Jargon I can take – its abbreviations I can’t stand

Posted on March 24, 2010 by Austin

NN blogger Jennifer Rohn has been writing recently about the use of jargon between scientists. As she points out, one of the points is to convey information succinctly from one person familiar with the vocabulary to one or more others who are equally familiar.

As I commented over at her post, I can live with the jargon. though it is important to be able to “translate” where necessary – as anyone who teaches undergraduate students, and/or who does any kind of public science communication, will be aware. Jenny made the latter point again in a recent follow-up comment.

This kind of “ability to talk parallel languages” thing is not taught very directly in science courses, which is sometimes a shame. Needing to be able to explain something in simple language can often be an aid to understanding. I am reminded of the undergraduate of a few years back who told me in a talk he was giving that researchers had worked out the transmembrane domain structure of the Cystic Fibrosis (CFTR) protein “by hydropathy analysis“. The way the student presented this made it clear he thought it was an experimental technique providing empirical evidence, rather that a predictive system (educated guessing) about the arrangement of the protein into domains and their topology through the membrane – predictions that would then need to be validated by biochemical and other experiments. If the student had known he would need to be able to explain the method, rather than just saying “hydropathy analysis”, then he probably would have understood the difference. Another way to see this, of course, is as a particular example of that old line:

“You never really understand something properly until you have to explain/teach it to someone else.” – a view I have a fair bit of sympathy with.

Medical courses are probably clearer than science ones about the need to be able to talk the parallel languages of “lay” and “jargon”. There is a famous line about medical students leaving University with twice the vocabulary that they started with, since they have acquired several thousands words’ worth of techno-medical-ese. But of course they also require the ability to explain things to people (i.e. patients) in plain language, so this is something one stresses over and over in the medical course, and indeed tries to test.

Anyway, I can live with jargon in science – just about – for the reasons Jenny and others have given. I feel less tolerant, however, of the mounting plague of abbreviations. In particular, the biochemists’ and molecular cell biologists’ relentless enthusiasm for abbreviations gets to me. I reckon that abbreviations are less universally recognised between scientists in related but different fields than are jargon technical terms, and I get particularly annoyed when people use tons of abbreviations in seminars without clarifying what they mean. I remember going to one seminar about vesicular trafficking in which the speaker used a dozen undefined abbreviation (I was counting) within the first ten minutes, comprehensively losing absolutely anyone in the audience who was not a trafficking fiend. You can probably imagine that the following forty minutes felt more like several hours.

I suspect I am not the only one who feels this way about abbreviations. To put the grumbling a bit more humorously, here is a tongue-in-cheek piece on the subject, written by a close friend of mine who writes occasionally in Physiology News under the pseudonym “Mark Cain”. It is a few years old now, having originally appeared in the Autumn of 2001.

I somehow doubt, though, that the number of abbreviations doing the rounds has decreased in the intervening years.

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“WHO IS JACK STAT ANYWAY?”

Here’s a question. Why can’t scientists communicate with one another (let alone with the public) without a bucketload of meaningless abbreviations?

How many times have you sat in a seminar when you realise the speaker has just used, without defining it, an abbreviation you’ve never heard of? And you’re lucky if it’s just one. Usually there are a whole bunch of abbreviations together. They come in packs, like buses do when you’ve been waiting in the rain for half an hour.

I hate abbreviations. I hate everything about them. I hate reading them in papers. I hate having to look them up in the huge lists printed at the start of papers. I hate hearing them in seminars.

Especially when I’ve just woken up and realise I’ve missed a full ten minutes-worth of choice abbreviations.

To add to the confusion, there are now so many abbreviations floating about in the biosciences that one finds the same, or almost the same, abbreviation meaning two completely different things.

An example: SOCS can stand for Suppressor of Cytokine Signalling or “Store-Operated Channels”.

But of course, getting scientists to break off their love affair with abbreviations is a bit like asking a roomful of 40-a-day smokers to quit. We users have all kinds of reasons why we need our abbreviations. It saves space in the journals. It stops us having to repeat long incomprehensible phrases, which can now be replaced by long incomprehensible abbreviations. The abbreviations are a shared coded language, serving to identify “people like us” – the ones who can understand the abbreviations. And of course abbreviations are useful in social situations when we’re talking to other scientists (i.e. people like us).

So despite the efforts of a few abbrevation-phobic journals – like the British Journal of Pharmacology – it seems unlikely that we will ever be able to kiss abbreviations goodbye. So I suppose I’ll have to learn to love them. Which raises the question: do they have any redeeming features?

Well, once in a while. Mainly when they make you laugh. Because a really choice abbreviation can conjure up something entirely different from what the person who coined it intended.

For instance, an abbreviation may sound ugly – like the distinctly nasty-sounding ECAC (“E-Cack”). Or illegal, like CRAC (“crack”). In fact there is a whole sub-family of abbreviations which could be confused with illegal substances, including ICE (interleukin-converting enzyme in scientific circles, a kind of amphetamine in parts of the USA) and JNK (“Junk”, no explanation necessary, or Jun N-terminal kinase).

Personally, I blame the biochemists for all this abbreviation business. Seriously, the rot started when the first biochemist was allowed to get away with referring to a protein by an abbreviation referring to its molecular weight on a gel. Because now we’re stuck with p53, p70, p120, p126 and innumerable others. Ever since that first p-something, biochemists have been the shock troops of abbreviation-ism. Biochemists love their abbreviations. And cell biologists are just as bad. Jak/Stat/Myc/Fos/Jun/Fyn – it sounds like a TV drama about flat-sharing young people with annoying nicknames. You can almost imagine the dialogue:

Hiya. Been out?

Yeah. Down the pub.

c-myc?

See Mick? Yeah – he’s coming over about six for a beer

c-fos?

See Fozz? That no-mark? We’re not inviting him, are we?

What about Fyn?

Finn the Irish lad? Not likely, mate.

Nah. And we’re not letting that !*!! Jack Stat tag along either.

Posted in Annoyances, Humour, The Life Scientific | Tagged | 24 Comments

They’ve got (a) form for that

Posted on March 5, 2010 by Austin

One of the things UK academics can probably all agree on – apart from that they are not yet entirely convinced by NN’s new MT4 blogging platform – is that meaningless oversight, audit, form-filling and box-ticking has risen inexorably in the last decade.

It seems that the Times Higher Education agrees as well: read one of the best leader articles I have seen in the THE for a while and you will get what I mean.

Red Tape: A Form of Distrust

Academics are vociferous in their condemnation of bureaucracy, especially when it tries to measure the unmeasurable. Obviously, higher education must be accountable to its public paymasters, but if the audit becomes the goal, human nature is such that people will put more effort into the things that can be audited – never mind the quality, feel the paperwork….

But banal and mind-numbing though it is, bureaucracy isn’t neutral. It is insidious, changing the nature of both teaching and research; it also, of course, has been used to push academics in uncomfortable directions.

The comments after the article make interesting reading. It appears that University administrators think the academics should stop bloody whingeing and do what the administrators tell them. For their own good, you understand. And because administrators know best.

The academics, as you would expect, are not impressed by what the administrators say.

A senior academic commenting as “Mark” sums it up nicely:

“In so many cases, the main justification for the paper work is that “we have to be seen to be doing”.  In other words, it doesn’t actually matter if the monitoring is working, it just matters that we have a sufficient paper trail to prove to others that we are doing it.”

To which I suspect many UK lecturers – in science and other subjects – will be shouting:

“Yes!”

Not, sadly, that that seems likely to change any of this rubbish anytime soon.
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PS If you didn’t spot the rather feeble pun in the title, read the definition here.

Posted in Annoyances, Grumbling, Universities | Tagged | 4 Comments

Tragic multiple shooting at the University of Alabama puts academic tenure review in the spotlight

Posted on February 13, 2010 by Austin

The US news networks, Twitter, and now US-based science blogs are aflame with the story of American neuroscientist and nitric oxide researcher, Dr Amy Bishop, who is reported to have been charged with murder after a mass shooting at the University of Alabama campus at Huntsville yesterday (Friday) afternoon. Nature’s Great Beyond blog has also carried the story

The facts are obviously still emerging, but those that seem clear are:

– Three members of the UoA Faculty (academic staff) are dead, and three other people are in hospital, two in critical condition;

– Dr Bishop, a tenure-track Assistant Professor in the Department, has been charged with capital murder;

– The shootings occurred at a Faculty (staff) meeting around 4 pm Friday;

– Bishop was up for academic tenure (i.e. was under consideration for confirmation in post for life or alternatively for being “let go”).

Several news stories reported that Bishop had heard on the Friday morning that she had been turned down for tenure. The New York Times reports that “according to a faculty member”:

”[Bishop] had applied for tenure, been turned down, and appealed the decision. She learned on Friday that she had been denied once again.”

Various reports claim that Bishop attended the Faculty meeting in the afternoon, when the shootings occurred. Those killed in the shooting were biology department chair Gopi Podila and professors Maria Ragland Davis and Adriel Johnson. A 9 mm handgun was reported to have been recovered from a rest room after the shootings. Other reports stated Bishop then called her husband, biotech start-up scientist Jim Anderson, to come and collect her. She was reportedly arrested in the parking lot.

Anderson and Bishop have four children.

In the latest twist, and one worthy of a novel or movie, several US news outlets carried a Boston Globe report that the Harvard-educated Bishop had been involved in the death by shooting of her younger brother in Massachusetts in 1986, when she was 20 and her brother was 18. The shooting was ruled accidental.

An updating news thread on the case can be found at the Huntsville Times website. while dicussion of the case is underway over at Science Blogs here at Pharyngula, or here, or on the open thread here. There are also blogs that have been looking at what Bishop’s students said about her on sites like ratemyprofessors.com

Some discussion, unsurprisingly, concerns the stresses of the US tenure review system. Gun control on US campuses and beyond is also being debated. I think what most caught my eye was that in the first online story I read about the tragedy on a US news network website, a UoA Huntsville student was quoted as saying they felt unsafe:

“Because campus authorities would not allow [me] to bring my own gun onto the campus.”

Posted in News, Universities | 56 Comments

Charles Darwin, the physiologists, and the Physiological Society – from the 1870s to the present

Posted on December 23, 2009 by Austin

Here is the Darwin piece I promised to kick the blog off properly. It started off as a piece for Physiology News, but has been adapted and extended. It isn’t quite finished to my satisfaction, and I am a little apprehensive that Henry (Gee) will tell me loads of it is wrong… …but I think I had better post it or it will not make it in 2009 at all.

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The year now drawing to an end marks the bicentenary of the birth of Charles Darwin (12 February 1809 – 19 April 1882), as well as the 150th anniversary of the publication of his most celebrated work, On The Origin of Species, which went on sale to booksellers on 22 November 1859.

Given the central position of evolution and natural selection in our understanding of biology, Darwin obviously has a strong claim to be the greatest of all biologists, English or otherwise. Both Science and Nature published a range of features celebrated the anniversary of Darwin’s birth early this year, as did most newspapers.

Much or all of the above will be known to most, or even all, NN readers. Some may also know that Darwin was a friend of the founders of the Physiological Society. I doubt many will know that he was elected as one of the first two Honorary Members of the Physiological Society at the Society’s third ever, and first formal (with a rule book) meeting. But Darwin’s connections with the Physiological Society, and its early members, also encompassed many detailed scientific exchanges.

Following his early voyages, Darwin spent most of his later career in his home at Down House in Kent, maintaining a voluminous scientific correspondence and many scientific collaborations. The Darwin correspondence project tells us:

“Darwin exchanged letters with around 2000 individuals over his lifetime…He rarely attended meetings of scientific societies, typically spent only two weeks a year in London, and only occasionally received fellow scientists into his home. And yet he was arguably one of the best informed scientists of the day…”

Darwin and the physiologists

Darwin’s long-term correspondents included John Burdon Sanderson, Professor of Physiology at UCL and latterly in Oxford, with whom Darwin discussed the possible use of electrical signals in plants. A younger physiologist who corresponded with and visited Darwin frequently was George Romanes (1848-1894), best known for his work on the locomotory system (muscles and their control) of Medusae (jellyfish).

Darwin’s interactions with Sanderson, Romanes, Michael Foster (founder of the Cambridge Physiological Laboratory and thus of the most celebrated “school of physiology”), and others amongst the founding members of the Physiological Society, are well described in a fascinating 1970 article by RD French, “Darwin and the physiologists, or the medusa and modern cardiology”. The article discusses the extent to which Darwin’s ideas on evolution and natural selection were absorbed by, and influenced, the physiologists of the second half of the 19th century.

We should remember that the term “physiology”, as it was used in the 1870s, would have included what we would now think of as biochemistry and pharmacology, and indeed cell biology. The early issues of the Journal of Physiology in the 1880s and 1890s are notable for a much wider range of subjects, and experimental organisms, than has been typical in the last 20-30 years.

Of the physiologists who corresponded with Darwin, Romanes’ work on jellyfish had a particularly clear evolutionary underpinning, as the analogies of the jellyfish “muscular bell” with rhythmic muscular systems in higher animals were obvious. As an example of these analogies, French’s article explores the influence of Romanes’ ideas upon the theories of cardiac conduction and rhythmicity then being developed by Walter (WH) Gaskell and others.

The Darwin influence is clear in the opening words of a celebrated August 1883 paper by Gaskell on tortoise heart. This paper was one of a series that demonstrated the “intrinsic rhythmicity” of the heart in higher animals (i.e. that rhythmicity was a property of the heart itself and not dependent on control from the brain and nervous system), and also the fact that the heart had not one but several sequential pacemakers, with the beat rate of the “highest” (fastest) pacemaker entraining (governing) the others. Writing little more than a year after Darwin’s death, Gaskell states:

“The views held by physiologists upon many points connected with the innervation of the heart have been too exclusively based upon observations upon a single type of heart, viz. that of the frog. It is therefore very advisable wherever possible to control these experiments by a corresponding elaborate series of observations upon the hearts of a large number of other animal types, and in this way to trace the evolution of function in the same way as the morphologist tracks that of structure.” (emphasis added)

Darwin and the Physiological Society

Perhaps Darwin’s greatest gift to physiologists, and to the fledgling Physiological Society, was his unequivocal support for animal experiments as a way of making advances in physiology and medicine. The founding of the Physiological Society was a direct result of the late Victorian vivisection controversy, and the 1875 Royal Commission on vivisection. Those interested in this history can find a summary of it on the Physiological Society’s website. The Royal Commission’s report became the basis for the Cruelty to Animals Act of 1876, which established the system of licences for experiments on living animals. Darwin gave evidence in person to the Royal Commission, stating his belief in the need for animal work:

“I am fully convinced that physiology can progress only by the aid of experiments on living animals. I cannot think of any one step which has been made in physiology without that aid. No doubt many surmises with regard to the circulation of the blood could be formed from the position of the valves in the veins, and so forth, but certainty such as is required for the progress of any science can be arrived at in the case of physiology only by means of experiments on living animals.”

Darwin went on to clarify that he was referring to experiments in which animals were properly anaesthetised, and to express his surprise at objections to such procedures:

“It is absolutely unintelligible to me on what ground the objection [to these experiments] is made in this country.”

The physiologists were very appreciative of Darwin’s support. The first informal meeting to discuss the founding of the Physiological Society, which took place at Burdon Sanderson’s London home on the 31st March, 1876, was attended both by Darwin’s most prominent scientific disciple, Thomas Henry Huxley, and also by Darwin’s third son Francis Darwin (1848-1925), then 28 yrs old. Francis Darwin, who assisted his father in much of his research and ultimately became a distinguished botanist and FRS, had been working for his MD Thesis in one of the London physiological laboratories. The meeting reconvened a few weeks later on April 26, with Huxley chairing, to ratify a rule book, including the rule that:

“Men of distinction in Science who have contributed to the advancement of Physiology are eligible for election as Honorary Members.”

The third preliminary meeting, held at Romanes’ house, identified those “who shall be invited to become members and attend the next meeting of the Society.” This group included both Thomas Huxley and Francis Darwin. The meeting also resolved to elect Charles Darwin as one of the first two Honorary Members. [The other was the early physiologist William Sharpey (1802-1880)]

Darwin later wrote to Romanes (on 29 May):

“I was very much gratified by the wholly unexpected honour of being elected one of the Honorary Members [of the Society].This mark of sympathy has pleased me to a very high degree”.

Darwin remained unswerving in his support for animal experimentation until the end of his life. In a celebrated letter published in the Times in 1881, a year before his death, he wrote:

“I know that physiology cannot possibly progress except by means of experiments on living animals, and I feel the deepest conviction that he who retards the progress of physiology commits a crime against mankind.”

This letter can be read at the Times online archive, along with accompanying material and a commentary by former Physiological Society President and Head of the MRC Prof Colin Blakemore.

Darwin’s death in 1882 was a cause of great sorrow among the scientific men of the day, including at the Physiological Society. Edward Sharpey-Schafer in his extended history of the early Physiological Society records the feeling of the members present at the following meeting:

“With respect to [Charles Darwin’s death] the draft of a resolution occurs in the Minute Book, written in pencil and nearly illegible, which probably expresses an attempt then and there to voice the feelings of the Society… The draft reads as follows: ” The effect produced in the scientific world by the death of Charles Darwin is so universal and profound that any formal motion in reference to it by this little Society would appear to be superfluous, if not impertinent.”

The same meeting in 1882 elected several new Honorary Members including, perhaps a little symbolically, Thomas Huxley. Huxley and Francis Darwin continued to attend Physiological Society Meetings thereafter, and physiology in the late 19th and early 20th century was also indebted to Darwin’s fifth son Horace (1851-1928), founder of the Cambridge Scientific Instrument Company, which manufactured apparatus for many of the Cambridge laboratories. Apart from these direct ties, a reading of Sharpey-Schafer’s history makes clear that the approbation and involvement of men of the standing of Charles Darwin and of Thomas Huxley was of great importance to the fledgling Physiological Society.

From the 1870s to the present day

Perhaps an appropriate place to close this brief summary of Darwin’s ties to physiologists and the Physiological Society is an editorial in Science earlier this year by past President of the Royal Society Robert (Baron) May and Paul Harvey. They noted:

”… Dobzhansky’s memorable injunction that nothing in biology makes sense except in the light of evolution.“

One can, I think, see their dictum exemplified in diverse ways in papers in the physiological journals down the years. In the words and ideas of Victorian physiologists like Gaskell; in the use of invertebrate preparations like barnacle muscle and the squid giant axon for the seminal studies of Hodgkin, Huxley and Katz on action potentials; in the comparative sequence analyses presented in modern papers studying the structure-function relationships of ion channels; and in countless other places.

Indeed, with the widespread availability of genome sequences, I think that there is likely to be an increase in cross-species perspectives on physiological function – at least at the level of individual proteins – over the next decade or two. So two hundred years on from his birth, Darwin’s influence on physiology is not just still present. I would say it was undergoing a revival.

Some years ago the evolutionary biologists in my own University caused a furore when they argued, in a curriculum review, that all our degrees in biological and biomedical sciences should be explicitly themed round evolution and natural selection. The furore was because they also argued that overall teaching time devoted to different phyla should be in direct proportion to the “amount” of the natural world that different phyla represented.

The idea never caught on, perhaps understandably in an era when it is biomedical sciences (and thus implicitly the study of humans and higher mammals) that largely drive undergraduate student recruitment into life science degrees – something that a lot of people, me included, pointed out to them

But I think I can see what they were getting at.

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REFERENCES

French RD (1970). “Darwin and the physiologists, or the medusa and modern cardiology” J of the History of Biology 3:253-274.

Gaskell, W. H. (1883). “On the Innervation of the Heart, with especial reference to the Heart of the Tortoise” J Physiol 4: 43-230

May RM & Harvey PH “Species Uncertainties” Science (2009) 323: 687.

Sharpey-Schafer E. (1927). “History of the Physiological Society during its First Fifty Years, 1876-1926. Part.1.” J Physiol. 1927; 64 (Suppl): 1–76.

PS A note on references and hotlinks:

I just spent about 2 hrs putting a lot more of these in, but forgot to save… and a browser crash blew the whole lot away. I thought I had saved it, actually, but I am learning my way around the NN blogging platform and it turns out I hadn’t. But I am staying calm. When a long-ago computer crash ate my PhD Thesis reference list that I’d spent two days typing in, I kicked a filing cabinet and put my back out for three months. So I’m staying calm. Anyway, the piece therefore appears here without a lot of the links, which I will add as I find the time. Sorry.

Posted in History, Physiology | 5 Comments

RIP Dan O’Bannon

Posted on December 18, 2009 by Austin

Any sci-fi film buffs on NN? I figure there must be a few.

Not real science, but a sad day for sci-fi film buffs today as the news just broke that screenwriter / director Dan O’Bannon has died aged 63.

O’Bannon’s obits may well give the biggest mentions to his screenwriting credits on seminal sci-fi movie Alien and the Schwarzenegger vehicle Total Recall. But in the Elliott family he will be remembered mostly as the other half (with director John Carpenter) of the team that produced the low-fi 70s sci-fi classic Dark Star,) a favourite movie of my younger brother and me ever since we first saw it in our teenage years. Dark Star has been one of those films we share lines from as private jokes – part of our shared history.

Dark Star started life as a USC film-school graduation short made on a shoestring budget by Carpenter and co-written with fellow film student O’Bannon. It was later expanded into a feature in 1974. You can read about the film here.) It can be seen in some ways as a parody of Kubrick’s 2001, and indeed of the whole idea of exciting adventure-filled “to boldly go” space travel of the future portrayed in Star Trek.

The running gag of Dark Star is the one about – what if space travel turned out to be really, really boring? With people stuck together for years, thoroughly fed up with one another’s company, eating monotonous food and doing monotonous things on a malfunctioning spaceship?

For those too young to have ever caught Dark Star, perhaps its most obvious descendant, at least on British TV, is the comedy series Red Dwarf (official website here) which seems to me to owe much of its “Waiting for Godot in space” premise to Dark Star. Of course, Red Dwarf has other obvious antecedants in 70s sci-fi, including Alien and another “space will drive you crazy” cult classic, the proto eco-movie Silent Running.

Perhaps the best known single sequence from Dark Star is the end of the film, featuring the philosophical and talkative bomb (see here and here). However, more of a flavour of the film overall can be got from this sequence, or this shorter one.

Anyway, if you’ve never seen Dark Star, it is well worth digging out on DVD or video (do they still have those?) to see what 70s film-makers could do with a quirky vision, next to no money, improvised-on-a-shoestring special effects (by O’Bannon) and an absurdist deadpan sense of humour.

If the film-makers were talents like Carpenter and O’Bannon, at least.

RIP Dan.

Posted in Procrastination, Science-fiction, Uncategorized | 3 Comments