Various positions

What use is there in keeping a blog if you can’t post your arbitrary idiosyncratic opinions as if you were an authority? Here is a list of opinions about life in the scientific community.

Social media for scientists

People who promote social media for scientists by humblebragging about how they got a glam journal paper because of Twitter should stop. An unknown PhD student from the middle of nowhere must be a lot more likely to get into trouble than get on a paper because of Twitter.

Speaking of that, who thinks that that writing an angry letter to someone’s boss is the appropriate response to disagreeing with someone on Twitter? Please stop with that.

Poster sessions

Poster sessions are a pain. Not only do you suffer the humiliation of not begin cool enough to give a talk, you also get to haul a poster tube to the conference. The trouble is that we can’t do away with poster sessions, because they fulfill the important function of letting a lot of people contribute to the conference so that they have a reason to go there.

Now cue comments of this kind: ”That’s not true! I’ve had some of my best conference conversations at poster sessions. Maybe you just don’t know how to make a poster …” It is true that I don’t know how to make a good poster. Regardless, my ad hoc hypothesis for why people say things like this is that they’re already known and connected enough to have good conversations anywhere at the conference, and that the poster served as a signpost for their colleagues to find them.

How can one make a poster session as good as possible? Try to make lots of space so people won’t have to elbow each other. Try to find a room that won’t be incredibly noisy and full of echos. Try to avoid having some posters hidden behind pillars and in corners.

Also, don’t organize a poster competition unless you also organize a keynote competition.

Theory

There is way way way too little theory in biology education, as far as I can tell. Much like computer programming — a little of which is recognized as a useful skill to have even for empirically minded biologists who are not going to be programming experts — it is very useful to be able to read a paper without skipping the equations, or tell whether a paper is throwing dust when it states that ”[unspecified] Theory predicts …” this or that. But somehow, materials for theory manage to be even more threatening than computer documentation, which is an impressive feat. If you disagree, please post in the comments a reference to an introduction to coalescent theory that is accessible for, say, a biology PhD student who hasn’t taken a probability course in a few years.

Language corrections

That thing when reviewers suggest that a paper be checked by a native English speaker, when they mean that it needs language editing, is rude. Find a way of phrasing it that won’t offend that one native English speaker who invariably is on the paper, but doesn’t have an English enough name and affiliation for you!

The open access ‘Plan S’ is decisive action to do the wrong thing

Plan S (as Wikipedia puts it: ‘not to be confused with S-plan‘) is an plan by the European Research Council and other European research funders to promote open access publishing. They say that key idea is:

After 1 January 2020 scientific publications on the results from research funded by public grants provided by national and European research councils and funding bodies must be published in compliant Open Access Journals or on compliant Open Access Platforms.

What Plan S is doing right, in my opinion:

  • Research funders have realised that they have weight they can throw around. They can force change on publishers by telling researchers what to and deciding what they will pay for and not pay for.
  • They emphasise copyright and strong licensing (i.e. cc:by) that give readers the rights to use and reproduce.
  • They want publishing costs to be covered by funders, and be capped to be somehow reasonable.

What Plan S is doing wrong, in my opinion, can be summarised by quoting their ninth principle:

The ‘hybrid’ model of publishing is not compliant with the above principles

First, let us talk terminology. ‘Gold’ open access is where the journal is exclusively open access. ‘Green’ is when the journal may not be open access normally, but allows you to put up an accessible copy of the paper somewhere else, for example your friendly institutional repository. These labels unhelpful. They aren’t natural mnemonics, and as you might expect, they are used inconsistently. More importantly, author-pays full open access is not some higher form of publishing, so I wouldn’t call it ‘gold’.

‘Hybrid’ publishing is when only some papers in a journal are open access. This would not be allowed under Plan S. This would prevent publishing in Science, Nature and Cell. Depending on your stance on publishing that may be upsetting or encouraging. Of course, it would also disqualify a set of society journals like Genetics, Heredity, and Evolution.

Why, one might ask? Is it important that open access publishing happens only in exclusively open access journals? I guess the idea is to prevent library-pays journals from getting paid twice by also charging authors for some papers.

I think that is confusing a means with an end. The goal should be to get the most accessible papers with the least amount of effort, and to push scientific publishing in a positive direction. I am not sure that monolithic author-pays publishers are all that much better than monolithic library-pays publishers, so why should we give them a particular advantage?

In my opinion, a better option would be along these lines: We should accept preprints as a form of cheap open access, make sure to format our preprints a bit nicer (I’ve sinned against this by uploading double-spaced manuscripts with the figures at the end), and pressure subscription journals to accept preprinting of the final text without delay. Maybe one could even get journals to accept the preprints to be distributed under permissive licenses. This may be a tall order, but maybe no less realistic than trying to dictate the size of the publishing fee.

We could have the best of both: scientific communities could keep publishing in those quality society journals that all of our colleagues read, and everyone would get free and convenient access to papers. The problem of unreasonable subscription fees will remain, and that needs other plans for joint library and university action. For those of us that have a bit of an iconoclastic streak, it would also leave the field open for new ideas in publishing, rather than prescribing certain journals with a particular business model.

I’m looking at a life unfold
Dreaming of the green and gold
Just like the ancient stone
Every sunrise I know
Those eyes you gave to me
That let me see
Where I come from
(Lianne La Havas)

Reading Strunk & White

I don’t remember who, but someone wrote that people who hand out the advice to read Strunk & White’s Elements of Style probably haven’t read it—the implication being that it’s not as good as its reputation. The names of famous works and authors often work as metonymies for common wisdom more than as references to their content, not just Strunk & White, but Machiavelli, The Modern Synthesis etc. The journal GENETICS, where I recently sent a couple of papers, have Strunk & White as part of the guidelines for authors, so I decided to read Strunk & White.

This is from the part that the GENETICS guidelines refer to, namely the famous ”Omit needless words” section:

Vigorous writing is concise. A sentence should contain no unnecessary words, a paragraph no unnecessary sentences, for the same reason that a drawing should have no unnecessary lines and a machine no unnecessary parts. This requires not that the writer make all sentences short, or avoid all detail and treat subjects only in outline, but that every word tell.

This is some good advice that is apt for scientific writing. All the rules that deal with vigorousness and conciseness would make life easier for all us readers of scientific papers:

15. Put statements in positive form.
16. Use definite, specific, concrete language.
17. Omit needless words.
18. Avoid a succession of loose sentences.
19. Express coordinate ideas in similar form.
20. Keep related words together.

Scientific writing is often too roundabout and guarded. I think that happens not because we’re trying to worm our way out of criticism, but because we have misguided notions about style that we get from reading heaps of badly written papers, and can’t shake without effort.

But there is also a ton of advice that is tedious and arbitrary. A problem with learning from authorities is that we end up reifying their pet peeves. The Elements of Style is full of them. There’s this thing you do when you state your opinion: You try to express it forcefully (forcibly, I guess, according to Strunk), but you are not Kantian about it. You don’t expect it to be elevated to a universal law. If it were, especially without the conditions that applied to those opinions, you might be unhappy with the results. Yes, we should omit unnecessary words, but for some authors, it may be more pressing to look for words to add, to elaborate, explain, and exemplify.

The same is true for graph-making (where should the y-axis end? what is the best way to show proportions?), the proper way to email university teachers as a student, the placement of figures in manuscripts to be reviewed, … In the absence of evidence, we substitute opinion, loudly spoken.

Different ways to cite papers

The journals Genetics and Nature Genetics seem to take opposite views on citations. See first this editorial from Nature Genetics: ”Neutral citation is poor scholarship”. It is strongly worded in a way that is surprising and entertaining:

The journal deplores and will decline to consider manuscripts that fail to identify the key findings of published articles and that—deliberately or inadvertently—omit the reason the prior work is cited.

(All the emphasis in all the quotes was added by me.)

The passage that suggests a difference in citation policy occurs at the end:

Authors are of course free to select the literature that is relevant to their current work and to cite in their arguments only those publications that meet their standards of evidence and quality.

Genetics, on the other hand, says this in the instructions for preparing a manuscript:

Authors are encouraged to:

  • cite the supporting literature completely rather than select a subset of citations;
  • provide important background citations, including relevant review papers (to help orient the non-specialist reader);
  • to cite similar work in other organisms.

I’m sure the editors of Genetics also don’t support scattershot citation of tangentially related papers (as in ”This field exists [1-20]”), but they seem to take a different stance on how to choose what to cite.

I wonder what the writers of the respective recommendations would make of these, in my opinion delightful, opening sentences (from Yun & Agrawal 2014). Note the absence of hundreds of citations.

Inbreeding depression has been estimated hundreds of times in a wide variety of taxa. From this body [of] work, it is clear that inbreeding depression is common but also that it is highly variable in magnitude.

Clearly, obviously

This is my kind of letter to Nature:

This is a friendly suggestion to colleagues across all scientific disciplines to think twice about ever again using the words ‘obviously’ and ‘clearly’ in scientific and technical writing. These words are largely unhelpful, particularly to students, who may be counterproductively discouraged if what is described is not in fact obvious or clear to them.

Clearly, this is easier said than done. It is common writers’ advice to remove adverbs, and to a lesser extent adjectives. These words may be pointless filler words, and when they’re not, there is a risk of telling the reader what to think in a manner that seems impolite. But they also do some work to make the text flow, and prose without them can seem sterile and disconnected.

If we could also get rid of ”surprisingly”, I would be happy.

Prata svenska

Nu när jag inte alls behöver prata om genetik på svenska känns det plötsligt extra viktigt att tänka på det.

Helst skulle jag förstås vilja kunna prata om genetik på svenska med termer som är begripliga, smidiga och inte känns konstlade. Vad som känns konstlat är naturligtvis en smakfråga. Ska man skriva ”enbaspolymorfier” eller ”snippar”? Det första låter som kanslihussvenska och det andra är ett lustigt ljud med genitala associationer.

Jag kan komma på alla möjliga svepskäl att inte prata om genetik på svenska — ”det låter töntigt”; ”det finns inte ord” — men de är inte särskilt bra. Det är också såklart sant att någon som jag är bättre på mitt modersmål än ett andra språk jag lärde mig skolan, och antagligen både tänker och skriver mer effektivt och nyanserat på svenska än på engelska.

Vilka är de bästa källorna till svenska genetiska termer? Jag antar att de flesta svensktalande genetiker gör som jag och litar till en blandning av: vad vi hört äldre akademiker säga, uppslagsverk som Nationalencyklopedin och Wikipedia, Biotermgruppens lista, kanske KI-bibliotekets svenska MeSH-termer och, om allt annat tryter, översättning från engelska enligt eget huvud.

Genetisk terminologi har flera besvärliga egenskaper. Dels finns det många låneord från latin och grekiska — epistasi, pleiotropi, eukaryot, … — som antagligen inte direkt är självförklarande ens för den som kan latin eller grekiska. ”Epistasi” förresten … Biotermgruppen kallar det ”epistas”, KI-MeSH skriver ”epistasi” och Wikipedia ”epistasis”. Naturligtvis använder genetiker inom olika specialområden samma ord på olika sätt också. ”Pleiotropi” betyder tre olika saker (Paaby & Rockman 2013). Eller var det sju olika saker (Hodkin 1998)?

Sedan finns det massor av ord som betyder ungefär samma sak. Vad är skillnaden på ”variant” och ”allel”? Betyder ”gen” samma sak som ”locus”, eller är det ”variant” och ”locus” som betyder samma sak? Det beror på vem som svarar.

Och till sist verkar genetiker tro att att det hjälper läsaren, eller får dem att verka klyftiga, om de myntar massor av förkortningar. Och sedan helst, som med snipparna ovan, förvandlar förkortningarna till roliga små läten. Snipp och BLUP och tork och kvark voro sex små dvärgar.

Griffin & Nesseth ”The science of Orphan Black: the official companion”

I didn’t know that science fiction series Orphan Black actually had a real Cosima: Cosima Herter, science consultant. After reading this interview and finishing season 5, I realised that there is also a new book I needed to read: The science of Orphan Black: The official companion by PhD candidate in development, stem cells and regenerative medicine Casey Griffin and science communicator Nina Nesseth with a foreword by Cosima Hertner.

(Warning: This post contains serious spoilers for Orphan Black, and a conceptual spoiler for GATTACA.)

One thing about science fiction struck me when I was watching the last episodes of Orphan Black: Sometimes it makes a lot more sense if we don’t believe everything the fictional scientists tell us. Like real scientists, they may be wrong, or they may be exaggerating. The genetically segregated future of GATTACA becomes no less chilling when you realise that the silly high predictive accuracies claimed are likely just propaganda from a oppressive society. And as you realise that the dying P.T. Westmorland is an imposter, you can break your suspension of disbelief about LIN28A as a fountain of youth gene … Of course, genetics is a little more complicated than that, and he is just another rich dude who wants science to make him live forever.

However, it wouldn’t be Orphan Black if there weren’t a basis in reality: there are several single gene mutations in model animals (e.g. Kenyon & al 1993) that can make them live a lot longer than normal, and LIN28A is involved in ageing (reviewed by Jun-Hao & al 2016). It’s not out of the question that an engineered single gene disruption that substantially increases longevity in humans could be possible. Not practical, and not necessarily without unpleasant side effects, but not out of the question.

Orphan Black was part slightly scary adventure, part festival of ideas about science and society, part character-driven web of relationships, and part, sadly, bricolage of clichés. I found when watching season five that I’d forgotten most of the plots of seasons two through four, and I will probably never make the effort to sit through them again. The first and last seasons make up for it, though.

The series seems to have been set on squeezing as many different biological concepts as possible in there, so the book has to try to do the same. It has not just clones and transgenes, but also gene therapy, stem cells, prion disease, telomeres, dopamine, ancient DNA, stem cells in cosmetics and so on. Two chapters try valiantly to make sense of the clone disease and the cure. It shows that the authors have encyclopedic knowledge of life science, with a special interest in development and stem cells.

But I think they slightly oversell how accurate the show is. Like when Cosima tells Scott to ”run a PCR on these samples, see if there are any genetic markers” and ”can you sequence for cytochrome c?”, and Scott replies ”the barcode gene? that’s the one we use for species differentiation” … That’s what screen science is like. The right words, but not always in the right order.

Cosima and Scott sciencing at university, before everything went pear-shaped. One of the good thing about Orphan Black was the scientist characters. There was a ton of them! The good ones, geniuses with sparse resources and self experimentation, the evil ones, well funded and deeply unethical, and Delphine. This scene is an exception in that it plays the cringe-inducing nerd angle. Cosima and Scott grew after than this.

There are some scientific oddities. They must be impossible to avoid. For example, the section on epigenetics treats it as a completely new field, sort of missing the history of the subfield. DNA methylation research was going on already in the 1970s (Gitschier 2009). Genomic imprinting, arguably the only solid example of transgenerational epigenetic effects in humans, and X inactivation were both being discovered during 70s and 80s (reviewed by Ferguson-Smith 2011). The book also makes a hash of genome sequencing, which is a shame but understandable. It would have taken a lot of effort to disentangle how sequencing worked when the fictional clone experiment started and how it got to how it works in season five, when Cosima runs Nanopore sequencing.

The idea of human cloning is evocative. Orphan Black flipped it on its head by making the main clone characters strikingly different. It also cleverly acknowledged that human cloning is a somewhat dated 20th century idea, and that the cutting edge of life science has moved on. But I wish the book had been harder on the premise of the clone experiment:

By cloning the human genome and fostering a set of experimental subjects from birth, the scientists behind the project would gain many insights into the inner workings of the human body, from the relay of genetic code into observable traits (called phenotypes), to the viability of manipulated DNA as a potential therapeutic tool, to the effects of environmental factors on genetics. It’s a scientifically beautiful setup to learn myriad things about ourselves as humans, and the doctors at Dyad were quick to jump at that opportunity. (Chapter 1)

This is the very problem. Of course, sometimes ethically atrocious fictional science would, in principle, generate useful knowledge. But when when fictional science is near useless, let’s not pretend that it would produce a lot of valuable knowledge. When it comes to genetics and complex traits like human health, small sample studies of this kind (even if it was using clones) would be utterly useless. Worse than useless, they would likely be biased and misleading.

Researchers still float the idea of a ”baseline”, though, but in the form of a cell line, where it makes more sense. See the the (Human) Genome Project-write (Boeke & al 2016), suggesting the construction of an ideal baseline cell line for understanding human genome function:

Additional pilot projects being considered include … developing a homozygous reference genome bearing the most common pan-human allele (or allele ancestral to a given human population) at each position to develop cells powered by ”baseline” human genomes. Comparison with this baseline will aid in dissecting complex phenotypes, such as disease susceptibility.

In the end, the most important part of science in science fiction isn’t to be a factually correct, nor to be a coherent prediction about the future. If Orphan Black has raised interest in science, and I’m sure it has, that is great. And if it has stimulated discussions about the relationship between biological science, culture and ethics, that is even better.

The timeline of when relevant scientific discoveries happened in the real world and in Orphan Black is great. The book has a partial bibliography. The ”Clone Club Q&A” boxes range from silly fun to great open questions.

Orphan Black was probably the best genetics TV show around, and this book is a wonderful companion piece.

Plaque at the Roslin Institute to the sheep that haunts Orphan Black. ”Baa.”

Literature

Boeke, JD et al (2016) The genome project-write. Science.

Ferguson-Smith, AC (2011) Genomic imprinting: the emergence of an epigenetic paradigm. Nature reviews Genetics.

Gitschier, J. (2009). On the track of DNA methylation: An interview with Adrian Bird. PLOS Genetics.

Jun-Hao, E. T., Gupta, R. R., & Shyh-Chang, N. (2016). Lin28 and let-7 in the Metabolic Physiology of Aging. Trends in Endocrinology & Metabolism.

Kenyon, C., Chang, J., Gensch, E., Rudner, A., & Tabtiang, R. (1993). A C. elegans mutant that lives twice as long as wild type. Nature, 366(6454), 461-464.