papers.

The second assumption is that more ethnic diversity in journals means better science. Well, that’s true in the sense that the more people who get the opportunities to become scientists, the higher the average quality of the science that is published. But I’m not at all convinced that members of any group, be they groups involving genders, religions, incomes, or ethnicity, have a special “point of view” based on their group identity that makes them do science differently. Science is science, and I don’t feel that Hispanics, say, have a different “way of knowing.” (There may be one exception here, that I’ve mentioned before: I think women scientists are responsible for shifting the focus in sexual selection from male traits alone to female preferences as well. But many men were also involved in this shift). In the end, the best science comes from giving everybody equal opportunities, not practicing remediation based on race at the publication level.

But the question is whether journals should be publishing more papers by members of minority groups. That is, is there a bias against, say, black or Hispanic authors that needs to be rectified by that form of “affirmative action” on the publication level—taking steps to accept more papers by minority authors?

It’s my opinion that the answer is “no”. This presumes that a paucity of papers by such authors is prima facie evidence for bias, when it may reflect only a paucity of minority-group members in the field, or of minority scientists submitting papers, or submitting fewer papers,—rather than reviewers deliberately discriminating against papers by minority authors.

It may be worth investigating this issue, but I consider it hardly worthwhile for two reasons.  First, figuring out whether a paucity of papers from minority group members is due to racism at the reviewing level is very hard to do, though not impossible (see below). More important, it’s certainly true that the disparity between the proportion of minority-group members in the population and the number of papers published by members of that group is due largely not to racism but to an underrepresentation of Blacks and Hispanics in science. Figuring out why that disparity exists is the best way to achieve more proportionality in science, if that is your goal. And that’s really where our efforts should be going.

Here are the data given in the NYT piece from two scientific organizations showing disparities between population proportions and publication/reviewer proportions. The article makes the point that most journals, though, do not keep records of the ethnicity of authors and reviewers. (To clarify for non-scientists, when scientists submit papers to a journal, those papers are sent to several reviewers—usually two or three—who are experts in the area of research. Based on the reviewers’ assessment of the paper, the editor then decides whether or not to publish it. If the decision is “yes,” there is often some revision of the paper required, either in the discussion or the scientific analysis.)

I’m going to discuss authors here, not reviewers, because it is the quality of authors‘ work that, by and large, constructs the quality of the journal. How do we know if a journal is discriminating against minority authors? You can’t simply use a difference between the proportion of people in the field, or the proportion of people submitting papers on the one hand, and the proportion of papers published on the other, as a criterion for bias. That’s because members of different groups may submit papers less often, or of lesser quality, and that this would lead to differential representation that would not reflect racism. Bias must be proven, not assumed.

There are two ways to solve this problem. The first is the equivalent of doing “blind” auditions for orchestras—auditions in which those seeking an orchestral chair perform behind a curtain. That “blind” system removes all bias against sex or race. To do this with a paper, you simply remove the names of the authors, their institution, and the acknowledgments from the manuscript, so the reviewers don’t know who wrote the paper. (There are, of course, ways to guess, like if an author cites herself repeatedly, but in many cases this will indeed lead to quality appraisal ignorant of the author’s race or gender.)

I hit upon that system in the late 1970s when I was a postdoc, full of piss and vinegar and concerned that papers were getting preferentially published not because of race, but because of reputation. My idea was that famous people had an easier time publishing their papers than small fish (like me!). I wrote letters—real letters—to the editors of about 30 journals in my field, proposing that manuscripts be reviewed blind this way. I got only one response, and that was from an editor who said that he preferred knowing the authors, because famous authors were more likely to submit better papers! That may be true on average, but it’s not the best way to ensure the quality of papers in a journal! In fact, famous authors may get by more easily with shoddier work because of their reputations.

At any rate, some journals have now wisely decided to adopt the blind-author technique, and more power to them! It seems to me a step in the right direction to eliminate animus not just against groups of people, but against your scientific “enemies” or in favor of your scientific “friends”. (Believe me, this kind of bias is rife in science.) While you can get around this system by guessing, I think it does help ensure objective reviewing and thus higher-quality papers. (I should add that the NYT music critic opposed blind auditions because he said that while it increased the proportion of women in orchestras, it didn’t eliminate racial inequities; his view was clearly that equity trumped orchestral quality.)

The other way would be to do an experiment submitting identical sets of manuscripts with fake names that give clues to the gender or ethnicity of the authors. If manuscripts with women or minority authors are rejected more often than the same manuscripts with “white” or “male” names, that surely indicates bias. This was what was done in a laborious study of grant reviewing, using made-up “black”, “white”, “male” and “female” names on identical proposals. The study showed no evidence of racial or gender bias in grant evaluation. Needless to say, you don’t hear much about this study, even though it was a good one, as the results went against people’s certainty that there must be sex and gender bias in reviewing.

That experiment could be done with paper reviewing too, and really must be done before you can start making implicit accusations of bias.  But I favor the blind-reviewing technique. You don’t have to do any experiments to see if that one makes things more equitable because, by eliminating a source of bias from the outset, it almost has to. It is my feeling that a “fake name” study wouldn’t show evidence of bias in pubication, but that’s my feeling alone. Better just to practice blind reviewing rather than speculate or do experiments.

In the end, my feeling is that affirmative action should not be applied to reviewing papers by people who already have doctorates, and, while I believe in affirmative action, I think it has to stop at some point in the hierarchy. My point comes after faculty hired hiring. I think it’s okay and useful to take race and gender into account when hiring junior faculty, as well as in college and grad-school admissions, but that’s where it stops. Ethnicity and gender should not be a consideration in getting tenure, full professorships, or in getting papers published—areas where merit alone should be the only criterion. Again, this is my view, and others may disagree.

Some of those who disagree think the whole system of a scientific meritocracy is flawed—that there isn’t even a scientific meritocracy. The NYT article says that:

Publishing papers in top-tier journals is crucial scholastic currency. But the process is deeply insular, often hinging on personal connections between journal editors and the researchers from whom they solicit and receive manuscripts.

“Science is publicized as a meritocracy: a larger, data-driven enterprise in which the best work and the best people float to the top,” Dr. Extavour said. In truth, she added, universal, objective standards are lacking, and “the access that authors have to editors is variable.”

To democratize this process, editors and reviewers need to level the playing field, in part by reflecting the diversity that journals claim they seek, Dr. Kamath said. “People think this is a cosmetic or surface issue,” she said. “But in reality, the very nature of your scholarship would change if you took diversity, equity and inclusion seriously.”

This whole section is to imply that there is little correlation between the merit of a paper and the chance of its being published. I think that’s a foolish conclusion, with the caaveats that Wu gives meant to imply a weak correlation at best. This is not my experience in reviewing papers or assessing published papers. Yes, sometimes a terrible paper gets published in a good journal, and a great paper gets rejected by a good journal, but there is surely a correlation between the quality of a paper and the chance that a. it will get published, and b. that it will get published in a prestigious journal.

No, to democratize the process, just do blind reviewing. That will go a ways toward eliminating bias. But even in the absence of that procedure, journals would be hard pressed to construct a system that would give preferential publication to papers by ethnic minorities. Regardless of what Katherine Wu thinks, science largely is a meritocracy, at least when it comes to publication, and I don’t think it would be good for science as a whole to bump papers up or down based on the race of their authors.

 

Paper retracted for title and wording: “Where there are girls, there are cats.”

July 9, 2020 • 1:30 pm

I haven’t seen the original version of this paper in Biological Conservation, which investigates the correlates of feral cat density in 30 Chinese universities, but a piece in Retraction Watch, below, implies that the title (and perhaps other bits of the paper) caused its retraction by Elsevier (the publisher) until until it was changed. The indictment: sexism—in particular, the frequent use of the term “girls”.

Retraction Watch, and the last link above, imply that the sticking point was indeed the paper’s title:

As promised, Biological Conservation has replaced a controversial paper on feral cats in China whose cringeworthy title — “Where there are girls, there are cats” — prompted an outcry on social media that resulted in a temporary retraction.

The new article boasts a different, non-gendered title: “Understanding how free-ranging cats interact with humans: A case study in China with management implications.” But it makes more or less the same point: Where there are women, there are more cats.

Cringeworthy? Well, why not call it “Where there are women, there are more cats”? Who’s running the railroad at RW?

The new ungendered paper (click on screenshot):

The abstract (with the sex aspect in bold, my emphasis):

The growing population of outdoor free-ranging cats poses increasing threats to biodiversity. While those threats are now well recognized, how human-cat interactions contribute to shape population dynamics have been overlooked. In this study, we explore major variables associated with the distribution of free-ranging cat density in 30 universities in Nanjing, Jiangsu Province, China. We specifically focus on possible even greater care devoted by women to the free-ranging cats. We found that, as expected, the density of feeding stations is positively associated to the density of free-ranging cats. More interestingly, the density of male students versus female students seemed to be non-randomly associated with the distribution of cats among universities. An online questionnaire confirmed that women were more concerned about the living conditions of free-ranging cats than men in China. Finally, a socialization test focusing on 27 free-ranging cats conducted by female and male observers suggests that cats may have the ability to adopt a friendlier behavior with female students. Our result suggests that human-cat relationships can be understood using multiple angles, including population dynamics, behavioral ecology and conservation psychology. Such a better understanding of human-cat interactions is necessary to develop relevant population management in urban context.

And a bit of the (new paper):

The TIRM model was selected for the analysis and we used the corresponding estimated density of the cats in each campus in the following analysis (Supplementary Table S2). The Pearson correlation test showed that the density of cats was significantly correlated to the student density (N = 30, r = 0.63, p < .001), to the feeding station density (N = 30, r = 0.85, p < .001), to the women density (N = 30, r = 0.78, p < .001) and also to the proportion of women (N = 30, r = 0.65, p < .001). However, it was not correlated to the percentage of greenery coverage of each campus (N = 30, r = 0.13, p = .49), to the density of men (N = 30, r = 0.26, p = .15) or to the survey season (N = 30, r = −0.07, p = .72). The percentage of total explained variance of those factors were ordered as follows: feeding station density (34.06%) > women density (22.44%) > proportion of women (17.78%) > student density (16.65%) > men density (6.52%) > season (1.44%) > percentage of green coverage (1.11%).

And the results from a questionnaire:

The 2038 online questionnaires showed that women had fed or rescued outdoor free-ranging cats more often than men (χ2 = 94.692, p < .001, df = 1, Fig. 1). Similarly, women tend to feed outdoor free-ranging cats more regularly (χ2 = 19.345, p < .001, df = 1, Fig. 1).

All in all, it looks like the authors found a statistically significant correlation between the density of feral cats and the density of women, and they could explain at least some of it, at least in theory, by the tendency of women to rescue and feed feral cats more often than men.

But that’s not good enough. Retraction Watch, which seems outraged by the original title, along with (of course!) social media, applauds the change:

The journal also published an editor’s note — in which they manage to keep the search engine optimization value of “Where there are girls, there are cats,” while disclaiming the title — explaining its actions. The editor, Vincent Devictor, didn’t respond to our request for comment when we reported on the withdrawal, and he is joined on the editorial by Danielle Descoteaux, of Elsevier, which publishes the journal.

Step one: blame language barriers for a poor decision that, as any editor should admit, falls squarely on their shoulders.

Was that decision really that poor? Or was it the “social media outcry” that made the journal retract the paper? You know the answer.

In truth, I am not that bothered by the title, which is pretty cute and, given the data, seems accurate as far as it goes—though had I written it I would have said “women” instead of girls. Nope, the title is dumbed down and gender-purified until it’s just the usual anodyne and tedious title we see so often. And the authors, of course, had to issue an apology:

. . . . we did not realize the topic is so sensitive, although at first we actually have tried our best to wirte [sic] the words… I firstly want to declare that I have not any sexism or even any thought of it, probably it is an English expression and culture difference that misleading readers since we are not native English speaker. For the title, may be catchier in our current version, it is like to say ‘more girls, more cats?’, just to catch readers that maybe cat density is related to sex ratio? In Chinese, it is very easy to understand and accept. I really don’t understand why human sex cannot be discussed in a paper, as we discuss more in animals research, or it is a culture difference…Not sure… 3, Actually in this paper, we just want to show a phenomenon, a point, a possible correlation, that cat density may be related to human social structure especially the sex ratio. I know correlation sometimes is not causation, but sometimes it is. Someone said feeding station is another more influencing factor, but who made these feeding stations? AT least from our observation, most are females in both universities and communities. Tell them more the fact that free ranging cat is invasive and affects biodiversity significantly and don’t feed them is very important. We have not any suggestions or ideas to control human sex, if I did not misunderstand some readers’ thoughts. Our suggestion is just to tell them the possible impact of feeding behavior to free ranging cats.

oooookay. . . .  so we live in a world where a title like that caused a social media outcry. Do these keyboard warriors ever rest? Yes, perhaps the use of the term “girls” was unwise, but really, people?

To wit:

Translation: “I used the term ‘girls’ which is regressive, counterrevolutionary, and contrary to the teachings of Chairman Meow.”

Another predatory journal in “deadly need” of a paper

June 17, 2020 • 8:30 am

I doubt that there’s a scientist alive who doesn’t get one of these predatory journal pleas on a regular basis. They’re never in my field (this one is in agriculture and soil science!), and they are in deadly need of a 2-page opinion piece for the next issue of their sub-sub-substandard journal.

I’d be tempted to submit something humorous, but a. it’s work and b. it would debase the scientific enterprise. Instead, I’ll show you the email for your delectation.

If you look up the location of the journal’s “offices” in San Francisco, you’ll find they are virtual offices, providing only the appearance of an office with a mailing address and someone to answer the telephone.

In other words, although the journal is real, it’s a predatory journal that exploits scientists who need papers on their c.v.s, making money by charging exorbitant publication fees. I suspect the real offices are overseas given the fractured English in the email (“deadly need”, “please tack the below link”, probably meaning “tick”), which of course means the email is lying.

Perhaps an enterprising reader would want to call up “Emma Megan” at the number and see what transpires.

World Journal of Agriculture and Soil Science <agri@irissciences.com>
Wed 6/17/2020 5:38 AM
To: Jerry Coyne

Dear Dr. Jerry A Coyne,

Greetings!

Hope you are doing very well!

Well, we are in deadly need of only one article to release Volume 5 Issue 2 before End of this Month. Is it possible for you to support us with your 2-page Opinion or Mini Review for this issue?

Please tack the below link to visit on our journal website
https://irispublishers.com/wjass/

Please acknowledge this email to submit your manuscript.

Emma Megan | Managing Editor
World Journal of Agriculture and Soil Science (WJASS) | [ISSN: 2641-6379]
Iris Publishers LLC,315 Montgomery Street, San Francisco, CA 94104, USA.
Web: irispublishers.com| Email Id: agri@irispublishers.com |Tel no: +1-628-201-9788

Hoax: a crazy hilarious paper in a predatory journal

April 16, 2020 • 12:30 pm

UPDATE: See this Twitter thread by the author for his hilarious interaction with the journal, including the “reviews”.

____________

This paper, pointed out earlier today by my Chicago colleague Brian Leiter, highlights one of the scandals of scientific publishing: predatory journals that will publish anything, allowing researchers to inflate their c.v.s while the journal rakes in outrageous “publication fees.”

The upside is that the paper is fricking hilarious, and so transparently nonscientific that it’s amazing that even an abysmal journal would publish it. Perhaps they don’t care—perhaps all they want is the dosh. But this paper is the result. Click on the screenshot below to go to the paper. Download it quickly, for I have a feeling it will be gone soon. . .

(If it disappears, you can always get a pdf from yours truly.)

Behold: “What’s the Deal with Birds?”

I mean, if the abstract and keywords don’t give it anyway, somebody’s asleep at the wheel:

Abstract

Many people wonder: what’s the deal with birds? This is a common query. Birds are pretty weird. I mean, they have feathers. WTF? Most other animals don’t have feathers. To investigate this issue, I looked at some birds. I looked at a woodpecker, a parrot, and a penguin. They were all pretty weird! In conclusion, we may never know the deal with birds, but further study is warranted.

Keywords:

birds, ornithology, behavior, phenotype, WTF, genomics, climate change

Remember, this is not a joke journal; it’s one that pretends to be serious. Here are a few tidbits (be sure you read the acknowledgments at the end of the paper):

 

And Figure 1, which is lovely.  Remember, the journal is presenting this as peer-reviewed and solid scientific work (well, clearly this one wasn’t peer-reviewed as it was received March 25, and published April 1!).

 

Given the publication date, could this be an April Fool’s paper? No, I don’t think so. The journal isn’t available through my library (of course), but the journal’s table of contents, which you can see, gives no indication that the paper is a hoax. Instead, the journal appears to be a repository for crap papers in all sorts of fields from authors all over the world. In fact, I just saw on Twitter this note from another biologist, Andrew Burchill, that Baldassarre telegraphed his intentions before he submitted “What’s the deal with birds?”.  (Note that, in my own tweet, the hoax paper was regarded as “sensitive content”!):

Greg did a bit of Googling and came up with what’s indented below:

Here’s the link to the publisher’s website– it’s a real hoot!
A statement of “Publication Ethics”!!
It’s not written by a fluent English-speaker. A sample sentence:
We want the outcome of integrity meeting integrity to be compounding source of factual information that will help the world become a better place.
And this (I suspect it’s the opposite of what they intended, but it’s nonetheless oddly fitting.):
Authors should ensure that the manuscript they’ve submitted to us should be under review anywhere else.
They claim to be based in San Francisco. I wouldn’t put money on it.

 

Science is loaded with these kinds of predatory journals; I get invitations to publish in them all the time, often in journals way outside my field, like microbiology or even obstetrics! Maybe if scientists kept loading them up with hoax papers like this one, it would hasten their demise.

By the way, the author’s name, Daniel T. Baldassarre, sounds like a hoax name, too, but he’s a real biologist, an assistant professor of zoology at the State University New York at Oswego, as he correctly notes in the paper’s header. (I’ve put his photo below).

Daniel Baldassare

One final remark. In the “grievance studies affair“, Helen Pluckrose, James Lindsay, and especially Peter Boghossian got into big trouble for “hoaxing” humanities journals with equally ludicrous papers.  Baldassarre won’t get into trouble (and shouldn’t), for his paper is in a clearly predatory journal.  But what’s the difference between a predatory scientific journal that will publish nonsense and humanities journals like Fat Studies or Gender, Place & Culture that publish nonsense but also purport to be venues for serious research? In effect, they both do the same thing: help researchers fatten their c.v.s with worthless research. Why should Boghossian et al. be excoriated for exposing the same kind of crappy journal standards that Baldassarre did?

Anything that exposes this kind of academic garbage, including clear hoax papers, is to be applauded, so long as the hoaxes are revealed (as they were with the Grievance Studies Trio) or are so palpably ridiculous (as with Baldassarre’s paper) that they couldn’t be anything other than a hoax.

h/t: Greg Mayer

My last research paper. Part 2: Results

January 28, 2020 • 10:30 am

A few days ago I began a two-part summary (it’s now become three parts!) of what will probably be my final “research” paper: the last paper in which I pushed Drosophila flies with my own hands to gather data. (This doesn’t mean it’ll be my final science paper.)

That post discussed the aims and the methods of our paper in Genetics, which you can see by clicking on the screenshot below, or by downloading the pdf here (the full reference is at the bottom). If you can’t see the paper, and don’t have the legal Unpaywall app, a judicious inquiry will produce a pdf for you.  After having written this post, I think that I will divide the discussion into three parts, as this has gotten a bit long. Today we’ll have the results, and within a few days I’ll write about what I see as the significance of the results (i.e., what’s called the “discussion” section of the paper).

The rationale of the experiment is described in detail in the previous post, and I won’t repeat it here. In short, we took two pairs of species, and for each pair, made a hybrid swarm consisting of individuals having half of the genome from each parental species, and half of the organelles and cytoplasm of each parental species (the contents of the cells). Each pair comprised one widespread species and one island species (D. simulans/D. mauritiana in one experiment and D. yakuba/D. santomea in the other). The object was to see if the hybrid swarm would revert back to one or the other parent species, remain as a group of “mongrels” that had both species’ genes segregating, or, perhaps, might evolve into a new lab species that was reproductively isolated from both parental species.

We made eight replicate “swarms” for each pair of species to see how repeatable the changes were. And we measured four sets of characters, each of which characterized and differentiated the two parental species:

1.) Morphological traits that differentiated each pair of species. There were five of these in the D. simulans/D. mauritiana pair and three in the D. santomea/D. yakuba pair. These were described in the previous post, and the graphs below also name them. Characters in the swarm (and pure species) were measured every five generations up to generation 20.

2.) Mating behavior. As described before, there is mating discrimination (and shortened copulation) between the members of each pair. We took males and females from the hybrid swarm and mated them to individuals of the pure parental species to see if the hybrids behaved like one pure species or another (we did this at Generation 21; we kept the swarms going for 24 generations).

For example, copulations between D. simulans males and D. mauritiana females are very short compared to copulations in the pure species. If hybrid-swarm males also show short copulation duration when mated to pure D. mauritiana females, we can conclude their mating traits have reverted to those of D. simulans. (They’d also be expected to show no mating discrimination against D. simulans but substantial mating discrimination against D. mauritiana.) We did this with both pair of species.

3.) Sterility in species crosses. When you cross members of both pairs of species, you get hybrid males that are sterile and females that are fertile. (This pattern is called “Haldane’s Rule”.) Sterility also persists in the hybrid swarms for a while as genes producing the malfunction get weeded out of the population by selection. We measured the sterility of males in the population at generation 20 compared to that of the pure species (in which males are perfectly fertile). More important, we looked at the sterility of hybrids produced in matings between swarm individuals and the two pure species (all at Generation 20). For example, if you cross individuals from the D. mauritiana/D. simulans swarm to the parental species and get fertile offspring with D. simulans but sterile offspring with D. mauritiana, then you know that the genotypic constitution for fertility in the swarm has reverted to that of D. simulans.

4.) DNA composition of hybrid swarm. As I wrote in the previous post, both pair of species are differentiated at many sites on their DNA. We could thus sequence samples of the hybrid swarm and see what proportion of each species’ genome remained in that swarm after 20 generations. We did this survey in all eight replicates for each of the two swarms, but only once, as this endeavor involved sequencing about 20 million bases. The analysis is a bit complicated and I needn’t go into it here.

The paper:

I’ll give the results of four tests below. They are all consistent and unequivocal: in every analysis, either the morphology, behavior, or DNA sequence of the swarm reverted to that of the “dominant” (mainland) species: D. simulans in one swarm in D. yakuba in the other. And this was true of all eight replicates of each swarm. Also, by generation 20, the DNA sequences of all replicates had reverted almost completely to that of the dominant species, though some DNA of the island species remained. That “relict” DNA was pretty consistent across replicates.

1.) Morphological traits. The two graphs below show the changes in morphology of the species-distinguishing traits occurring in all the swarm replicates over 20 generations (measurements were taken at generation 0, 5, 10, 15, and 20). The first plot shows the D. mauritiana/D. simulans swarm and the second the D. yakuba/D. santomea swarm. We also measured the morphology of both pure species as controls over time; these values are the straight and dotted lines at top and bottom (these values stayed pretty constant, as the traits are species-specific.) The hybrid replicates at each generation are shown as open circles, with the means among replicates plotted as best-fit lines, with each replicate being a different color.

In the first plot below, the values of pure D. mauritiana traits are the dotted lines; those of pure D. simulans traits are the solid lines. And you see that the hybrid swarm at generation 0 is largely intermediate between the lines, as it should be (forehead width, however, remains close to that of pure D. mauritiana for 10 generations before reverting to the D. simulans value).

The important result is that, over time, every replicate for every character reverted to the D. simulans value. The changes are especially marked between generation 10 and 15. By generation 20, the values of all traits are essentially those of pure D. simulans. For these traits the hybrids have, then, evolved to have all the trait values of D. simulans. The swarm looks like pure D. simulans individuals.

 

And this is the plot for traits in the D. yakuba/D. santomea swarm, with pure D. yakuba values being the solid line and those of D. santomea the dotted line. Again, the traits begin as intermediate in the first generation and then gradually take on the values of the dominant species (D. yakuba) after 20 generations. This is true in all eight replicates. In particular, the pigmentation of flies in the swarm winds up just as dark as that of pure D. yakuba individuals (a score of about 600 on a 1200-point maximum scale), rather than being almost unpigmented like D. santomea (that pure species has an average pigmentation score of 49). The characters change at different rates over time. For example, change in pigmentation is smooth over time but that of hypandrial bristles reverts within 5 generations to the value for D. yakuba.

 

2.) Mating behavior. I can summarize briefly: in all aspects of mating and copulation behavior, the hybrid swarms reverted to the “dominant” mainland species in all replicates by generation 21. In other words, in the D. yakuba/D. santoma swarm all the individuals behaved like pure D. yakuba flies, and in the D. simulans/D. mauritiana swarm all the individuals behaved like pure D. simulans individuals. This is true for both males and females. So we have reversion to the pure species in not just morphology, but in mating behavior.

3.) Sterility in species crosses. Again, in all the replicates of both hybrid swarms, individuals reverted to the fertility characteristics of the “dominant” mainland species by generation 20. For example, looking at the individuals in the 8 replicate D. simulans/D. mauritiana swarms, all swarm males produced fertile male offspring when crossed with D. simulans females but sterile male offspring when crossed with D. mauritiana females. The same held when we crossed hybrid-swarm females to either D. simulans or D. mauritiana males. And likewise again with the D.santomea/D. yakuba swarm: by the end of the experiment, both swarm males and swarm females behaved in their fertility relationships like pure D. yakuba individuals. Again, we observe ubiquitous and replicable reversion to the “dominant” mainland species.

4.) DNA composition of hybrid swarm. The assay at Generation 20 showed that in all the swarms of both species, the DNA of the island species had largely been eliminated, so that the genomes of the swarm were almost entirely that of the dominant species. However, some island-species genome remained in both replicates, as expected since some of it is “neutral” and wouldn’t be subject to selection one way or another. Here, for example, is the proportion of ancestry in each replicate (two bars for each replicate depending on which reference genome we used), with the dominant species’ DNA in yellow and island-species DNA in red. Very little of the island-species DNA remains, and what remains is present “segregating”, i.e., sites having one copy of island DNA and the other copy of mainland DNA at a given position (remember, there are two copies of every gene). Clearly, DNA from the island species is on the way out.

 

(From paper): Genetic ancestry rapidly and consistently regressed to that of one of the two parental species in all admixed populations. (A) The proportion of sites either fixing for D. simulans ancestry or still segregating for both parental species’ ancestry in each of the eight admixed D. mauritiana/simulans populations. (B) The proportion of sites either fixing for D. yakuba ancestry or still segregating for both parental species’ ancestry in each of the eight admixed D. santomea/yakuba populations. Sites were considered to still be segregating for both parental species’ ancestry if any of the ploidy = 8 genotypes 2 | 6 through 6 | 2 received a posterior probability >1/3. The left bar for each population summarizes results obtained when mapping to either the D. mauritiana (A) or the D. santomea reference genomes (B). Bars to the right, for each population, summarize results obtained when mapping to either the D. simulans (A) or D. yakuba (B) reference genomes.

Here is a broad genome scan, with each vertical line representing a 5000-base window, with its species composition indicated in yellow (dominant species DNA present) or red (island species DNA present, but not in very high frequency). I’ve put the caption from the paper here, too. As you read down each of the two figures, you see the DNA on that particular chromosome arm among the eight replicates (there are four chromosomes, with the X having only one arm, the second and third having two arms each, and the fourth being very small).

 

(From paper): Genome-wide distribution of ancestry in all admixed populations. Heatmaps showing ancestry estimates summarized in 5-kb genomic windows for each chromosome or chromosomal arm in the D. simulans (A) and D. yakuba (B) reference genomes. Each row is a different admixed population and colors reflect ancestry ranging from 0 (fixed for “minor” parent ancestry) to 1 (fixed for “major” parent ancestry). The bottom row summarizes the number of populations that showed evidence of a given genomic window still segregating for both parental species’ ancestry (i.e., ancestry estimate < 0.8).

As you see, the vast bulk of the genome is yellow, coming from the dominant species (the red bars stick out, but they are not nearly as frequent as they look against the pure yellow background).

One also sees that particular regions of the genome tend to remain “segregating” across all replicates: for example the tip of the third chromosome in the D. simulans/D. mauritiana swarm and the middle of the right arm of the second chromosome in the D. yakuba/ D. santomea swarm.

Finally, to show you the meager amount of foreign genome remaining in most parts of the genome, here is a plot showing, for each of the five chromosome arms, how much of the swarm genome was segregating: i.e., what proportion of the DNA had some sequence from both species (it was almost all “heterozygous”, with one copy of the mainland sequence and one of the island sequence). The eight replicates are given different symbols for each arm.

As you see, for almost all chromosome sites except for some replicates of chromosome arm 3L in the D. simulans/D. mauritiana swarm and arm 2R in the D. yakuba/D. santomea swarm, on average less than 5% of the island species DNA remained. In all arms but one in the D. yakuba/D. santomea swarm, almost no foreign DNA remained.

What’s also notable is that the amount of foreign DNA on the X (“sex”) chromosome was the lowest in both swarms. This may be because the X chromosome contains a number of genes producing hybrid male sterility, and thus “island” DNA was quickly eliminated by selection. (Also, since the X is present in only one copy in males, both recessive and dominant “sterility genes” are fully expressed, so they’re eliminated much more quickly.)

(Caption from paper): The proportion of genomic windows where both parental species’ ancestry still segregated varied across chromosomes. Each point represents the proportion of 5-kb genomic windows that have evidence for both parental ancestries still segregating after 20 generations following initial hybridization between the parental species. (A) D. simulans/D. mauritiana; (B) D. yakuba/D. santomea.

 

The Big Conclusion: In all replicates in both swarms, and for all traits measured—morphological, mating behavior, fertility relationships, and DNA sequence—the traits and the DNA of the swarm evolved (reverted) in the laboratory back to that of one pure species. And in all cases that pure species was the “dominant” mainland species: D. simulans in one swarm and D. yakuba in the other. We did not get a “hybrid” species, but rather got back a population whose DNA was largely that of a pure species. The results were markedly consistent among replicates, and the overall results very similar in both swarms.

In the next (and last) post, I’ll try to describe the significance of these results, and float some theories about why, in all cases, our swarms reverted to the dominant mainland species instead of the island species.

If you’ve gotten this far, thanks for reading!

________________

Matute, D. R., A. A. Comeault, E. Earley, A. Serrato-Capuchina, D. Peede, A. Monroy-Eklund, W. Huang, C. D. Jones, T. F. C. Mackay, and J. A. Coyne. 2020. Rapid and predictable evolution of admixed populations between two Drosophila species pairs. Genetics 214:211-230.

Another ripoff journal and science publisher

August 18, 2019 • 2:30 pm

So I need this article for my upcoming lectures on Antarctic biology. Sadly, the journal (Current Protein and Peptide Science) isn’t in our university’s e-library, so I have to either buy it (see below) or request it via Interlibrary loan. I will of course do the latter, so readers needn’t send it to me, and I certainly wouldn’t want to encourage bypassing ripoff journal paywalls.

But I was curious about the “Purchase PDF” button. When you click on it, you get this:

FIFTY EIGHT DOLLARS THEY WANT! And the article is only 22 pages long. That’s more than $2 a page for a pdf!

This is highway robbery, I tell you. But these inflated prices are typical if you don’t have a library or private subscription. (The company, by the way, is Bentham Science.)

Now the authors are from Hong Kong, so I doubt that any American taxpayer money was used to fund the research, but that is often the case and that’s DOUBLE highway robbery. If you pay taxes to support research, the results of that research—the publication—should be free to everyone. It’s your money, folks!

Not only that, but this journal may (I’m not sure) charge authors to publish their paper. And where does the publication fee come from? You guessed it: Joe Taxpayer. (There is a place on grant proposals to ask for money to publish papers.)

Scientific publishing is a huge racket, and what ripoff prices like this one do is impede the progress and dissemination of scientific knowledge. Bentham Science can take a number get in line, and kiss my tuchas.

I was so mad that I issued one of my rare tweets:

h/t: Nilou

Dong-ta-ra-con-ching! An insane paper, accepted by a Springer-Verlag journal, is now retracted

July 26, 2019 • 8:45 am

Reader Jonathan called my attention to post on the website Symptoms of the Universe by a physicist named Philip Moriarty. It points out what may be the craziest paper ever accepted by a decent mainstream science journal—at least in the last few decades. (I’m assuming that the journal Parasitology Research is reputable, though I may be wrong.)

Click on the screenshot to see Moriarty’s piece:

According to the article’s abstract, the authors, eight scientists from Korea, tested a “remediated” drug, mebendazole, against a ciliate parasite that infected a farmed food fish. They thought that by treating the drug in a weird way (read on), they might increase its efficacy and thus the production of fish. The results showed a marginal increase in efficacy and a reduction of deleterious side effects. The problem was how they “remediated” the drug:

Click on the page below to see the now-retracted paper:

The issue, as Moriarty notes with some screen captures, is the way the drug was treated. Read and weep (or laugh loudly):

What? Did the scientists wear tinfoil hats when they did the experiment? And what were the reviewers thinking when they read this? But wait! There’s more: a nice diagram of how they focused “Dong-ta-ra-con-ching” on the drug. I don’t see any trees here, and I have no idea what a “putor program” is, nor do I want to read enough to find out.

The authors conclude this:

The present study is the first study to demonstrate that the toxicity of MBZ could be reduced by remediation of component elements using the FOGF energy that is present in nature. Regardless of the fact that this new approach was initially examined in the marine environment, it has considerable potential for future application to reduce side effects that can occur in medical products applied in both veterinary and human medicines, and also the side effects that can occur during development of numerous new drugs, consequently resulting in the suspension of development.

Yeah, right. Perhaps chemotherapy drugs should now be treated by focusing energy using silkworm poop. . . .

An article at Retraction Watch that discusses this paper reports that the paper was in review for four months before it was accepted. Here’s the journal’s retraction notice (click on screenshot):

Trying to find out how the deuce this paper got accepted, Retraction Watch wrote the editors of the journal, who didn’t respond. Springer Nature (the relevant division of Springer) did, but their response was less than satisfying:

We asked the journal’s editors, Una Ryan of Murdoch University in Australia and Julia Walochnik of the Medical University of Vienna, why it took post-publication peer review to determine that the paper was nonsense. In other words, what exactly were the peer reviewers, editors, and publisher — that’s Springer Nature — doing between March 5, 2018, when the paper was submitted, and July 6, 2018, when it was accepted?

The editors did not respond, but apparently forwarded our email to Springer Nature. A spokesperson for the publisher responded:

In the interests of being fair and following due process, the paper was sent for a post publication peer review, following which all authors agreed to retract the paper as stated in the retraction note.  We treat all correspondence on integrity matters as confidential and cannot comment on details of the peer review process.

Seriously? What they’re doing here is trying to hide their big mistake. Sure the reviewers and details of the correspondence could be kept confidential, but the outline of what happened can certainly be revealed, like “the reviewers didn’t see this procedure” or “the scientists admitted they made it up.” As it is, everyone gets exculpated—who would see this retraction were it not for Retraction Watch and Moriarty?—and the scientists, who should be laughed out of the field, go blithely along exposing other stuff to dong-ta-ra-con-ching. Oy!

Do note that I’ve had my own run-ins with Springer involving retraction, as a while back the firm published an equally bonkers creationist paper in its journal International Journal of Anthropology and Ethnology, and, when I reported it to Springer, the firm at first defended it. But I persisted, and eventually the paper was retracted, though it’s still on the website. (I once thought it should be taken down, but perhaps it should stand as a monument to blinkered religiously-based dismissing of evolution.)

I add that Springer’s operating profit is enormous: 34%, and that’s not even the highest profit among gouging scientific publishers (Elsevier makes 36% and Wiley 40%).  Because of this, I have signed petitions and personally vowed not to work for Elsevier and Springer (I haven’t received requests from Wiley but won’t work for them, either). I found this out after Springer asked me to review a book proposal for them, an onerous task, and then offered me an e-book as payment. Using scientists to do their reviewing and editing for them, either for free or for trifles like e-books, which cost them nothing, is of course the way companies like Elsevier and Springer make their bloated profits, which are further inflated by charging libraries enormous amounts of money to carry their journals.

This is one reason I’m glad I retired, as I don’t have to deal with importuning from companies like this. And, as you see, Springer does everything it can to keep its retractions under wraps.

Study published in Science isn’t replicated; journal refuses to publish the failure to replicate

June 26, 2019 • 2:30 pm

Posting will probably be lighter than usual (even during my travels) over the next ten days, as I’m weary of arising at 4:30 to write posts, and, more important, I’m off to the Big Island soon for traveling and snorkeling. I’ll try to keep the Hili dialogues going, although it’s tough without Grania, but bear with me until July 9.

Today’s Execrable Science Story comes from Bloomberg, which you can access by clicking on the headline below:

As the article reports, 11 years ago Science published a paper by a group of psychologists that, says Bloomberg, claimed to find biological differences between liberals and conservatives. The paper is this one, and you can get a free pdf by clicking on the screenshot:

From Bloomberg:

According to the paper, conservatives tended to react more to “sudden noises” and “threatening visual images.” This result, which suggests that political liberalism and conservatism spring from deep, indelible sources rather than reactions to the issues of the day, suggests that polarization will never end — that the populace will always be divided into two camps, separated by a gulf of biology.

This is the kind of paper that demands replication, and indeed, when two groups tried to replicate the results, they failed:

Fast forward a decade, though, and the claim is unraveling. In a working paper published this month, another team of psychologists attempted to repeat the experiment, and also conducted other similar experiments. They failed to find any evidence linking physical-threat perception with political ideology. But when they tried to publish their paper, Science desk-rejected it — that is, the editors refused to even send the paper out for peer review, claiming that the replication study simply wasn’t noteworthy enough to be published in a top journal. Meanwhile, another team of researchers also recently tried to replicate the original study, and failed. So even though at this point the evidence proving a biological basis for liberalism and conservatism seems to have been invalidated, it’s unclear whether this fact will make it into the public conversation.

The “desk-rejected” link takes you to a Slate article by all four of the rejected paper’s authors, who provide a good justification for publishing their paper. But it wasn’t even reviewed by Science! As the authors say in Slate:

We did not expect Science to immediately publish the paper, but because our findings cast doubt on an influential study published in its pages, we thought the editorial team would at least send it out for peer review.

It did not. About a week later, we received a summary rejection with the explanation that the Science advisory board of academics and editorial team felt that since the publication of this article the field has moved on and that, while they concluded that we had offered a conclusive replication of the original study, it would be better suited for a less visible subfield journal.

We wrote back asking them to consider at least sending our work out for review. (They could still reject it if the reviewers found fatal flaws in our replications.) We argued that the original article continues to be highly influential and is often featured in popular science pieces in the lay media (for instance, here, here, here, and here), where the research is translated into a claim that physiology allows one to predict liberals and conservatives with a high degree of accuracy. We believe that Science has a responsibility to set the record straight in the same way that a newspaper does when it publishes something that doesn’t stand up to scrutiny. We were rebuffed without a reason and with a vague suggestion that the journal’s policy on handling replications might change at some point in the future.

There’s not much more to add to this. Science has behaved shamefully, with its usual hauteur and diffidence. They are a bunch of self-iimportant gits. They won’t, I suspect, even add a note to the original paper that it had failed replication; and that is the minimal thing to do to call attention to the issue.

And what if the failures to replicate don’t get published? (I hope and expect that they will.). For science to progress, false or questionable results must be put into the public domain, for that’s the only way to ensure that the truth will out. By allowing a possibly incorrect result to stand uncorrected, Science is degrading the entire scientific enterprise. Their behavior is reprehensible.

I should add that, according to the replicators, the paper’s original authors were supportive of the efforts to publish the failure of replication. It’s the damn journal—I call it a “magazine”—that’s to blame here.

The publisher Springer tries to stiff me

May 14, 2019 • 8:45 am

There’s not much news today except for what you already know: Trump is imposing ridiculous tariffs on China, which will, contrary to his stupid claim, cost U.S. citizens more. Tariffs are never a good idea. And Doris Day died.  The big news from Chicago is that all ten of my ducklings are still alive and thriving, which goes a long way toward counteracting the bad news.

In the absence of news, here’s a personal rant, which I’ve made before. Commercial scientific publishers like Springer and Elsevier are well known for gouging both scientists and university libraries by charging huge amounts for subscriptions to journals, for “publication charges” (what you pay when you publish a paper in their journals), and for online reprints. I recently discovered, for instance, that the University of Chicago Library, which is not impecunious and is well stocked with journals, can’t afford to carry Nature Ecology & Evolution, an important journal in my field. That’s because its publisher, like all Nature journals, is Springer, and is charging more money for the journal than our library can afford. (This is not a predatory journal or an obscure one; it’s one I would read if I had access.)

As I wrote in 2016, the profit margins of commercial science publishers are obscene. My beef at that time, which still holds, was this:

I’ve long complained about the bloated profits of commercial scientific publishers, which can be as high as 40%. That’s obscene if you realize that other companies which actually make a product make far less money, that the scientific publishers get that money by not only charging authors to publish there, but having their scientific papers refereed and improved by reviewers who are paid nothing. Those reviewers—and I’ve done plenty of gratis reviewing for journals like Nature and Current Biology, as well as for journals issued by less greedy publishers—are done out of a sense of “public service”. Profit-hungry journals like to play on our sense of duty and public service, all the while raking in huge profits by using scientists to do the journal’s job for free. And remember that these journals charge people for access to papers that are, by and large, funded by government grants—by the taxpayer. It’s reprehensible that the public who funds such research is denied access to the results of that research.  (Some funding organizations, however, allow journals to charge for access for only one year. But even that is too much.) Commercial publishing of taxpayer-funded research is a travesty unless the profits, beyond those needed to pay salaries and run the company, are plowed back into more science.

But young scientists, who need to make their reputations by publishing in well-known journals like Cell and Nature, have no choice, for their hiring, tenure, and promotion often depend on what journals accept their papers. Sadly, many of the “high quality” journals are put out by greedy publishers. And it’s not just young scientists, either: organizations that hand out grants often look at where you’ve published your papers before deciding whether to give you further funds.

I’ve complained about this before, especially about the company Elsevier, one of the greediest scientific publishers around (see here). Eventually I, and 16,383 other scientists (the number is growing), pledged to do no more work for Elsevier until they adopted reasonable business practice instead of gouging scientists. Even editors have fought back: as I reported last November, “all six editors and 31 editorial board members of Lingua, a highly reputed linguistics journal that has the misfortune to be published by Elsevier, have resigned in protest of high library and bundling fees and of Elsevier’s refusal to convert the journal to open access.”

Companies like Springer and Elsevier are, unlike society journals or university-published journals, purely capitalistic: their aim is not to disseminate science, but to make money. And they do. Here are the profits I reported in the post above; note that I can’t be sure that these figures hold now, nor that they were absolutely accurate in 2016. But this is what I had:

Want to know the obscene level of profits these companies make? From Sauropod Vertebrata Picture of the Week, we have a listing of the profits of well known technical scientific publishers. These are from 2012 and represent profits as a percentage of revenue:

Here’s a comparison of profits from various companies, including nonscientific ones, listed on Alex Holcombe’s blog in 2013; they’re compared to profits of other companies. [JAC: I believe these are profits as a percentage of revenues.]

As pointed out in the article I’ll shortly summarize, Elsevier made a profit of $1.13 billion dollars in 2014—1.3 times the entire annual budget of the Howard Hughes Medical Institute.

One way that companies like Springer fatten their purses is by getting scientists to do reviewing for them, and then paying them nothing or almost nothing. What this means, in effect, is that scientists are working as no-wage slaves so that commercial scientific publishers can make more money. Here’s an email I got yesterday from an editor at Springer (names changed to protect the capitalists):

From: [NAME REDACTED]
Sent: Monday, May 13, 2019 2:50 PM
To: Jerry Coyne
Subject: Population Genetics-Historical Fiction

Dear Prof Coyne,

Greetings from New York.  Please allow me to introduce myself as an editor in Life Sciences at Springer.  As you may know, Springer is an international publisher of scholarly research and reference works in a variety of academic disciplines.

We have recently received a book proposal entitled [TITLE AND DESCRIPTION OF BOOK REDACTED]. Given your academic interest in this field, I wonder if you are available to review this unique project for scope and suitability for publication (2 pages plus sample chapters).  I am delighted to offer any ebook of your choice from Springer (valued at $250 or less) as a token of my gratitude.  In the event that you are unable to review for us,  please feel free to suggest a colleague who might be a suitable alternative.

I look forward to hearing from you, and thank you in advance for your time and consideration.

With best wishes,
[Name REDACTED]

Note what they’re offering. In return for several hours of work (I’d have to review a short book proposal but also “sample chapters”, which are long and take time), I get an ebook of my choice. Now what does that cost Springer? Nothing! Once an ebook is produced, handing out one free copy to a reviewer has a marginal cost of zero. (And I don’t even read books online.) In other words, they’re asking me to put in several hours of work in return for bupkes. Nobody else who invested so much time in acquiring scientific expertise would be expected to work for nothing. But journals like this one do, counting on our “sense of duty as scientists.” (Some companies do offer real books, but often of a value less than that of a reviewer’s time, especially given that the cost of a book to a publisher is about half what you’d pay in a bookstore or online.)

Well, I will and do exercise a sense of duty for journals that aren’t run for profit, but not for companies like Springer. I wrote them this reply:

Sorry, but the offer of an e-book, which costs you virtually nothing, is hardly reasonable payment for what would be at the minimum several hours of work on my part. I should make at least as much as a plumber, don’t you think?

And I don’t have an e-reader.

I consider such offers pure exploitation of academics so that your already obscenely large profits (34% of revenue) can become even larger. When you offer a decent stipend instead of e-books, then maybe you’ll get more takers.

I’ll add that your journals cost so much that our library at the University of Chicago cannot even afford to take Nature Ecology & Evolution, which is a journal right in my area.

I can see why you make so much profit: you pay book reviewers virtually nothing.

Yours,
Jerry Coyne

The Great Science Publishing Scandal

May 4, 2019 • 10:30 am

by Matthew Cobb

Earlier this week, BBC Radio 4 broadcast a programme I made, along with producer Deborah Cohen, about how scientific publishing works, the problems associated with it, and why everyone should be concerned about it. Click on this picture and you will be able to listen to the programme from anywhere in the world.

You might think this is a fairly niche issue, but if you or anyone in your family has a disease and you want to read up on the latest treatments, you will find that, unless you work or study at a rich university, you may not have access to the material, which is behind a paywall.

The programme is not primarily about the massive profits of the publishers* but about something much more interesting – how we got to this situation, and how academics (not just scientists) are complicit in the system. We also explore various alternatives, including Sci-Hub, a site run by a Kazakh hacker, which has stolen the whole of the academic literature, pretty much, and gives it away for free. But as one of my interviewees put it in a quote we didn’t use – “Stolen from whom?”

The programme is only 28 minutes long, and the response so far has been very positive. Those who are particularly keen on one or another Open Access option have been disappointed that the programme is not either more polemical or more focused on one solution. I felt that explaining the complexities of the problem to the general listener would be more interesting.

_______
* For example, in 2017, the largest academic publishing company, Elsevier, made £913 million profit, up £60 million from 2016. Its 2017 profit margin was 36.8%. The raw material underlying that profit – the academic articles and their reviewing – was provided free of charge by academics, often from research that was funded by the public either through taxes or through donations to charities.