30 January 2023

DORA at ten: Publisher ban roundtable

On a bit of a whim, I proposed an event for the 10th anniversary events around the Declaration of Research Assessment (DORA).

And they said yes?

And now I have to do this. Mark your calendars and if you’re interested in being part of the roundtable, email me!

Publisher bans and DORA

Publisher bans and DORA

Publishers like MDPI, Frontiers, and Hindawi have experienced enormous growth in the number of submissions from researchers, which would suggest they they are meeting needs of the research community and providing good value to researchers. But multiple institutions have told scientists that research in journals from these publishers will no longer “count” for assessment. Such policies suggest that these are “predatory” publishers that do not perform the basic functions of academic journals. The publishers dispute this, as do many authors whose work appears in their journals. Many authors believe that choosing where to publishing their findings is part of their academic freedom. Blacklisting publishers with hundreds of journals may be too blunt an instrument for research assessment and inconsistent with DORA. Are there cases where such bans are valid and useful to the community?

This event will be held as an online round-table discussion followed by a moderated Q & A session.

I’ve been ripped off! OMICS journal messes up my work

Matt Hodgkinson drew my attention of that fact that one of my articles on authorship has been ripped off and turned into mush by someone in OMICS. (Lightly edited)

Allied Business Academies, a.k.a. Allied Academies, are another publisher to avoid. Quelle surprise, as they’re a brand of the notorious publisher OMICS.

Compare: Zen Faulkes’s 2018 article, “Resolving authorship disputes by mediation and arbitration” with Laura Sandra’s 2021 article, “Alternative Dispute Resolution in Academic Publishing”, in Journal of Organizational Culture Communications and Conflict.

Ms. Sandra, of course, does not exist.

I am always glad when someone finds my work worthy enough to re-use, but I have to say: This is not what I had in mind.

It is weird to see my work in this garbled form. I can recognize some of the elements of my paper, but it’s like they’ve been put through a blender, no doubt to avoid setting off plagiarism detectors. My original paper was 7 typeset pages with 95 references. “Sandra’s” version is a page and a half with three references. 

I have not included a link to the OMICS article because they don’t need the clicks. Go read my paper instead. I think it has something useful to say.

Reference

Faulkes Z. 2018. Resolving authorship disputes by mediation and arbitration. Research Integrity and Peer Review 3(1): 12. https://doi.org/10.1186/s41073-018-0057-z

External links

Matt Hodgkinson on LinkedIn

Why my new paper on award-winning conference posters is short

You know, sometimes you have plans for a project. Big plans. And sometimes those pan out. And sometimes, you are pleased that at least something came out.

I have a new little paper about conference posters out today.

It started when Paige Jarreau wrote somewhere (can’t remember if I saw it first on her Twitter or a Slack channel) that she was going to be organizing a special collection on visual narratives in science communication. And I thought, “Hey, I could use this to make the point that even though posters are a form of visual communication, they are usually very heavy on text.”

I submitted an abstract for a proposal to see if it fit the project. I had an idea for checking out a few posters every week over the summer to build up a little database. 

I didn’t want just a hodge-podge of random posters. I wanted distinct sets that were publicly archived. I had already bookmarked a few conferences that archived their posters.

Then reality set in. Some of my bookmarks had already succumbed to link rot, and the posters were no longer available. The semester started, and it was a hard semester in terms of preparation. So instead of posters from multiple conferences, I ended up with just one conference. But I think it was an interesting set of posters, because they were award winners from one of the biggest conferences in the world. Surely these would be awesome!

I hadn’t gotten as far or as detailed as I originally planned. But this project had a deadline, and 50% of something is better than 100% of nothing. I wrote the paper and submitted it. 

Things got worse, time wise, when reviews came back. It wasn’t rejected! But then, not only was class preparation had gotten more time-consuming, not less. I just couldn’t get to the revisions. Then there was a family emergency, so I got an extension.

Unfortunately, I was already so far behind that I missed one opportunity to make the paper better. 

One reviewer suggested a work I hadn’t heard about. But it wasn’t online or in the library. And it wasn’t a short article. It would take time to read. I decided not to wait until I could get the interlibrary loan. I submitted the revision without it. I have since gotten the work and... argh, it was so on point. It would have been a completely logical thing to include and discuss in my paper.

It’s going to be one of those losses that will haunt me until I put it right somehow.

I hope the paper has something to offer. It gave me more ideas for how I could push forward with bigger, better analyses in the future.

Reference

Faulkes Z. 2023. The “wall of text” visual structure of academic conference posters. Frontiers in Communication 8. https://doi.org/10.3389/fcomm.2023.1063345

14 January 2023

Publisher bans: A repeating pattern of attack on academic freedom

Last week, a couple of websites reported that a couple of departments at Zhejiang Gongshang University were not going to count publications appearing in three large open access publishers: MDPI, Frontiers, and Hindawi.

The policy appears to be leaked from internal memos. I searched the university site for the memo, and Google reports a result, but it is hidden behind an institutional login, so I can’t see the rationale behind this move.

This is the third attempt I know of to stop researchers from using certain publishers. I say again, publishers. And this doesn’t include the Chinese Academy of Sciences flagging dozens of journals as “risky.” 

You know, back when European funding agencies were announcing so-called “Plan S” to promote open access publication, some folks got all huffy 😤 about how vital it was to academic freedom that researchers be able to exercise choice in where they chose to publish their results. How dare a funding agency tell a researcher that they can’t publish in journals like Nature or Science, just because they are not open access! 

If that principle of researchers being able to choose their journal is important, then we are seeing a lot of attacks on academic freedom. But not many people seem to care. Far from being concerned, a lot of researchers seem to think banning researchers from using particular publishers is a great idea. That’s kind of blowing my mind. 🤯

Have these people not heard of the Declaration on Research Assessment (DORA)? It says, we “need to assess research on its own merits rather than on the basis of the journal in which the research is published.” The same principle should extend to publishers. If we shouldn’t judge research based on the journal it is in, we shouldn’t judge research based on the publisher of the journal, either.

For what it’s worth, I’ve tracked a lot of the criticism of MDPI in particular here on the blog. There are valid reasons to be concerned about editorial practices. But on the other hand, I’ve read a lot of useful papers in journals from all three of the publishers that Zhejiang Gongshang University are trying to blacklist.

Hat tip to Mario Barbatti and Richard Sever.

P.S.—Weirdly, when I searched the university for references to this new policy, one of the hits was to an open access library that said, “Most of these papers come from internationally renowned publishing institutions, including Hindawi, PlosOne, MDPI, Scientific Research Publishing and some high-quality articles from Biomed.” (Emphasis added.) So the library knows not what administrators are doing?

Update, 18 January 2023: I ran a couple of polls asking if people considered being able to choose their publication venue to be important to their academic freedom.

People on Twitter voted “Yes” more than twice as much as “No.” The vote on Mastadon was smaller but even more lopsided.

External links

Related posts

University tells scholars what journals to publish in

31 December 2022

The mind of a worm, the mind of a human, and mind uploading

In 1986, a key paper on the nervous system of the nematode worm Caenorhabditis elegans appeared. It was a fairly complete description of the entire nervous system of the animal: it counted all the neurons (302 then) and a good first pass at counting neural connections (5000 chemical synapses, 600 electrical synapses, and 2000 synapses to muscles).

The paper was subtitled, “The mind of a worm.” 

This subtitle was despite there being nothing about the behaviour or internal states of the species. It was all anatomy.

I think it was called that for a couple of reasons. 

First, co-author Sydney Brenner was a playful writer. He wrote a great column for Current Biology for many years that often showed his wit.

Second, it represented a hope in invertebrate neuroethology that understanding the neural connections of an organism would allow you an almost complete ability to predict the behaviour of that organism. A few papers since have used the phrase “mind of a worm” in homage to the 1986 paper.

So the subtitle was probably a joke, but one the represented a real goal of invertebrate neuroethology: to crack the neural circuitry of animals. Then we’d understand behaviour.

Fast forward to 2022. Our understanding of nervous systems is better. Technology has gotten batter. But a preprint about C. elegans released this year says, “We find that functional connectivity differs from predictions based on anatomy.” 

Wait, what? Wasn’t the promise that that once we had the neural connections, we would have near omniscience about the behaviour of thise worm?

In the world of invertebrate neuroethology. this is kind of yesterday’s news. It’s been decades since neuroethologists gave up on the idea that neural circuitry alone would give you a relatively complete understanding of behaviour. I suspect that idea was already wobbly in 1986 but was pretty clearly abandoned by the 1990s. It was killed by things like the study of neuromodulation in the stomatogastric nervous systems of decapod crustaceans.

But it seems that the news has yet to reach other fields in neuroscience.

After my last post on mind uploading, Ken Hayworth helpfully sent me a link to an article he wrote about mind uploading. I appreciated the writing, particularly this concise summary.

The core of the scientific argument: I am my connectome and (aldehyde stabilized cryopreservation) preserves the connectome

Most of what I said in my review of a book length treatment of the connectome argument is relevant here. In brief:

Invertebrate neuroethology has already tested the connectome hypothesis. The connectome hypothesis didn’t exactly fail, but it certainly under performed. Knowing the connectome of a worm has not revealed the mind of a worm.

The only reason to think, “Sure, the connectome didn’t give us everything we wanted to know in small neural circuits in invertebrates, but it will totally work in humans” is special pleading.

External links

Vitrifying the Connectomic Self: A case for developing Aldehyde Stabilized Cryopreservation into a medical procedure (PDF)

References

Randi F, Sharma AK, Dvali S, Leifer AM. 2022. A functional connectivity atlas of C. elegans measured by neural activation. https://doi.org/10.48550/arXiv.2208.04790

Related posts

Brainbrawl! The Connectome review

If you know how to do mind uploading, please do tell us

 


27 December 2022

If you know how to do mind uploading, please do tell us

Here we go again.

Ken Hayworth is mad that more neuroscientists aren’t working on the problem of immortality.

(I)t is still really bugging me that we could ALL likely get to the future together (via quality brain preservation and far future mind uploading) if only the neuroscience community would start taking its own findings seriously and consider the implications.

He seems to think that neuroscientists are avoiding this topic because we are all secretly dualists?

Neuroscientists should not succumb to magical thinking about the mind/brain.

I don’t know any other working neuroscientists who think the brain in magic. Citation needed.

Neuroscientists should know that we already have the tools to preserve brains fantastically well at the ultrastructural and molecular levels using aldehyde fixation.

But Hayworth does not say how he can demonstrate that the current level of detail of preservation is “enough” detail. Sure, synaptic connections will be important. What about resting membrane potential? Gasotransmitter levels? Blood flow? Can any of those be captured in a static preserved brain?

Of course mind uploading will be possible in the future… just read the damn literature on models of brain function… they are all computational.

But Hayworth does not say how he can demonstrate how structural information can be converted into a computational model.

Why refuse to openly discuss/debate what should be considered the most important long-term application of your research?

Here I am, discussing it. I’ve answered a lot of questions about mind uploading on Quora. Let’s see... (Searches Quora) In no particular order:

Is mind uploading digital immortality a real possibility for the future?  

How is it possible to copy our brains into computers?

How realistic is mind uploading and what should I learn in order to research it?

Why is there no focus on uploading our brains to travel in efficient small spaceships? Should we fund mind uploading research for this end purpose?

Are we working on a way to upload brilliant minds in various scientific disciplines into a digital repository to hasten scientific advancement?

Does quantum computing make it possible to upload a neural net of your brain into a simulation so that when your body dies a copy of your brain itself could live forever in a computer network with other people?

Could thoughts and memories be digitalized at some point?

What is the current state of progress on mind uploading? What are the specific major obstacles and progress on each? 

How long will it be until I can upload my consciousness?

Why are people so against the idea of mind uploading and even question its possibility? 

Do any laws of physics prevent mind uploading?

What percent chance is there that whole brain emulation or mind uploading to a neural prosthetic will be feasible by 2048?

Will human consciousness ever be transferable to a new body or a machine e.g. a robot cyborg computer or avatar? Can-you transfer your own consciousness and memory and leave your biological body without creating two selves

Can the-mind be uploaded to a computer?

What do we need to know in order to be able to upload a human mind? 

It is like physicists refusing to discuss the possibility of fusion power plants. It is like NASA refusing to contemplate human settlements on Mars.

Rocket from Frau im Mond
Hayworth thinks mind uploading is a mere engineering problem – like space travel in the 1920s. It was pretty clear that you could get into space with a big old rocket. (A movie about going to the moon, Frau im Mond, was made in 1929.) Conceptually, we knew how to solve the problem. Creating the rockets was a mere engineering problem. 

But I argue that mind uploading in the 2020s is not like space travel in the 1920s. “Mind uploading” is an unsolved conceptual problem, as far as I can see. That is, it’s more like NASA admitting they don’t know how to create artificial gravity or faster-than light travel than refusing to think about sending humans to Mars.

Liquid fueled rockets were flying in the 1920s. What’s the “mind uploading” equivalent of Goddard’s rocket? Can Hayworth point to a single working model of taking a preserved nervous system and successfully reconstituting it as a complete digital model that can faithfully reproduce behaviour?

For me, science is the art of the solvable. If there is anything I have learned in science, it’s that the only way to tackle big questions is by tackling small questions.

And I am selfish. I want to contribute to problems I can solve in my lifetime. Or, at least, see some significant progress towards solving. I don’t want to chase pipe dreams of the “far future.”

Many a career has been wrecked on the rock of “big ideas.” Immortality is a exactly such a rock. 

 Do you have scientific objections that will stand open scrutiny?

Wait. Burden of proof is on the claimant. If Hayworth thinks mind uploading is possible, it is up to him to specify why it is possible. In considerably more detail than a six tweet thread.

Human life not worth saving?

Hayworth may consider a biologically based computer model to be a life. But many will not. Nowhere in his description is how this “uploaded mind” will interact with the world. Hayworth probably considers Alex Murphy’s existence in RoboCop not just acceptable, but positively luxurious:

Alex Murphy’s remaining body in RoboCop (2014) showing he has his head, lungs, and little else.

I don’t think a disembodied simulation of a dead brain warrants the name “life.”

Related posts

Overselling the connectome

Brainbrawl! The Connectome review

Brainbrawl round-up

“Mind uploading” company will kill you for a US$10,000 deposit, and it’s as crazy as it sounds

22 December 2022

Belated Dalek Day

 Ooh, it’s been a while since I’ve used the “personality quizzes” label on here...

Yes, I am a day behind on Dalek Day, the 59th anniversary of the best television monsters. I should have posted my results for the “Which Dalek are you?” quiz yesterday, but better late than never.

You are... the Emperor Dalek! A true leader of armies, the face of the mighty Dalek Empire, you are truly unstoppable! Although confident and often grandstanding, you are bred for war and the ultimate conquest of the entire galaxy.  However, not all empires (and Emperors) last forever…


19 December 2022

Grad schools should not require students to publish to graduate

Indian flag with "Truth alone triumps" in Hindi
Times Higher Education and other news venues is reporting on changes to doctoral programs in India, one of which is not requiring doctoral students to publish work as a requirement to graduate. This change was recommended back in 2019, but only just took effect.

While this is described as maybe the most controversial of several reforms to India’s doctoral programs, only one person is quoted speaking against it.

Dr Mukherjee said that this was the wrong approach. “If we want good quality research, and are worried about the rise of predatory journals that cash in on the students’ need to publish, the concern is the predatory journals,” she said.

Most of the article is about what students have to do to enter doctoral programs, not about what you need to do to complete it.

The news story is a good kick in the pants to me to finish this post, which I have been thinking about and drafting for months. Because India is far from the only place that has been requiring its doctoral students to publish papers to get their degrees.

A while ago, I asked about what graduate programs required their students to publish before they were eligible to graduate. I was surprised that the practice was quite widespread, and by the number of publications some institutions require their students to put out to graduate.

The highest requirement reported was three first-author published papers with two more submitted (five total). Another reported authorship on four papers, of which two have to be first author. But even requiring a paper or two was much more widespread than I expected.

This replies to my Twitter thread were abundant and helpful, so you might want to look through them.

A little later, DrugMonkey ran a poll that indicated a little more than half of programs required a publication to graduate.

To be blunt, I think requiring publications before a degree is awarded is bad, and I think India made the right move.

Publication requirements are extremely unfriendly to students. Neither a student nor supervisor nor university has any control over the peer review and editorial process. So it is entirely possible for a student’s graduation to be delayed through no fault of the student. And there is a real financial cost in many cases for students have to pay tuition and expenses for extra semesters, when all the work is done.

Worse, there is a completely predictable outcome of publication requirements. A publication requirement creates an incentive for fast publication and high acceptance, both of which are most easily achieved by shoddy work and editorial shortcuts.

Researchers found 88% of “approved” journals were problematic. India Express reported  did other investigations that suggested India was a major source of articles for dubious publishers. More than one person has suggested that such requirements are partly responsible for the enormous growth of MDPI and similar publishers.

I am annoyed hearing researchers loudly tell others not to publish in MDPI or Frontiers or what have you, and then get upset that these publishers are growing all the time. But they don’t seem to look at things like graduate publication requirements that create a vast, worldwide market for the services of journal articles where decisions are fast and acceptance is likely.

I completely understand the counter arguments. Training a student to produce professional level academic work is the point of a doctorate. The best way to prove that work is publishable is to publish it. It is harder to argue, “That shouldn’t have been published” than “That won’t be published.” 

I also get that public institutions are always being asked to justify their expenses to prove they are not wasting taxpayer money. Journal articles are a “product” that is easily tracked and counted.

I am all in favour of getting graduate students to publish. This should absolutely be the goal and students should be encouraged – or even pushed (with kindness) – to write up work and get it in the hands of editors. 

But Goodhart’s law comes in action once again. When something becomes used as a measure, it stops being a good measure.

Reference

Patwardhan B, Nagarkar S, Gadre SR, Lakhotia SC, Katoch VM, Moher D. 2018. A critical analysis of the ‘UGC-approved list of journals’. Current Science 114(6): 1299-1303. https://www.jstor.org/stable/26797335

External links

India axes publication goal for PhDs to tackle predatory journals (Registration required)

Not mandatory to publish in journals before final PhD thesis: UGC

No paper, no PhD? India rethinks graduate student policy

10 December 2022

New podcast interview on aquarium crayfish

Have you ever wondered what would happen if you released your pet out into the wild? Unfortunately, certain animals are dangerous to introduce into new ecosystems. Out of the one hundred worst invasive species in Europe, seven are species of crayfish. Crayfish are commonly traded as aquarium pets, but sadly, they are often mishandled and released into non-native environments. Being a keystone species, their introduction drastically damages these ecosystems. Despite this, the crayfish pet trade is a poorly regulated process that encourages irresponsible pet trading. Zen Faulkes elucidates and offers solutions for the flawed crayfish trade. Using the advertising websites Kijiji, eBay, Craigslist, and Aquabid, Faulkes monitored crayfish sales and found that, indeed, non-indigenous species are being sold in Canada, as the top selling species, Marmorkrebs, is not native to North America. Additionally, legislation did not guarantee a decrease in sales and was not well enforced. Faulkes continues to monitor crayfish sales and their effects as new legislation develops in hopes of raising awareness and assessing the risks related to this pet trade. Faulkes recommends using a multi-pronged approach to address this issue, encouraging low-risk trade, law enforcement, and education. Bringing awareness to readers is the first step in this process, so be responsible pet owners, and don't release your aquarium pets into foreign waters.

Back in October, I recorded a podcast interview with three University of Ottawa students about my papers about crayfish in the aquarium trade. It was tons of fun to do, and I hope that comes across in the recording!

BEaTS Research Radio's Podcast: Come to their aid! - The crayfish pet trade - Special Episode

https://beatsresearchradio.buzzsprout.com/591520/11837184

Thanks to Julie Pan, Malithi Thanthridge, and Ishika Tripathi for their great questions, and editing our conversation down to a tight 15 minutes.