30 December 2016

2016: Where did the work go?

There are reasons aplenty to hate this wretched year, but I’m just going to focus on the professional side for me. 2016 was a year I felt like I just couldn’t get stuff done.

On paper, it was not a horrible year. On paper, the book Freshwater Crayfish was released, which I co-edited and had a couple of chapters in. But in reality, the physical copy of that book was released in August 2015.

I also had one other book chapter, in Science Blogging: The Essential Guide, back in February. But the production on that book had dragged on for so long (I first blogged that it was coming out late in 2014) that it certainly didn’t feel like it was something new.

My frustrations were compounded because I had submitted a couple of papers early in the year; one early January, in fact. But for reasons that do not need exploring at this juncture, the editorial process for both of them dragged out longer than usual and they won’t see the light of day until 2017.

(At least, I hope they will appear in 2017. One journal that has accepted one of my articles still has items in its pre-print queue today, 30 December 2016, that are dated 30 December 2015. A whole year as a “forthcoming” article? That sucks.)

The number of blog posts was down here on NeuroDojo, but holding reasonably steady on Marmorkrebs and Better Posters. I have a lot of blog posts that I started but wasn’t able to finish.

I did teach a lot this year. I just got through the heaviest teaching load in a semester I’ve had in a very long time (and am so pleased nobody yelled at me, which I was convinced was about to happen any day). I did two graduate classes that were new to me for the first time ever. I taught a grad course in summer. And I taught the #SciFund poster class for the second time.

For me, professionally, 2016 feels like “the one that got away.”

23 December 2016

The open access “sting” by Science, three years on

In 2013, writer John Bohannon published a Science article where the main drawing card was an obviously bad paper that he got accepted or published in multiple junk journals. He was not the first, nor has he been the last, to set out to punk crappy journals with obviously bad papers. It’s practically a scientific genre in its own right now.

I grabbed four of the papers that made it through the production process (despite Bohannon’s efforts to keep them out of the literature) for teaching purposes. I was recently reminded of those papers, and went looking for them again.

Let’s start with Indandah et al., 7-chloronorlichexanthone inhibits the growth of murine SV40 transformed lymphoid sarcoma Cells in vitro, in Medicinal Chemistry:

The journal is still there, but there is no hint of the retraction. There’s just a gap in the page numbering.

Next, Magaya et al.,Arthogalin inhibits the growth of murine malignant prostate sarcoma cells in vitro, from Journal Of Pharmacy And Pharmacological Research.

The entire publisher website is gone. The same is true for Nonjah et al., Nephrosterinic acid inhibits the growth of murine malignant pleural sarcoma cells in vitro.

The entire Scientific Journal of Medical Science is gone, gone, gone.

With this track record, I was surprised to see one journal acting like a real journal: being transparent and taking responsibility. The Journal of Biochemical and Pharmacological Research still exists, first of all. You need to drill down to find their page for Onnoocom et al. contribution, Schizopeltic acid inhibits the growth of murine polyploid pulmonary blastoma cells in vitro. But when you do:

The journal acknowledges that the paper was there in its table of contents, but the links for the abstract and PDF both lead to a retraction notice:

JBPR has been a victim of bogus submissions; and this paper is one of those and is hereby retracted. The editor in chief takes full responsibility for accepting this bogus manuscript for publication in JBPR. We sincerely assure readers that something like this will not occur again.

The last line makes me raise my eyebrows a bit. No journal can assure readers that they won’t make this mistake again. It’s just not possible to have a 100% failsafe fraud detection system.

Yes, journals should be criticized when they publish deeply flawed papers. But how they respond to those errors matters, too. It is possible that some junk journals are actually new journals run by people with good intentions but little experience that have the potential to improve. I’m not saying a single retraction notice makes a journal reputable,

Related posts

Open access or vanity press, the Science “sting” edition
Using “journal sting” papers for teaching

22 December 2016

Truth and justice at universities, not “or”

A friend whose opinion I trust asked people what they thought of a talk by Jonathan Haidt. Haidt’s summary of the talk is here. His thesis is universities can search for truth or be agents for social justice, but not both. Weirdly, Haidt says that individuals can pursue both truth and justice, but an institution cannot, for reasons that are never explored.

Haidt says there are few conservatives in university positions, citing Higher Education Research Institute data. Haidt then presumes that being on one political side precludes understanding of others. He does this by demonstrating that much reasoning is “motivated,” which is an idea that has lots of empirical support. However, he makes hasty generalization in arguing that because people often engage in motivated reasoning, they always do this. He makes another hasty generalization by arguing that only other people can dissuade researcher from incorrect views, neglecting the possibility that evidence can do so.

And this is about the last portion of Haidt’s talk that is driven by data.

Haidt is concerned that the political homogeneity of universities will trickle down to students. Evidence does not support this. Professors may largely lean to the political left, but their students are not much affected by this. See here and here.

He goes on to make lots of similar assertions about how students and professors are scared. “Professors all over the country are changing their teaching,” he claims. But his assertions are just that: assertions. He presents no data to support these claims. Well, unless you count a screenshot of a Vox article. (One which did not go unchallenged, incidentally.)

Haidt goes on to expound his thesis to say that universities have created a culture of victimhood, and how universities teach that other people are literally “members of good and bad groups.” He does so again through selected anecdotes, not data.

Haidt clearly implies that teaching that people can be “members of good and bad groups” is somehow wrong. He presumes that all political views have prima facie validity. He ignores many cases of political ideas have been shown to be empirically, factually wrong, but that are still bandied about as “common sense” by politicians. I would also like to ask Haidt would be whether he thinks German Nazis of the 1940s were just misunderstood.

At one point, Haidt says, “I’m not denying there’s oppression,” but I can’t help but wonder why this is a throwaway sentence compared to the amount of time he spends attempting to build the case for “victim culture.” He argues that certain statements are inviolable, like, “America has endemic racism / sexism,” but doesn’t address whether or not that is true. Again, Haidt is apparently operating from the point of view that has as as starting point that “America is racist / sexist” and “America is not racist / sexist” are equally plausible.

He says certain patterns that might be correlated with racism or sexism are “invitations to get to work” to find out if they are true or not. I like that Haidt is advocates empiricism, but what is missing is at what point hypotheses should be abandoned. We have seen the “Doubt is our product” strategy used many times to bring faux respectibility to discredited ideas.

Haidt also takes the liberty of defining “social justice” as he has experienced it. I suggest it is at least plausible that other people might disagree with his definition.

Haidt claims he is not on the left or the right. My impression is that Haidt, in trying to understand the origins of political disagreement, has attempted to be fair in understanding the basis for political viewpoints. Unfortunately, I think that objectivity in seeking the basis for people’s views has made him unwilling to critique them unevenly, leaving him to proclaim, “Everyone does it.” But as David Frum wrote:

“They all lie” is a sentiment that most benefits the most egregious liars.

I agree with many of the individual cases Haidt presents. But this is not surprising when you build your case on the best supporting anecdotes.

Weirdly, at the very end, Haidt unravels his own thesis, saying you can only effect change if you commit to truth. But again, this is a throwaway line that runs counter to his headline (which is 90% of communication effort). Haidt’s headline argument would make academia irrelevant. We can only tell the truth as long as it doesn’t matter. If we try to effect change, we’re spin doctors.

External links

Why Universities Must Choose One Telos: Truth or Social Justice
The moral roots of liberals and conservatives

19 December 2016

The tyranny of free time

“Have a nice break.”

I know students and other mean well, but “breaks” are very stressful for me.

I’m sure I’ve complained about this before, but work rarely stops. Before classes start up again, I have a conference (SICB in New Orleans), potentially an NSF pre-proposal to write, and two projects where data collection ends on 1 January that I can start writing up.

Second, and increasingly so, I feel pressure to make the best use of my time on things other than work.

“Hey, I have nothing slated for today! Should I do my laundry? Go shopping? Write a blog post? Play a video game? Read a book? Watch those DVD bonus features? Netflix binge on that show I’ve been meaning to catch up on? Work out at the wellness center? Clear all the crap out of my office? Clear all the crap out of my apartment?”

At least with work, I know what I am supposed to be doing. With my time, things are not so clear.

16 December 2016

Misunderstanding antibiotic resistance

Even people who try to incorporate evolutionary thinking into their research struggle with the concepts, it seems.

Thomas Wittum was interviewed on Quirks and Quarks about finding bacteria in a pig farm that were resistant to one of the “last resort” antibiotics. He repeatedly put forward the idea that these bacteria must have been introduced there from a human health care facility, like a hospital, where these particular classes of antibiotics are used the most.

This notion come perilously close to the idea that organisms evolve features that they “need.” The thinking seems to go that antibiotic resistant bacteria must come from hospitals, because why would bacteria is someplace without those antiobiotics have resistance to them?

This misses the concept of “standing variation”: that any population can have variation in a trait in the absence of any selection pressure for one version of the trait or the other. If you look at classic cases of dark coloured insects, like peppered moths, flourishing in industrial areas (industrial melanization, for those who know the fancy words), populations always had some dark insects around before industrialization. That’s standing variation. Later, the dark colour provided an advantage as the landscape got darker. But the key point is that the insects didn’t newly evolve dark colouration as regions became industrialized, because they needed it.

Similarly, it is possible that these farm bacteria came had antibiotic resistance “out of the box,” so to speak. The resistance would do very little in the farm setting, but... if those bacteria were in an environment where those antibiotics were released, they would suddenly have a huge advantage.

Having said that, it is entirely possible that the antibiotic resistance did come from a hospital or someplace similar. The manuscript itself (Mollenkopf et al., in press) doesn’t address the source of the bacteria, or the antibiotic resisting gene. But it’s not a good assumption that if we create a new antibiotic, there will be no bacteria that will be able to survive it at the start. Some bacteria might, by chance, already have a way to evade the antibiotics.


Mollenkopf DF, Stull JW, Mathys DA, Bowman AS, Feicht SM, Grooters SV, Daniels JB, Wittum TE. Carbapenemase-producing Enterobacteriaceae recovered from the environment of a swine farrow-to-finish operation in the United States. Antimicrobial Agents and Chemotherapy: in press. http://dx.doi.org/10.1128/AAC.01298-16

External links

Drug resistant "superbug" gene found on pig farm

Picture from here.

15 December 2016

SACS speaks

SACS, the accreditation agency for UTRGV has released its document about why the institution has been placed on probation. There isn’t much in the way of new information in the document.

From what I have gathered in news reports, one potential issue is that after UTRGV was established in Fall 2015, the University of Texas Brownsville was apparently still “officially” still a degree granting entity. This was done because Texas Southmost College, which had been joint with UTB for some time, had no accreditation of its own, and keeping UTB going “on paper” allowed TSC to keep going. But the question was, “If UTB still existed, why didn’t students get degrees from UTB instead of UTRGV?”


The University of Texas Rio Grande Valley... was placed on Probation following receipt of self-disclosed information submitted as part of a withdrawn merger application
and receipt of a completed Institutional Summary Form. Prior to the institution’s next review by SACSCOC’s Board of Trustees in December 2017, a Special Committee will conduct an on-site evaluation of the institution’s compliance with the Principles of Accreditation(.) ...

Probation is the most serious sanction imposed by SACSCOC’s Board of Trustees short of loss of accreditation. ... The maximum consecutive time that an institution may be on Probation is two years. In December 2017, the University of Texas Rio Grande Valley will conclude 12 months on Probation. ...

What will happen in December 2017? SACSCOC’s Board of Trustees will consider the accreditation status of the University of Texas Rio Grande Valley following review of a Monitoring Report submitted by the institution addressing the standards cited above for non-compliance, and the report of a Special Committee that will visit the institution in fall 2017. The Board will have the following options: (1) remove the institution from Probation without an additional report; (2) continue accreditation, continue Probation, authorize a Special Committee, and request an additional report; and (3) remove the institution from membership for failure to comply with the Principles of Accreditation.

Related posts

UTRGV placed on probation by accrediting agency
UTRGV’s accreditation probation details emerge
“We will...”

External links

Disclosure Statement Regarding the Status of UNIVERSITY OF TEXAS RIO GRANDE VALLEY

09 December 2016

“We will...”

When UTRGV launched, it started a public campaign around the phrase, “We will.” It’s all over the place with claims about the things “we will” do. It’s on the Twitter account...

By the student press.

It’s even used by boring administrative stuff like strategic planning...

And student financial aid reminders.

In light of the accreditation probation , I thought it was time for an inspirational new addition to the “We will” campaign.

(I always thought “We will” was an ironic choice of tagline, because it indicated not that we were doing anything, just that we had plans to do it eventually, someday, sometime.)

Related posts

UTRGV placed on probation by accrediting agency
UTRGV’s accreditation probation details emerge

08 December 2016

UTRGV’s accreditation probation details emerge

Local station KRGV and Inside Higher Ed report on what the University of Texas Rio Grande Valley has done to get into hot water with the accreditation agency, SACS.

And it’s not just the “timing issue” that president Guy Bailey claimed it was.

The SACC Coordinator of Communications Pamela Cravey explained a few.

“For failure to comply with principle 1.1 integrity, comprehensive standard 3.4.4 acceptance of academic credit, comprehensive standard 3.4.7 consortia relationships contractual agreement,” she said.

Inside Higher Ed calls the list of shortcomings “unusually long.”

(T)o judge by SACS's laundry list of areas in which the new institution is falling short of the accreditor's requirements and standards, UT Rio Grande Valley appears to be a work in progress.

A spokeswoman for SACS cited a full 10 major areas in which the new Texas campus had faltered, including such basic things as assuring that it “operates with integrity in all areas.” Other areas of difficulty included complying with federal financial aid audits and ensuring that the institution's degrees are based on instruction it offers itself (rather than by other institutions).

My reaction might be summarized as: “Holy sh*t.” I mean, to be accused of a lack of integrity? Judging from the quote above, it appears to be section 1.1, which would make it literally the first thing on the list that universities are supposed to do. I have heard, but not confirmed, that there is a lower level of concern, “warning.” If there is, we kind of blew past that.

UTRGV is not the only university on the list, as Inside Higher Ed notes. There are nine others, but UTRGV is unusual in that it is part of a state university system, serves the most students, and was launched with very high goals of creating a new research university.

What I wouldn’t give to be a fly on the wall of the University of Texas System board rooms these days.

At the start of the semester, the UT system was praising UTRGV for its first year, which it called “stellar.”

In the middle of the semester, we learn that the med school isn’t going well and UTRGV mispent millions of dollars.

At the end of the semester, we’re getting warning shots that our legitimacy as an institution is in question.

Update: The campus newspaper, The Rider, has published the full list of ten points of concern:

  • Integrity (Principle 1.1)
  • Acceptance of academic credits (Comprehensive standards 3.4.4)
  • Consortial relationships/contractual agreements (Comprehensive standards 3.4.7)
  • Institutional credits for a degree (Comprehensive standards 3.5.2)
  • Institutional credits for a graduate degree (Comprehensive standards 3.6.3)
  • Financial aid audits (Comprehensive standards 3.10.2)
  • Substantive change (Comprehensive standards 3.12.1)
  • Advertising, Student Recruitment, and Representation of Accredited Status policy compliance, (Comprehensive standards 3.13)
  • Publication of accreditation status (Comprehensive standards 3.14.1)
  • Recruitment materials (Federal requirement 4.6)

The Rider also reports the faculty senate will be meeting with the president soon.

Update, 9 December 2016: Local newspaper The Monitor wrote an unusually pissy editorial complaining that SACS should have released all the details of the concerns that put the institution on probation, and demanding more information.

Meanwhile, mark your calendars for 15 December, when SACS is planning on posting more about the issue:

(Pamela Cravey) said her agency will post “a public disclosure statement” on its website on Dec. 15 providing additional insight.

These statements include an update and explanation of actions taken and what it means for the institution, but the violations are not typically listed, based on statements currently available.

Another update, 9 December 2016: The Faculty Senate emailed the faculty today after meeting with President Bailey. They described the situation thus:

The concerns shared at this point in time center on the transfer of UTB students to UTRGV to meet the expectations of the timeline set by Texas legislature. It took longer for Texas Southmost College to gain independent accreditation than expected. If UTB had been abolished on August 31, 2015 (the date UTPA was abolished), all TSC students would have lost their financial aid. This meant that UTB could not be abolished until a later date even though it had no students. ...

We found President Bailey to be very straightforward about the situation. He provided us with detailed documented timelines starting in July 2013 through September 2016. Our institutions had been in communication with SACSCOC consistently throughout this process. He reassured us that there are no concerns with faculty, programs, students or financial aid.

Update, 11 December 2016: Local paper The Monitor has obtained new documents relating to UTRGV’s accreditation issues.

Because UTB would remain an accredited institution after the creation of UTRGV, there were discussions of transferring all UTB students to UTRGV to avoid “teach-outs,” which would be agreements with UTB and TSC to teach bachelor’s, master’s and doctoral programs at UTRGV. The next move would be to consolidate or merge UTB with UTRGV.

“Discussed the benefits of just moving all to UTRGV to avoid teach-out and facilitate the award of financial aid,” the log of a Feb. 23, 2015 meeting states.

This meeting was attended by UTRGV officials Bailey, Brown, Provost Havidan Rodriguez, and SACSCOC’s Armstrong, and Director for Legal Affairs Carol Luthman.

A year later, however, during a conference call between Brown, Donat and Armstrong, the SACSCOC officials seemed confused by what transpired during that Feb. 23, meeting.

“No UTB Students in fall 2015; this was not their understanding from the February 23, 2015 meeting,” states the log of a May 4, 2016 call. “Need to respond by clearly describing our understanding of the February 23, 2015 meeting and provide documentation that had been transparent on how UTB operates.”

It still doesn’t address why “integrity” is concern number one.

Minor annoyance: the story repeats the myth that UTRGV is the first university created this century.

Related posts

Show me what you value
Our med school is not going smoothly
Physics fraud
UTRGV placed on probation by accrediting agency

External links

UTRGV Reassures Students Probation Period Won’t Affect Them
A Watchdog Bites
UTRGV may have violated 10 standards on path to probation EDITORIAL: UTRGV probation questions need specifics
UTRGV probation fears dispelled

06 December 2016

UTRGV placed on probation by accrediting agency

This is not good.

University president Guy Bailey sent an email to the campus today informing us that the university had been placed on probation by SACS, the regional accrediting agency.

The reasons for this are not clear. When I went to the SACS website, there are no details about this that I could find. Bailey referred to some “timing issues” around the separation of legacy university, UT Brownsville, from Texas Southmost College. But how that split affects the sort of things accreditation is supposed to measure, like financial stability, instructor qualifications, adequate assessment, it not at all clear.

UTRGV has to stay accredited. It’s just non-negotiable for students, faculty, and administration. A non-accredited university is just a diploma mill, and has no real standing.

More details are supposedly coming next month. So this is a story to watch closely.

External links

Accrediting agency places University of Texas Rio Grande Valley on probation

05 December 2016

Polisplaining science

At the National Review, Julie Kelly says scientists should stop playing politics.

I’d be fine with that if politicians stopped playing scientist.

How many times have we seen politicians expressing opinions about the facts around scientific issues? Not policy issues around science, or funding science, or anything else that is a legitimate domain of politicians, “polisplaining” scientists. Politicians throwing snowballs to claim “global warming isn’t real” kind of stuff.

Hey politicians, you came into my house, and called my work, and the work of my colleagues, “lies straight from the pit of hell.” You routinely hold up the work of scientists for public ridicule as examples of taxpayer waste (even when it cost $48 in spare parts). Don’t antagonize scientists and expect us to say nothing.

Kelly warns that the public doesn’t trust scientists on some issues. The article kind of implies that public trust in scientists is in freefall. But in most polls in developed countries, scientists regularly come out as one of the most trusted professions.

In the United Kingdom, poll results came out today putting scientists as one of the most trusted professions. Politicians in general? Last.

In the United States, the poll phrasing isn’t quite equivalent. Even so, college teachers (which, since most scientists are professors, is reasonably close) got more than 50% of people rating them as very trustworthy, while members of Congress rated 8%.

While public trust in scientists is higher than that of politicians, I do agree that scientists should want to keep public trust. That’s important. But if the public doesn’t trust scientists on some issues, whose fault is that? There are documented cases of deliberate, politically motivated disinformation campaigns to convince people not to trust scientists. And that came from the political right.

External links

04 December 2016

Campuses as sanctuaries

My campus is about 85% Hispanic, and we are one of the closest to the US/Mexico border. So we have an unusual perspective on a lot of issues concerning immigration. I’m mostly just quoting this story because I think it’s going to be an interesting one in the next few months.

The Faculty Senate of the University of Texas Rio Grande Valley unanimously passed a resolution Friday endorsing the idea of a sanctuary campus. ... The resolution was passed in response to a recent petition signed by more than 1,500 students that asks President Guy Bailey to prohibit campus police or immigration authorities from asking students about immigration status.

My prediction is that President Bailey will do nothing. Because:

Gov. Greg Abbott tweeted in opposition to “sanctuary campuses” Thursday vowing to cut state funding from any state institution that assumes a sanctuary status.

As far as I’ve been able to observe, money seems to be President Bailey’s major motivator for doing anything as an adminstrator. Even the threat of losing state money will probably be enough to ensure compliance from institutions.

The Vice President of Young Republicans at UTRGV Jaime Garcia called the petition reckless.
“We could have stayed UTPA and UTB but we merged to get access to the funds that the bigger schools get here in Texas,” Garcia said.

Non sequiter. I don’t see how the merger is related to any of these issues. It’s also frustrating to see a petition – names on a piece of paper – one of the most notoriously sedate forms of political activism there is, being branded as “reckless.”

Update, 5 December 2016: Called it.

“There is no problem right now, and so, you stand a much greater chance of creating a problem if you make that declaration,” (UTRGV President Guy) Bailey said in an interview Wednesday.

Let’s not take a stand because something might happen. Gah.

Additional, 5 December 2016: In an email to faculty, the faculty senate noted of its resolution:

We do not use the term “University Sanctuary”, but do support our students, faculty and staff. ... We felt that we needed to step-up and not wait until later. We want everyone to know where we stand on this issue.

Well... they do use “Sanctuary campus” to describe what other institutions have done. Here’s the text:

WHEREAS the University of Texas Rio Grande Valley (UTRGV) has a mission to “Transform the Rio Grande Valley” through an “accessible educational environment;”

WHEREAS, UTRGV has a goal to foster sustainable community-university relationships and lists “Diversity, Access, and Inclusion” as values;

WHEREAS the Senate and our academic community and peers across the country are concerned about the recent increase in hate crimes and inflammatory language around the United States since the presidential campaign;

WHEREAS there have been repeated examples of threats against women, LGBTQIA-identified individuals, specific ethnic and religious groups, and immigrants during and after a divisive presidential election;

WHEREAS President Bailey sent out a memo on 11/16 that stated, “Please join me in ensuring that all members of the UTRGV community embrace our commitment to a diverse, inclusive, safe, and supportive learning and working environment.” He referred to this list of University policies that support this commitment:

WHEREAS the U.S. president elect has openly discussed eliminating the DACA program that supports our undocumented students and has championed the rapid increase in the deportation of undocumented immigrant community members which could negatively impact our community, our students and their families, our staff and their families, our faculty and friends;

WHEREAS UTRGV has a goal to “Cultivate a welcoming, inclusive, and nurturing climate for all faculty and staff” including a commitment to “foster a supportive family-friendly climate;”

WHEREAS the internal 2011 memo indicates that U.S. Immigration and Customs Enforcement officers are subject to certain restrictions upon entering college campuses should be affirmed post-election; https://www.ice.gov/doclib/ero-outreach/pdf/10029.2-policy.pdf

WHEREAS the president-elect has campaigned on banning Muslims from entering the United States and his cabinet members have in the past suggested a registry of Muslim American citizens;

WHEREAS UTRGV has a focus on Globalization with a goal to “Foster a globally-connected university culture” with an initiative to “Increase the number of global partnerships that align with university priorities;”

WHEREAS UTRGV and its students have benefitted from the 2001 decision signed by Rick Perry that allows undocumented students to establish residency and enjoy in-state tuition, and later he and the Texas legislature allowed these students some access to the Texas Grant program, decisions which increased access to educational opportunities in our community;

WHEREAS over 28 university campuses have declared their campuses Sanctuary Campuses and many more (over 100) in the process of declaring;

WHEREAS UTRGV has the highest number of Senate Bill students in Texas;

THEREFORE, be it resolved that UTRGV be designated an All-Inclusive Campus, where all Vaquer@s are welcomed and supported.

To that end, the Faculty Senate of the University of Texas Rio Grande Valley, call upon the university administration to take the following actions and/or make these assurances, to the extent legally possible:

  1. that the university assign a specific administrative office to assist our DACA students and other students who lack the protections of citizenship on a strictly confidential basis.
  2. that the administration send a clear, public message that UTRGV will not tolerate xenophobic, misogynistic, homophobic, transphobic, ableist, Islamophobic, and racist comments and actions on campus, and that we as a university will not tolerate religious persecution or the trivialization of sexual assault.
  3. that the university continue its efforts towards being an allied campus and continue its trainings and inclusivity initiatives for LGBTQIA-identified students, faculty, and staff.
  4. that the university avoid compliance with a registry of Muslim citizens, and that the university carry on with its pre-election (11/8/16) processes for admitting international students.
  5. that the university make a public commitment to continue protecting student privacy and announce an assurance that it not release any records regarding the immigration status of students and their family members to institutions or authorities who would restrict a student’s opportunity for a quality education.
  6. that the university publicly advocate for the continued resident tuition designation for undocumented students and Texas Grant consideration for Dreamer students at the forthcoming state legislative sessions.
  7. that campus police will not question anyone’s immigration status or religious affiliation, nor will it enter into systematic partnerships or agreements with outside agencies, including ICE and the Department of Homeland Security, to question the legal status or religious affiliation of our students, faculty, or staff.

*We use Vaquer@s to include all gender identities.

This document was aided greatly by the Petition sent by UTRGV’s Minority Affairs Council, LUCHA (La Unión Chicanx Hijxs de Aztlán), Center for Mexican American Studies, Mexican American Studies Program, Center for Bilingual Studies, Muslim Students’ Association, WAKE-UP (Women Artistically Kollecting Experiencias-Unidas Prosperando), Voto Latino, and BESO (Bilingual Education Student Organization) to President Bailey on 11/17/16.

Credit goes to the University of Oregon FS resolution on the same issue for some of the format and language of this resolution.

Update, 13 December 2016: On 9 December, President Bailey sent around an email that basically affirmed that he would do nothing except the stuff the university was already committed to doing.

This message is a response to those concerns and is meant to make absolutely clear that UTRGV is committed to placing student success and safety at the heart of the institution. The UTRGV community includes students, faculty, and staff of many backgrounds, and UTRGV welcomes and celebrates what each person brings to campus.

The following are current practices at UTRGV. We reaffirm these practices as part of our commitment to an inclusive campus community: [snip]

External links

UTRGV faculty senate unanimously backs 'sanctuary campus' campaign
Bailey: Not a good time to declare UTRGV a sanctuary campus
UTRGV not likely to be deemed ‘sanctuary’ campus
UTRGV not a sanctuary institution fit

02 December 2016

Post fact politics catches up to science communication

There was been much hand-wringing in political discussion the last few weeks about how we are living in a “post fact” world dominated by “fake news.”

Well, hi-di-ho, people, welcome to science education and science communication of the last few decades.

Fake news? Evolutionary biologists have been putting up with people saying things like, “There are no transitional fossils” for-frickin’-ever. Even when you show them Archaeopteryx. We’ve been putting up with the Discovery Institute and Answers in Genesis who attack established science and chug along regardless of scientific facts and countless debunkings.

We’ve been through the argument that, “If only people knew the facts, people would act different. The facts speak for themselves,” and seen how that has failed, and failed, and failed to budge public opinion on some of the best understood science out there. Unfortunately, even among scientists, this attitude of “The facts speak for themselves” is still common. People who say otherwise, like Randy Olson and Matthew C. Nisbet, have received way more criticism for pointing this out than they deserve.

Now the same strategies are not just confined to being deployed in a few hot button scientific topics, they’ve metastasized over the whole body politic in multiple countries.

It’s to our shame that we science educators and science communicators didn’t figure out effective ways to deal with those kinds of issues.

Additional, 5 December 2016: A new piece in the Guardian about how algorithms are delivering news on the Internet convinces me that, in some ways, what we’re seeing in qualitatively different from the misinformation that scientists have faced for the past decade. It’s deeper and more organized.

I think there are still powerful lessons from science communication, though: when trying to persuade, facts alone are not very persuasive.

I worry that policy wonks will go through the same long battles over “facts” and “evidence” that scientists have, and just believe that the facts will speak for themselves. They won’t. Facts need fierce advocates.

External links

Google, democracy and the truth about internet search

Picture from here.

29 November 2016

Tuesday Crustie: Shiny

If I’d known Moana had a giant decorator crab in it, I’d have pre-ordered tickets.

Tamatoa also gets the second best song in the movie, although even it pales in comparison to “You’re Welcome.”

28 November 2016

Are footnotes a way to game the Impact Factor?

One of Bradley Voytek’s 99 problems is strange journal demands:

Major journal said we can’t cite biorxiv papers; instead must reference them via footnotes.

I have been rankled by journals’ refusals to cite non-traditional sources before. But this journal wasn’t refusing to acknowledge to a source. It was refusing to acknowledge a source in a certain way.

This puzzled me momentarily, but I have a hypothesis. Any time a journal talks about fiddling with citations, there is a prime suspect as to why: the journal Impact Factor. I strongly suspect that footnotes aren’t counted in the calculations of journal Impact Factor like terminal references are, even though footnotes and a reference list in this case would serve the same purpose: to credit a source so that people can find it.

What a journal might have to gain by keeping pre-print servers out of citations? It doesn’t enhance the journal’s own Impact Factor. It doesn’t enhance anyone’s Impact Factor, for that matter. Denying citations to pre-print servers seems futile, since pre-print servers don’t have Impact Factors.

While pre-print servers don’t have Impact Factors, including citations to them might make it easier to collect data about their use. There seems little doubt that the majority of citation analysis is done by text mining and algorithms, rather than by hand. (Notwithstanding the contention by Brembs et al. (2013) that Impact Factors are often negotiated.)

For journals, the very act of data collection about pre-print servers might feel threatening to them. There are some researchers who want journals to die across the board and wouldn’t mind if pre-print servers (or something like them) rose up to take their place. If it becomes clear through citation analysis that more and more studies on pre-printe servers are being cited as reliable sources of information, the uncomfortable question for journals arises:

“What are journals for, exactly?”

Update, 29 November 2016: Bradley Voytek reports that the situation has changed:

The journal editors discussed and changed their policies to allow preprints with DOIs.

How interesting.


Brembs B, Button K, Munafò M. 2013. Deep impact: unintended consequences of journal rank. Frontiers in Human Neuroscience: http://dx.doi.org/10.3389/fnhum.2013.00291

Related posts

Why can’t I cite Mythbusters?

Picture from here.

No lead is safe

I normally tell people that I hate football. But homesickness makes you do funny things, so I tuned into the last quarter of the Grey Cup last night.

I was rewarded.

At some point, when the lead was still pretty big for Ottawa, one of the commentators said a CFL motto was, “No lead is safe.” I sort of snickered when I heard that. I would not have believed Calgary could score two touchdowns is less than two minutes, with the last coming in with something like 20 seconds left on the clock to force the game into overtime. What a thriller! At that point, it didn’t matter who won, you just had a great championship game.

The Redblacks are new, formed after I moved to the US. I looked a few things up about the team while the game was in progress. When I went to Wikipedia, I wondered if I was on some sort of time delay, because the entry said, “In the 104th Grey Cup, the Redblacks brought the Grey Cup back to Ottawa for the first time in 40 years.” What...? But... but... the game was still going.

When I cam back a few minutes later to get a screen grab of the jumped gun, I saw someone already had some fun with Wikipedia (click to enlarge):

Of course, Redblacks had the last laugh on the irate wiki contributor, pulling off the overtime win.

Even this football hater can’t resist an underdog victory. Congratulations to the Redblacks on their first Grey Cup win!

External links

Redblacks pull off huge upset to win 104th Grey Cup in OT
Redblacks player lays on the field long after everyone leaves, perfectly wrapping up the Grey Cup

22 November 2016

Watch me now

A “watchlist” has one major job: to intimidate. And boy, Professor Watchlist does that in spades.

The mission of Professor Watchlist is to expose and document college professors who discriminate against conservative students, promote anti-American values, and advance leftist propaganda in the classroom. 

And just like that, we’re in a new era of McCarthyism. The website is horribly vague on what confirmation or vetting goes into this list, what an “anti-American” value is, or what constitutes “leftist propaganda.”

I agree with one thing on this list: professors shouldn’t discriminate against conservative students. Because professors shouldn’t discriminate against anyone.

But hey, conservative students, your ideas have to compete in the free market of ideas and be supported with facts and evidence. That is, conservative students, you don’t get to cry “Discrimination!” if I say, “Evolution is the best scientific explanation we have for diversity of life on this planet” because you happen to be a conservative young Earth creationist.

The website says it’s a project of TurningPoint USA, but the link to it is not always predictable. A link on Twitter informed me that this is the brainchild of one Charlie Kirk.

I clicked on one entry at random, and it linked out to a site called Campus Reform, which I’m pretty sure I’d seen before. It’s part of the Leadership Institute, which describes itself as “Training conservative activists, students, and leaders since 1979.”

I agree with Dr. Becca. Universities need to talk about sites like this, publicly. I was also toying with something Trina McMahon did: flooding the site with “tips.”

And perhaps this is an apt moment to repost this:

Update, 23 November 2016: One of the creators of Professor Watchlist, Alana Mastrangelo, is super happy that people have taken to trolling the “tips” section of the website. Free publicity.

Another creator of Professor Watchlist, Crystal Clanton claims that the tip line to inform the site’s creators, “I pray for your deaths every day.”

To anyone who would consider writing something like this:

You’re not helping. Knock it off.

External links

Professor Watchlist

The 21-Year-Old Becoming a Major Player in Conservative Politics (from 2015)
David Perry discussing the Watchlist
Heather Cox Richardson on being added to the Watchlist
Exposing 'crazy radical professors': 12 of the best #trollprofwatchlist tweets
Professor Watchlist Is Seen as Threat to Academic Freedom
Teaching in a time of professor watchlists
Academic witch hunts are back: The new McCarthyism, a sign of the stupidity of the post-truth era

21 November 2016

Keeping to schedule

My university publishes an academic calendar of holidays and exams well in advance of the semester. The university is closed this Thursday and Friday (American Thanksgiving). But since last week I’ve had a steady stream of students asking me if we are having classes on Wednesday, and I even got one asking me, “Are we having class today?” (Monday.)

My answer is, “Yes, the university is open and class is happening as usual, as per university policy.”

“Other professors are cancelling class that day.”

I cannot tell you how much this annoys me. I’m not so much annoyed by the students asking, but by my colleagues.

Professors who cancel classes because it’s close to a holiday aren’t being professional. People in other jobs and other professions don’t just get to randomly not show up to work. But professors can cancel class pretty much whenever they want. And someone would probably need to cancel a lot of classes before a department chair or other administrator caught on and commented. This is the sort of thing that gets legislators breathing down our necks with arguments that professors have no accountability.

It bothers me because students are getting short changed. Students pay tuition for a certain number of contact hour, and they should be upset that they are not getting the instruction and face time that they are paying for. I suspect that few students think of it this way, probably because many still see their relationship with professors as an adversarial one. A cancelled class is just less work, rather than missed opportunities to learn. Unfortunately, professors who cancel classes because it’s close to a holiday set a bad example and encourage this “classes are just another thing I have to do” view.

So no, my classes are not cancelled this week. Because I am a professional who takes my obligations seriously.

18 November 2016

How I learned advanced math from a fake documentary

Q. Are pseudoscience shows like Ancient aliens having a negative effect on the scientific literacy of Americans? (From Quora.)

If you want to rank the biggest negative impacts on the scientific literacy of Americans, I would not put pseudoscientific television documentaries on basic cable at the top of the list.

If you look at the issues where the public disagrees with scientists the most (climate change, evolution, vaccines, genetic modification of food), it’s not because they don’t have access to facts or that basic cable documentaries have mislead them. It’s because those issues have become political issues, and political leaders and political pundits actively promote narratives that are not scientifically justified.

That said, sensationalist TV shows like this do have an impact, and that effect is probably generally negative. Andrew David Thaler writes about some of the long term effects here: The Politics of Fake Documentaries. See also: Fish tales: Combating fake science in popular media.


Here’s the thing. This “ancient aliens” genre is not new. It reaches back at least to the late 1960s when Chariots of the Gods? was published, and the early 1970s, when books like this were published:

Now, I read that book as a kid. Yes, there’s a lot of rubbish in it, and I was pretty gullible. I thought a lot of it was plausible. Hey, what did I know, I was a kid. Did reading that book hurt my science literacy?

Well, in all the credulous interpretations of archaeological data (“This ancient gold trinket described as a bird, but it looks like a jet plane!”), there’s a chapter that I think was called “Shortcuts in space-time” or something like that. And that’s the chapter I remember most about that book. It introduced me to the concept of a tesseract. That’s real mathematics and real science, and it stuck with me because as I learned more, I learned that those ideas were real.

That book was unscientific. But it made me curious. And I learned some new science that I probably wouldn’t have otherwise been exposed to until university, if then. And when I got to university, I discovered The Skeptical Inquirer and learned to be a little less gullible.

I’m not arguing that those are a good means of science education. But they are works of art more than science, and art – and our reactions to it – are complex.

17 November 2016

Why is neuroscience teaching software so bad?

Neuroscience is a discipline that is very well suited to using computer models. There are all sorts of elegant mathematical descriptions of how neurons generate action potentials, how signals propagate along the length of a neuron, how signals from neurons add up and contribute to firing action potentials or not, and more.

So why do so many pieces of software created to teach neuroscience suck so much?

Now let me say this: the teaching value of the software is often excellent. The problem is that the implementation is rough, twitchy, and out of date. So maybe my question is better phrased as, why does neuroscience teaching software suck in the context of using them today, in 2016?

Let me give a few examples. This year and last I’ve used Swimmy (Grisham et al. 2008). Students have to crack the neural circuit that makes a fish swim. It is an awesome exercise that challenges my students intellectually.

But when it starts...

You’re presented an MS-DOS command line. 1990s memory whiplash right there. The interface consists of lots and lots of windows you have to resize manually. And the Mac version is so out of date that it doesn’t run properly any more.

I tried some software at The Mind Project, including Virtual EEG (Miller et al. 2008). Virtual EEG has a cool and interesting premise. You can create different sets of pictures (say, photos of objects and photos of people), and the program shows averages of real EEG data that was generated by people viewing those pictures. But, again, the interface is kind of clunky and twitchy. It’s written in Java, and it still runs, but I ran into some refresh issues such that screens often didn’t refresh and display properly. It all worked, but was such a chore to get to the stuff I wanted.

Realizing that these efforts were done the better part of a decade ago, I went looking for mobile apps.

I only found one promising candidate, Neuronify (pictured above). This one, at first glance, seemed very promising. It runs on Android and iOS. The user interface is very clean. But it feels more like a neurophysiological sandbox for playing around than a teaching tool. You build stuff rather than being puzzles to solve. The commands are very limited. You can inject current into a cell, but you can’t specify by how much, for instance. I’m sure I could put it to good use, but I need to think about how to use it effectively.

The contrast between teaching software and textbooks is profound. Textbook publishers have massive teams keeping the content and presentation up to date. There are new editions every few years. Say what you will about the cost, nobody would deny the typical university textbook is a professional looking, polished document.

Compared to the effort that goes into textbooks, most teaching software feels like the equivalent of a bunch of photocopied pages, printed off an old dot matrix printer, stapled together. It’s done by a small team, done once for some fairly specific teaching purpose, and nobody invests any effort in keeping up to date after it’s out and some small paper in an educational journal is published. So even those of us who decide to use the software have to pay the pixel tax.

I want students to struggle. But I want students to struggle with the inherent complexities of cellular neuroscience. Students don’t type in command lines to run Pokémon Go or Snapchat, and I don’t want them struggling with command lines in class. It’s the least important thing of all.


Grisham W, Schottler NA, Krasne FB. 2008. SWIMMY: Free software for teaching neurophysiology of neuronal circuits. Journal of Undergraduate Neuroscience Education 7(1): A1-A. https://mdcune.psych.ucla.edu/modules/swimmy/swimmy-extras/grisham-etal-junef2008.pdf

Miller BR, Troyer M, Busey T. 2008. Virtual EEG: A software-based electroencephalogram designed for undergraduate neuroscience-related courses. The Journal of Undergraduate Neuroscience
Education 7(1): A19-A25. http://june.funfaculty.org/index.php/june/article/viewFile/629/628

External links

The Mind Project (including Virtual EEG)
A pixel artist renounces pixel art

16 November 2016

The academic equivalent of “voter fraud”

In the recent American federal elections, some jurisdictions had relatively new legislation ostensibly aimed at preventing voter fraud. Critics argued that additional restrictions and costs made the laws more effective at blocking citizens with a legitimate right to vote than preventing people from voting illegally. And that the citizens preferentially blocked – usually poor people – were more likely to vote for the opposition party than the one that put the legislation in place.

And every study I saw indicated that voter fraud was vanishingly rare: 0.00000132% according to one study.

So huge effort is put into stopping a tiny number of potential cheats that possibly harms other honest participants in the system.

I’m wondering if the same can be said of higher education.

I was at a workshop for a teaching technology update yesterday. And when I’m at workshops like this, someone invariably launches into some sort of scenario – often quite an elaborate one – where students could use the technology to cheat.

It’s not that they necessarily have seen students cheating in the ways they describe, but they are worried that they could. So instructors go through contortions and set up elaborate safeguards and barriers and obstacles to try to catch cheats on the premise that cheating is pervasive.

The problem of cheating is not a problem created by students. The problem is created by higher education’s need to push a huge number of students through the system with as few instructors as possible. This forces instructors to use crummy evaluation techniques, like multiple choice pencil and paper exams.

As Yung Tae Kim reminds us, there is no cheating in skateboarding. You are evaluated on actual, immediate, real world performance, not pencil and paper tests. What would cheating in skateboarding even mean?

External links

The Misleading Myth of Voter Fraud in American Elections

Voter Fraud: Non-Existent Problem or Election-Threatening Epidemic?
Study Finds No Evidence of Widespread Voter Fraud
Yung Tae Kim: Skateboarding Physicist & Educator
Physics of Skateboading

Image from here.

15 November 2016

Peer review pariah, update

One of the good things about having a long running blog is that you rediscover stuff you wrote and can update it.

Back, um, “some time ago” (six years now crap I’m old), I dealt with the question of whether peer reviewers are overburdened. That is, there are too many papers and not enough people willing to review them all. At the time, I was suspect of the claims that being asked to review one to three papers a month was normal.

This question came up again on Twitter today. Since it’s been a few years, I wondered if I was still a pariah. I got the impression I was being asked to review more now...

And I am. The trendline is definitely upward. But it’s still far less than the “one to three papers a month” figure that people were claiming. I might hit the “one per month” around 2022.

I was part of the reviewer “talent pool” in the early 2000s, but got very few invites. I am the same guy now as then, so what’s changed? I think I’m getting asked to do more reviews because of the time spent in the academic system. And I was, luckily, able to step up my own publication game around 2010, which may have contributed to my “name visibility” among editorial boards.

I know some people on Twitter who are on journal editorial boards, and they do indeed complain about finding reviewers. But I wonder how well editors use the available talent pool. I would bet that journal peer review invitations are biased against:

  • Faculty who are not at American universities. (Update, 21 November 2016: Warne (2016) reports proportionately more peer review is performed by American researchers than Chinese ones.)
  • Faculty who are not at English-speaking universities.
  • Faculty at undergraduate institutions.
  • Post-doctoral fellows and graduate students.
  • Women reviewers.
  • Minority reviewers.

Update, 21 November 2016: Table 1 in Okike et al. (2016) shows more than ten men for every one woman reviewing manuscripts. Hat tip to Laura Jurgens.

Update, 5 December 2016: This tweeted list of “Top reviewers” from the journal Neurospsychopharmacology has nine men and one woman. Hat tip to Bita Maghaddam.

Update, 23 March 2017: Big new study in eLife by Helmer and coleagues (2017) supports that the hypothesis that “women are underrepresented in the peer-review process.”


Helmer M, Schottdorf M, Neef A, Battaglia D. 2017. Gender bias in scholarly peer review. eLife 6: e21718. http://dx.doi.org/10.7554/eLife.21718

Okike K, Hug KT, Kocher MS, Leopold SS. 2016. Single-blind vs double-blind peer review in the setting of author prestige. JAMA 316(12): 1315-1316. http:/dx.doi.org/10.1001/jama.2016.11014

Warne V. 2016. Rewarding reviewers – sense or sensibility? A Wiley study explained. Learned Publishing 29(1): 41-50. http://dx.doi.org/10.1002/leap.1002

Related posts

Peer review pariah

14 November 2016

Who’s going to hero up?

We tell the tale of heroes to remind ourselves that we also can be great.
John Wick, Legend of the Five Rings roleplaying game

Seriously, holy shit, how do you grow up loving Superman and think bullying is OK?

How do you read X-Men your whole life and think hating your neighbors because they are different is just fine?

How do you see every Star Trek episode and be riddled with xenophobia?

How do you have those people as your heroes your whole life, and then spit on everything they try to teach us? ...

My one slim hope is that maybe someday, something Spider-Man or Optimus Prime or Luke Cage said will get through and find a spark. Maybe be a reminder that most of our great fictional heroes wouldn’t behave like this.

They save people, they help people. They fight for people.

External links

How can you love Superman and still be an intolerant bully?
Superdames comics

10 November 2016

Favourite Quora answers

The search function on Quora sucks, and so I’m collecting some of my favourite answers here so I can find them again later.


Evolutionary biology

Academic writing