On mutations

Venter had more than one point mutation to deal with:

mutation.jpg

Posted in Science | 8 Comments

On synthesis

Oh my God, we’re all going to die, exclaimed the Daily Mail today.

Well, we are all going to die some day, but not because of the paper from the J. Craig Venter Institute, published in Science.

I’m having a little trouble understanding the fuss. Admittedly it’s a quite stunning technical achievement, but it doesn’t really tell us anything, does it? It’s simply a brute-force approach to turning one single-celled organism into a different one, isn’t it? Like nuclear transfer, refined to its bare essentials. A technical tour-de-force, and a stunning example of what we can do when we try, and it’s probably ironed out a lot of problems for the rest of us, but it’s more a triumph of marketing than anything else (a bit like the human genome first draft, perhaps?).

It’s not even as if the method is particularly applicable or transferable–dozens of researchers, ten years and 40 million nicker, for, as @Tideliar put it,

just the worlds biggest BAC. Please get a grip.

I will be impressed when, starting only with abiotic chemicals, Venter produces flowers from a genetically-modified top hat. Or am I missing something, and I should expect to see the army of radioactive gorillas marching down up Tottenham Court Road next Tuesday?

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Posted in Rants, Science | 21 Comments

On defecting

Jenny has a new shiny. It’s a device for imaging chemiluminescence–a standard procedure in any lab that works with proteins. The traditional way of doing this is on film, but it seems a lot quicker, safer and environmentally-friendlier to do it with one of the imaging gizmos.

Except…

Except I’m a little bit worried. I was reading a paper just now, trying to figure out how to summarize it for our Faculty Dailies, and came across this figure:

Pixels

Now I have no idea how this image was obtained (the Methods section mentions neither film nor fancy-schmancy new devices), but either way that is one butt-ugly blot (BUB for short). I am worried that it is obtained with a FSND, because you really have to be a bit of an imbecile to get that level of pixellation when digitizing a blot by scanning a film. I wouldn’t ever want to publish something that looked like that–accusations of over-processing aside, it simply looks wrong.

Are we likely to see more BUBs as FSNDs gain in popularity? Is a whole way of life and aesthetic pleasure at stake here? Say it ain’t so, Jenny.

Say it ain’t so.

Posted in Rants, Science | 20 Comments

On the profit motive

It’s just not funny any more.

This tweet:

Dangerous advice. Fever of +105F go to the ER! RT @homeopathyworks: Hot baby, less is better for your Children’s fevers http://om.ly/jgzJ

made me fall off my chair. The argument is that if a child has a fever of 105°F (40.5°C) or more, you should give them … water. The retweeted twitterer (‘twat’?) ‘@homeopathyworks’ says in her profile

Joette Calabrese is a certified homeopath, she has become a trusted voice in achieving robust health that is decidedly educated, experienced and committed.

Tell me, would you trust someone who recommends giving just water to your feverish child?

We should note that homeopaths often take the moral high ground, attacking ‘big pharma’ for selling drugs and making lots of money of the back of illnesses. It’s been pointed out time and time again by people with two brain cells to rub together that the homeopaths are also making money, and indeed their profit margins are probably much greater (because there’s no active ingredient).

But I didn’t realize just how much more money homeopaths are making.

Take this fever ‘remedy’ for example. On the Boots website, you can get a packet of ‘pillules’ for five quid. That should clear your fever within five days according to the dosage instructions (let’s ignore the fact that most, non-life threatening, fevers are self-limiting over that period anyway). And most homeopaths will tell you that you should go along to their ‘surgery’ and get the stuff made up the ‘proper’ way, which means you’re looking at substantially more dosh than that.

Aspirin caplets are 75p. If you take them at the recommended dose a pack will last you two days. Even if you bought three packs (to last five days) that’s still only £2.25; plus you get an active ingredient.

So who are the immoral money-grabbers now: ‘big pharma’ or homeopaths?

But seriously, if you have a temperature of 105 you should be in hospital already. As another twitter friend of mine put it,

They’ve obviously not read the book – stupid people are supposed to remove themselves from the genepool, not innocent children.

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Posted in Homeopathy, Rants, Science-less Sunday | 29 Comments

On copyediting

Copyediting is an activity that when not being actively maligned tends to be overlooked. But it’s a necessary step in science communication and publishing because clarity of expression is pretty darned crucial to getting your message across and avoiding misunderstandings. It’s doubly important when the language of publication is not the native language of the authors.

A shame, then, that even top journals do not employ copyeditors. Take the following sentence, that I found in an EMBO J abstract earlier today:

Abasic sites represent the most frequent DNA lesions in the genome that have high mutagenic potential and lead to mutations commonly found in human cancers.

Tell me, reading that, are abasic sites the most frequent DNA lesions, or are they rather the most frequent lesions that have high mutagenic potential and/or lead to cancers? I had to go and look it up, because proper journalism involves getting your facts straight and if I get something wrong then the excrement truly hits the air circulation device.

From the same abstract, I also found this wonderfully tortuous construction:

This amino acid templating mechanism was corroborated by switching to pyrimidine specificity because of mutation of the templating tyrosine into tryptophan. The tyrosine is located in motif B and highly conserved throughout evolution from bacteria to humans indicating a general amino acid templating mechanism for bypass of non-instructive lesions by DNA polymerases at least from this sequence family.

I know what you mean, but man, that’s painful.

This is not the authors’ fault. Were I to write an article for a German language publication I would hope that a good German speaker would be editing my prose to check for precisely that kind of ambiguity. Which means that I’d expect a copyeditor to be on staff (or based in India), which in turn (because these people need to eat occasionally) means that either I have to pay to publish, or pay to read.

And you know what? This is why science publication should never, ever be kostenlos, no matter where you stand in the Open Access debate.

Posted in Literature, Rants | 28 Comments

On unfortunate juxtapositions

Caffe

There’s an Italian cafe/deli round the corner. It’s a quiet place, which seems to suit the proprietors well in a Black Books-sort of way (although without the personality defects): they open when they feel like it and there are rarely more than three people in at any one time. They do a fine line in double espressos and ciabattas, and sell cheese.

As we perused the cheese counter last weekend we came across something neither of us had heard of before–taleggio cheese. Sounded interesting, and through the wonders of the internets, iPhones and (despite local mad environmentalists objecting to phone masts) a wavering GPRS signal we found out that it is a ‘semi-soft, washed-rind cheese from the Valteggio region in northern Italy.’ Sounded good, and Bernard the East End/Italian proprietor said it would go well in a salad, so that’s what we’re having with dinner tonight.

The unfortunate side of this story is the actual website I found describing the taleggio. The URL is www.artisanalcheese.com, and if that doesn’t make you laugh, maybe the following rambling anecdote might give you a clue.

{FX: wavy lines}

Back when online publication of journals (how did we get from cheese to journals? Well, never mind) was still relatively new and exciting, my boss at the time was editoring a certain journal. And because online publication was still relatively new and exciting, he and the rest of them were quite interested in hit counts for the papers (article-level metrics; way before PLoS got in on the act). And they noticed, as the story was related to me, one paper getting masses of hits. As in orders of magnitude more than the rest. ‘Strange,’ they thought, ‘what’s so exciting about Molecular dissection, tissue localization and Ca2+ binding of the ryanodine receptor of Caenorhabditis elegans ?’

Then someone read the abstract, and all became clear. This quiet, unassuming paper, which was getting absolutely hammered by search engines, happens to bear, in the abstract (which is freely searchable, even if the rest of the paper isn’t) the line (and bear in mind that ‘and’ is usually treated as an operator, not a search term)

CeRyR was found in the body wall, pharyngeal, vulval, anal and sex muscles of adult worms and also found to be present in embryonic muscle, but not in non-muscle cells.

There’s a moral here, but I can’t think what it is.

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Posted in Science-less Sunday | 17 Comments

On Memories

Scurry has written about memories. The skies over London have been similarly homeopathic this weekend–clear blue skies (like water), with no aeroplanes (like homeopathic preparations).

The Memory of Air Flight.

I went up Stave Hill yesterday and shot the video you see above. Usually the skies of London are criss-crossed with contrails: City Airport is to the east, just beyond Canary Wharf and Heathrow is southwest of us. Both very busy airports. But yesterday there was nothing. If I said that if you looked carefully you could see where the aeroplanes used to fly, you’d laugh at me, and rightly so. No memory of flight, there.

But the muppets are still at it. Homeopaths without borders? Oh please. If this isn’t a joke, it’s immoral and obscene. Playing on the good name of Médecins Sans Frontières to go and wave dehydrated water (yes, I know) at people who really need proper, medical help. Just in case you wondered, Muppets without borders is “Not associated with Doctors Without Borders”.

Oh, that’s all right then. Excuse me, I think I need to go and have a decidedly non-homeopathic vodka.

Posted in Homeopathy, Rants, Science-less Sunday | 14 Comments

On Peer Review

(This is a guest blog I wrote for the Research Information Network.)

I’m a fan of peer review.

There, I’ve said it. And I’m not saying it in the way that Sir Winston Churchill famously spoke of democracy; ‘the worst form of government except for all those others that have been tried.’ I’m also not talking as one with no experience of the peer review process, nor one with uniformly good (or bad) experience–I’ve had papers accepted without hesitation, I’ve had others improved substantially by the review process, and I’ve had a manuscript bounced around for two years until we found a sympathetic editor and reviewers who understood just what the bloody hell we were talking about.

I suspect that my experience matches that of the vast majority of jobbing scientists. We don’t have particular axes to grind, we just want to get our stuff published in as ‘good’ a journal as possible (and there’s a whole other can of fish to worry about) and we want to move on to the next experiment. Truth be known, we’d also like to see what our colleagues and, well, peers make of our work, and maybe even make constructive comments before the entire world gets to see it.

I’m also not a football fan of peer review. I won’t support this system unthinkingly, against all comers, waving my blue and white scarf above my head and throwing rolls of toilet paper at the opposition (actually, that attitude seems to characterize most opponents of peer review, but more on them in a bit). No; I recognize there are problems, and I’m certain it could be improved. Just don’t ask me how: I don’t know, for example, if single or double blind review, or complete openness would improve matters or make them worse, all things considered.

The thing is, peer review has been getting a bit of stick recently. Medical journals, especially, seem to get very worked up about it. The matter of Medical Hypotheses is another case in point. The Editor, Bruce G. Charlton, is embroiled in a fight with Elsevier, the publisher. Elsevier wants to make it peer reviewed, and Charlton thinks that will destroy the spirit of Medical Hypotheses. As if one editor is going to be in any way ‘better’ at assessing a manuscript’s ‘worth’ or ‘rightness’ (not newsworthiness–that’s different entirely and it’s something the crew at, say, Nature do very well) than any three peers–and let’s be explicit here, in this sense ‘peers’ means ‘experts in their field’, right? Anyway, I’m not overly concerned about the pros and cons of that case (except to point out that every professional in the field knows exactly how much worth to place on anything published there. It’s only the press–and the naif–that get confused about such things): rather I’d like to look (briefly, because it’s far too painful to spend much time on) at some of the comments on the Nature news article.

First, the repeated assertion that Nature, by virtue of having full-time editors, does not do peer review is patently ludicrous. How anyone who practises science could hold that opinion, moreover repeat it in a very public forum, is beyond me. At least the commenter had the grace to admit he was wrong, but this demonstrates the sheer level of misinformation and ignorance surrounding the entire issue. How can we have a reasonable debate when even those involved don’t know what they are talking about?

Second, we have the frothing-at-the-mouth prophets:

Peer Review should be universally rejected by all scientists and researchers as the thought control experiment that it is. Science is not Consensus! Truth cannot be discovered by vote no mater how smart the electorate thinks it is.

Right. There is so much wrong in those three little sentences that I really don’t know where to begin. Let’s just say that it’s another exemplar of people Just Not Getting It.

It gets better. It always does:

Peer Review as a concept, is no more than an easy way to influence, suppress, and control the direction and funding of scientific research. It is no less than tyranny and must be rejected as such.

Uh, OK, keep taking the tablets–actually no, get some different ones because those aren’t working.

Please, just one more?

Both Socrates and Galileo were “Peer Reviewed”. We all know how well that worked out.

Ah here we are. We’re dealing with someone who has had an obviously quite brilliant Idea that nobody will publish, let alone listen to, and the problem is not the Idea but peer review! If I had a quid for every loon who emailed me his theory on how everybody is wrong and how he (invariably a ‘he’; ‘she’s are far too sensible) has found the secret to life the universe and 42, only he can’t publish it because of the tyranny of peer review, and look how nobody believed Socrates or Galileo or Einstein, oh God especially poor old Einstein; well, I’d have fifteen pounds and sixty pence (that last one was a particularly sad and tragic affair).

Look, people: we’ve moved on from arresting or murdering people for having wacky scientific ideas–at least in the West. There is no conspiracy, no shadowy cabal that stops you publishing anything (and indeed, the internet makes publishing ridiculously easy). It’s far more likely, all things considered, that your Idea is so much dingo juice and you’re suffering a severe case of sour grapes. If your Idea is, actually, good; then Time will prove you right. It always does. But my money is on you being a wacko.

Even the company I work for is not trying to replace the initial round of peer review. Yes, our Chairman jumpstarted the Open Access revolution (and you’ll see why I was keen to establish my own bona fides, above), and yes, we’re really interested in what I’m calling post-publication peer review–assessing the likely impact and importance of the scientific output soon after the point of publication–but even we recognize the value of peer review as it stands today (notwithstanding arguments about anonymity and the like).

Ah! A voice of sanity and reason:

But people whose ideas, popular or not, that are backed up by sloppy research, or no research at all, should not be published until they can come up with the proper evidence supporting their claims. Coming up with adequate supporting evidence is another driving force behind science and ensures its credibility.

The point of peer review, actually, is neither to suppress nor promote good, bad, wacky, conventional, nuclear or world-changing Ideas. The major question that peer review is designed to answer, and is best at answering, is, “Is it done right?” It’s not some vast conspiracy to keep ideas down, nor to deny lunatics a forum or grant money. It’s there to help workaday scientists (some of whom will have brilliant, paradigm-shifting Ideas) do their research, without having to wade through a Stygian morass of ill thought-out crap.

We have to know our limitations, of course. Peer review suffers terribly from poison-pen reviewers. A field I worked in was almost destroyed because one PI kept trashing the community’s papers in review stage (she turned out to be mentally ill; that, also, is a story for another day). But that’s no reason to throw the F1 out with the autoclave bags. We need to identify and fix the problems with peer review, not destroy it entirely.

I need to address one last misconception. Peer review, done properly, might guarantee that work is done correctly and to the best of our ability and best intentions, but it will not tell you if a particular finding is right–that’s the job of other experimenters everywhere; to repeat the experiments and to build on them. Indeed, a friend of mine has been known to say, in public even, that most things in Nature are wrong. (And he should know–he’s a Nature editor.) He’s right of course–everything published will be superseded. But the point is, and the point we’re in danger of losing sight of to our great detriment as jobbing scientists, is that peer review done even half-arsedly cuts out a whole pile of junk and lets us get on with the real business of Science; that of finding shit out.

Posted in Literature, Rants | 41 Comments