Is it fair to compare "Alternative Facts" with "Alternative Medicine"

I came across this “meme” on Facebook today:

“The very concept of alternative medicine exists to create a double standard where the rules of science and evidence are stood on their head specifically to manufacture the result that is desired by cranks, charlatans, snake-oil salesmen, and self-proclaimed gurus. There is no alternative medicine. There is just medicine. Either it works or it doesn’t work.”
-Steven Novella

The inevitable retort was: but what about some “natural/traditional” medicines that have not been thoroughly studied. These might work. So, surely it’s an unfair comparison?

My response to that is this:

When people bullshit based on their gut feelings, they can also be right sometimes. It’s only when someone looks into it do we know whether it is actually fact or fiction. “Folk medicine” and natural products may have good (or bad!) effects but it is wrong to imply that they are medicine until we know whether/when they work.

In the same way that an opinion is not an “alternative fact”, a natural product that somebody thinks might do something is not “alternative medicine”.

Then, of course, there is the less generous - but even more apt - comparison of bare-faced lies with bare-faced fraudulent treatments like homeopathy - things demonstrably false that are being badged at truth under the label “alternative”.

I just hope that the war on “Alternative Facts” is more successful than the war on “Alternative Medicine”. The real problem with taking action based on made up stuff is that reality doesn’t care how well-meaning you are, or how much you want it to be true. Hopefully, America will not suffer too much at the hands of reality before Trump and/or his cronies realise this.

Stay angry Britain - but at your politicians, not each other

This is a call to voter on both sides: stay angry about Brexit and hold those ultimately responsible to account. I am not talking about Leave voters, or the Remain voters who won't shut up. I am talking about our political leaders who, despite often being pictured pint-in-hand for PR purposes, couldn't organise the proverbial piss up in a brewery.†

Donald Trump and Marie Le Pen aside, it is pretty clear that the Brexit affair is a national embarrassment. But I don't feel embarrassed by the decision itself - even if I think it's terrible - I feel embarrassed by the way that politicians appear* to have handed responsibility of the biggest political decision of our generation to the Great British public but then neither (1) adequately equipped to make an informed decision, (2) taken precautions to ensure that people were voting for what they thought, nor (3) put any plans in place to deal with anything other than the expected Remain victory. [*The vote was actually only a recommendation to parliament, who still make the ultimate decision.]

Remain supporters feel justifiably angry that the nation was duped into what they see as a calamitous decision of unprecedented proportions. But Leave supporters should feel equally angry. For, whilst you technically "won", the manner of your victory - underpinned by false promises and undermined by subsequent back-tracking and recriminations - removes any real mandate to act unilaterally on the outcome. Do you really want to hang onto a “victory” achieved only by cheating? Do you want to be the 1986 Maradona of British politics? Well, forgive me if I don’t consider that in-line with a traditional British sense of fair play.

Democracy is about compromise but if we're not careful we'll end up with a compromise that makes no one happy - of exactly the sort that "Project Fear" predicted. As Boris has implied, Britain is likely to try hard to maintain free trade, which means no change to borders (that we already control!) or the influence of EU law, but leaves us sitting on the outside peering in, rather than driving reforms and agendas.

It is in the interests of both camps to acknowledge that this referendum was a terrible idea, poorly executed. Such complex and wide-ranging decisions should not be based on a single vote on a single day. Nor should either side be allowed to get away with telling blatant lies. We need to stay passionate about the legitimate issues behind the Leave success - housing, education, jobs and healthcare - and push our politicians together to come clean about the causes and the solutions. If it turns out that the EU and immigrants are not simply scapegoats, or if the real facts about immigration and EU interference still leaving you wanting to leave, let’s vote Leave again and move forward together.

Above all else, let us drive for political reform to make Britain more democratic, which means abandoning first-past-the-post voting and replacing the House of Lords with an elected body, at the very least. I would also like to see voting become mandatory as in Australia, but with the option to abstain on the day.

To the politicians of Britain, I make this plea: don't follow through with Brexit purely because you are scared of appearing weak and undemocratic. That, ironically, is the weak and undemocratic thing to do. If you want to appear strong, and really want a democratic answer to the Brexit question, it is time to (wo)man up and admit that the whole way the referendum was conducted was a fiasco of gigantic proportions.

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†Footnote. The exception to “Stay angry Britain - but not at each other” is the racist arseholes across the country who have taken the Brexit vote as a mandate to racially abuse anyone they don’t like the look of. Leave and Remain voters must unite to counter this ugly trend and come together to make one thing clear: the person not welcome in my country is the British racist, not the target of their abuse.

Asking for a second referendum isn't about being a "bad loser" or undemocratic - quite the opposite

So, the unthinkable happened and Brexit won. This has triggered many people to sign a petition calling for a second referendum. This is not a daft as it seems, as the referendum itself is not legally binding and had no firm actions attached to either result. Indeed, back in May Farage suggested that the Leave camp might do the same if Remain won by a small margin.

However, this request has triggered a flood of outcries from Leave voters, with accusations of Remain supporters being “bad losers” or failing to embrace democracy because the people had spoken. I saw this one on Facebook from a second-degree contact, for example:

Why is this even a thing?! http://www.bbc.co.uk/news/uk-politics-eu-referendum-36629324

The people voted democratically and Leave got over 1.2million more votes. If you don’t like that, tough, you lost. That’s how democracy works. If you think that should be overturned, well maybe the voting system of North Korea will be more to your taste? I’m sure they’ll be happy to have you.

Apologies for the rant, I just wanted to say something about these childish people who can’t take “no” for an answer.

It is a valid question and, whilst I think it was meant rhetorically, here is my answer of why this is “a thing”…

The North Korea analogy is interesting. Imagine a vote in which leaders lie to the population, supported by propaganda machines of a biased and controlled media. Imagine this succeeds in getting the population to vote against their best interests. That is not democracy at work. That is a powerful elite, manipulating the political landscape to their own ends. That is major sections of the Leave campaign. (Not all: there were some genuine reasons for voting Leave. This is not about that - it’s about whether the people voting Leave were voting for those genuine reasons.)

This is not about being bad losers. This is about being passionate about the terrible decision that we are on the brink of. This about genuine fear of economic collapse, fragmentation of the UK and Europe, the rise of right-wing nationalism and xenophobic/divisive agendas, the collapse of the Northern Ireland peace process, the loss of workers rights as we “deregulate” and hand more power to the powerful. Look at America with its lack of decent holidays, parental leave or free healthcare. Not for Britain, thank you.

Imagine a bus and the occupants had voted to jump a ravine as a “shortcut” - despite mechanics, physicists and engineers warning that it probably won’t make the jump, and geographers pointing out that the probable landing point is further away from the destination. If you were in that bus and convinced it was about to plunge you all to destruction, you would scream pretty loud to reconsider.

Nor is this about elitist arrogance of the middle classes. Being confident in the overwhelming consensus opinion of experts who have studied certain fields for years - including all the uncertainty of outcomes - is not arrogance. Some rich privileged bloke in a suit, who studied Classics without any formal training in economics or law, believing that he knows better than those experts - that’s elitist arrogance.

Regular laws in the UK go through several readings and often get sent back to the Commons for a second vote. This has much more far-reaching consequences and unlike those laws cannot be undone, so the idea of some reflection and an “are you sure?” vote is not remotely undemocratic.

Democracy is about the will of the people, it is not about blindly seeing through the results of every single vote no matter what the consequences. If, as I and many others feel, a vote does not truly reflect the will of the people then damn straight it is our democratic right and responsibility to fight the result. (Politically, not physically, of course.)

The request is not to keep voting until Remain wins - it is to keep voting until there is a big majority. It is asking for people to be certain of their choice. If the Leave campaign are so confident that the people have spoken, they should have no problem with letting them speak again.

We, the people, all want what’s best for our country, not for our “leaders”. I suspect the majority on both sides actually want the same things - the disagreement lies in how to achieve them. When the leaders of the “winning” side have demonstrably lied about the consequences of their victory (and are now rapidly back-tracking, having not expected that victory), the anger, frustration and ire at the reaction of the “losers” would be better directed at those leaders, who now need to be held to account.

Should we give those who now realise they were mislead the chance to change their mind? Should we give those fools who feel that they should have voted and now regret not doing so the chance to undo their mistake? Normally, no. They would get their chance come the next election, and maybe they will have learnt their lesson. But here, there is no next election, no chance to make amends for a mistake - hence we are asking for one.

You may feel that people do not deserve a second chance. You may feel that we should be stuck with the decision even if it transpires that a majority actually oppose it, once they are in a position to make an informed decision. After all, them’s the rules, right? Well, that would be a victory for bureaucracy, but it hardly seems in the spirit of democracy.

Perhaps we Remainers are wrong. Perhaps the Leave supporters really do understand the implications of their choice and would do the same again, now that the reality is beginning to bite. Perhaps the EU and immigrants are not just scapegoats for problems with different solutions. So be it. But let’s not be so gung-ho as to sell our nation’s future down the river because it would be too painful to take a long, hard look at the manner in which we have just conducted the most important political decision of our generation.

To get Britain out of its current mess is going to take both sides working together. That means talking to each other, not shouting at each other. To have a chance of success, that solution needs more that 52% of the nation on board. So, do the democratic thing: keep the conversation going until we reach national consensus. Sign the petition.

If you are British, please fight the government plans to make all schools into academies

If you don’t know the problem, read Mark Steel’s excellent column:

Thank God our schools have finally been liberated by our national free spirit George Osborne

Now, please sign either or both of these petitions:

• Hold a public inquiry and a referendum over turning all schools into academies

The government has announced that every school in England will become an academy. This was not in their manifesto and is therefore a completely undemocratic move.

• Scrap plans to force state schools to become academies

State schools are accountable to parents, the local community and to local authorities. By forcing schools to become academies the accountability will be to a trust and to accountants. Her Majesty Chief Inspector of schools has concerns over education provided in academies and so should you.

I hate posting so much about depressing politics but blame the Tories. I simply cannot comprehend how they can think this is good for the children or the country. The only plausible explanation is pure self-interest and greed, wanting to give even more to their rich mates. How this can happen in a supposed democracy is terrifying. If nothing else, it has highlighted how sick the system really is.

In the modern age, there really is no excuse for hands-on democracy with the people voting (electronically) on important issues like this. (The problem, of course, is that the people with the power to change things are the ones who will be most disadvantaged by giving up some of their power.) https://petition.parliament.uk/ is a start, I guess.

Are data scientists just "research parasites"?

Although it passed me by at the time, the New England Journal of Medicine - a highly respected top-tier medical journal - featured an editorial on data sharing¹ in January. It was so bad, that the International Society for Computational Biology (ISCB) felt the need to respond in the most recent issue of PLoS Computational Biology². I’m glad they did, for the editorial was awful.

It starts quite well:

The aerial view of the concept of data sharing is beautiful. What could be better than having high-quality information carefully reexamined for the possibility that new nuggets of useful data are lying there, previously unseen? The potential for leveraging existing results for even more benefit pays appropriate increased tribute to the patients who put themselves at risk to generate the data. The moral imperative to honor their collective sacrifice is the trump card that takes this trick.

But then rapidly goes downhill:

However, many of us who have actually conducted clinical research, managed clinical studies and data collection and analysis, and curated data sets have concerns about the details. The first concern is that someone not involved in the generation and collection of the data may not understand the choices made in defining the parameters. Special problems arise if data are to be combined from independent studies and considered comparable. How heterogeneous were the study populations? Were the eligibility criteria the same? Can it be assumed that the differences in study populations, data collection and analysis, and treatments, both protocol-specified and unspecified, can be ignored?

Many of us who have actually conducted data analysis would retort: if you have concerns about the details then you should be making those details clear. If choices are important, explain them! For sure, you cannot just blindly combine multiple datasets that have different biases etc. but what decent scientist would do that (without an explicit caveat regarding that assumption)?

Longo and Drazen seem to be implying that all data scientists are bad scientists. As I’ve said before, Bioinformatics is just like bench science and should be treated as such. If you are making dodgy assumptions about data, you are doing it wrong. (Though people do make mistakes - the data collectors too.)

It gets worse:

A second concern held by some is that a new class of research person will emerge — people who had nothing to do with the design and execution of the study but use another group’s data for their own ends, possibly stealing from the research productivity planned by the data gatherers, or even use the data to try to disprove what the original investigators had posited. There is concern among some front-line researchers that the system will be taken over by what some researchers have characterized as “research parasites.”

Apparently, some people might think I am a “research parasite” because I sometimes analyse other people’s (published) data without talking to them about it. I’m glad the ISCB called them out on this. Newsflash: science only makes progress by people trying to disprove what other researchers (and, ideally, themselves) have posited. Science is a shared endeavour. If someone uses your data to do something (good), good! If you don’t want that, embargo the data or delay publication. Then question your motives; if glory is what you seek, perhaps you’re in the wrong profession?

A researcher frightened of “stolen productivity” is perhaps a researcher struggling for ideas. (I’d love someone else to answer some of the questions I have kicking around so that I could move on to the next thing!) A researcher scared of someone trying “to disprove what the original investigators had posited” has bigger problems.

The rest of the editorial is not so bad, as it tells the tale of a fruitful collaboration between “new investigators” and “the investigators holding the data”. Of course, this is the ideal scenario, short of generating the data themselves. The fact that the authors felt the need to stress this - and the language used of “symbiosis” versus “parasitism” - demonstrates that Longo and Drazen are utterly clueless about the modus operandi of the disciplines they discredit. Whilst ideal, direct collaboration is not always feasible. Sometimes - when the original investigators are too attached to their pet hypothesis or conclusion - it is not desirable.

They end:

How would data sharing work best? We think it should happen symbiotically, not parasitically. Start with a novel idea, one that is not an obvious extension of the reported work. Second, identify potential collaborators whose collected data may be useful in assessing the hypothesis and propose a collaboration. Third, work together to test the new hypothesis. Fourth, report the new findings with relevant co-authorship to acknowledge both the group that proposed the new idea and the investigative group that accrued the data that allowed it to be tested. What is learned may be beautiful even when seen from close up.

This sounds OK - and the described model may even be data sharing at its best - but the implication that anything short of this ideal is somehow inadequate is naive and unhelpful.

First, one person’s novel idea is another person’s obvious extension. And anyway, why should having one idea give you automatic rights to all obvious extensions?! Why should the rest of us trust the data gatherers to do a good job - especially if they exhibit attitudes towards data akin to these authors?

Second, identifying a potential collaborator does not guarantee collaboration. Ironically, the kind of paranoid narcissist that would use a term like “research parasite” is unlikely to be open to collaboration.

Thirdly, citation is a form of co-authorship that acknowledges “the investigative group that accrued the data”. Wanting full co-authorship where additional intellectual input is not required is just greedy. (And a note to the narcissist: self-citations are generally seen as lower impact than citations by wholly independent groups.)

Longo and Drazen should stick to commenting on what they know, whatever that is, and leave data scientists to worry about how they conduct themselves. With this editorial, they have done everyone - not least of which themselves - a deep disservice.

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1. Longo D.L., Drazen J.M. Data Sharing. N Engl J Med, 2016. 374(3): p. 276–7. doi:10.1056/NEJMe1516564.

2. Berger B, Gaasterland T, Lengauer T, Orengo C, Gaeta B, Markel S, et al. (2016) ISCB’s Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing. PLoS Comput Biol 12(3): e1004816. doi:10.1371/journal.pcbi.1004816.

The solution to extremism is not more extremism

Like all civilised beings, I was dismayed (if not shocked) at the recent events in Brussels. Until our world is rid of religious extremism, I fear that such terrorist atrocities will always be a part of it. However, the way to combat religious extremism is not political extremism.

Terrible as these events were, the damage and death toll are slight compared to a natural disaster, or even a bad plane crash. Just as we do not stop flying, or living in earthquake zones, neither should we go for a Trumpesque (albeit temporary) ban on muslim immigrants nor a right-wing blame-immigrants-for-everything backlash against refugees.

Caitlin Moran nailed it with a tweet:

Always good, on days like this, to remind everyone that the guys blowing up Brussels are THE PEOPLE THE REFUGEES ARE RUNNING AWAY FROM

— Caitlin Moran (@caitlinmoran) March 22, 2016

Of course, some people missed the point, retorting that the terrorists were home-grown extremists - even more reason not to blame the refugees - or that not all of them are fleeing ISIS. To me, though, the sentiment is sound. Caitlin is not talking about those specific guys, but rather the kind of regressive human who sees indiscriminate violence (whether motivated by religious or political ideologies) as an acceptable means to their desired end.

More recently, the poet Brian Bilston summed it up even better, with the preface:

Here is a new poem entitled “Refugees”.

Please bear with it.

If the terrorists succeed in making us lose our humanity and sink to their level, they win. If we live in a climate of fear due to an inflated sense of the risk posed by a scattering of abhorrent individuals, they win. Surely, a civilised society can do better than that?

A vote for Brexit is a vote against the next generation

At its heart, is “Brexit” really any more complicated than whether you are self-centred and introspective (leave*) versus you care about the world and the next generation (stay)?

There is only really one thing in this world worth really worrying about, and that’s Climate Change. Make no mistake: this really could destroy civilisation. Really. Unless it is either stopped or mitigated, all that other stuff - jobs, health, education, even wars - is just polishing a turd.

Fighting climate change needs increased international cooperation. It needs national governments being held accountable through international agreements and organisations. The Brexiters and Trumps of this world are happy to feed off everyone else’s misery to line their own pockets. They will hopefully be dead before the shit really hits the fan. Hopefully, so will I. Our children won’t.

Humanity has progressed greatly over the past few hundred years. Knowledge, healthcare and the potential for political influence has been opened up (in developed countries, at least) to the masses. Let’s not support individuals who hark back to mythical “glory” days in which only the established elite had anything. In former times, when America or Britain was perceived as “great”, this was always at the cost of the poor and minorities. It was about lording it over your (perceived) inferiors, both nationally and internationally. It was about the status and riches of ruling classes. It was about powerful people sending powerless people to die in their millions for pointless causes. It was about gaining superiority in the game of “us versus them”.

In the 21st Century, greatness must mean something different. It must be about the state of the lowest citizen, not the highest. There is no “them” - there is only “us”. Nations and countries are arbitrary boundaries, drawn up for bureaucratic and political reasons, with no actual basis. Race is a myth. People are people, the world over.

Unless we realise this, we are all doomed. When the wings fall off and the plane crashes from the sky, it doesn’t matter whether you’re in business class or economy.

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* There will of course be some UK “winners” in the Brexit scenario, who will benefit from the removal of competition and/or want to be a bigger fish in a smaller pond. However, to think that Brexit serves the nation’s self-interest, you probably need to add “deluded” to the attribute list, as John Major makes clear.

ICBCSB 2015: Another scam conference comes to Australia

I am a bioinformatician working in Sydney, Australia. I recently helped to organise the ABACBS2015 conference in Sydney, where ABACBS stands for the Australian Bioinformatics And Computational Biology Society, of which I am a member. I am also part of the New South Wales Systems Biology Initiative. You may therefore find it surprising to know that I found it surprising to find out that in December, Sydney NSW will be host to "ICBCSB 2015 : 17th International Conference on Bioinformatics, Computational and Systems Biology".

This is not the only surprising thing about ICBCSB 2015. For Sydney is actually at least the 15th 17th International Conference on Bioinformatics, Computational and Systems Biology (ICBCSB 2015). Next week, the conference is being held in Madrid. Last month, there was the 17th International Conference on Bioinformatics, Computational and Systems Biology in Bali. And Prague. And Chicago. And Istanbul. The 17th International Conference on Bioinformatics, Computational and Systems Biology (ICBCSB 2015) has also been in Venice, London, New York, Berlin, and Geneva and will be held in Penang and Dubai. And that’s just in the first two pages of a Google Search - there are more (including Lisbon and Stockholm).

This makes OMIC Group Conferences look positively legit. Indeed, the organisers of all 15+ ICBCSB 2015 conferences - the World Academy of Science, Engineering and Technology (WASET) - seem to be basing their conference business model on that of OMICS. Or perhaps it was the other way round. Either way, if you replaced the WASET logo on the website with OMICS Group, nothing would seem out of place.

If you have ever attended a (real) scientific conference, pick one of those past conferences at random, for example Berlin, and click on the conference photos page, then tell me if you have ever seen anything so depressing in your life. And remember: these are the photos they chose to put up, so presumably show the conference in its best light. Given the number of group photos of (all?) the delegates, I wonder whether they had time for much else other than publicity shots. And in case you are thinking: “those are probably just the invited speakers”, I would bet good money that the delegates were all invited - and still had to pay top dollar to attend.

Finally, in case you have any doubt, just Google “WASET scam”. It does not make for happy reading.

If you are in bioinformatics or systems biology, please spread the word far and wide about these conferences and why they should be avoided at all costs. The sooner we starve the likes of OMICS Group and WASET of naïve unsuspecting scientists to prey on, the sooner these parasites will f#@k right off. There are plenty enough legit conferences to choose from. (Yes, it makes me angry.)

And if you have already signed up for Sydney ICBCSB 2015, do not despair. As luck would have it, there is a real bioinformatics event being held in Sydney that same week: BioInfoSummer 2015. It’s more of a workshop than a conference but there will be plenty of opportunities to discuss science with some excellent bioinformaticians and systems biologists. At least that way, you won’t waste the plane ticket and hotel costs, even if WASET won’t give you a refund for pulling out. (Not likely!)

Is there an important difference between bioinformatics and computational biology?

No.

Bioinformatics is just like bench science and should be treated as such

A bad workman blames his tools. A bad life scientist blames bioinformatics. OK, so that’s a little unfair but so is the level of criticism levelled at bioinformatics by people who should know better. If you are a bioinformatician, it is inevitable that you will run up against the question of whether you ever do “real” science.

If you are unlucky, it will be as blunt as that. At the end of a bioinformatics seminar earlier this year, someone actually asked (in what was meant to be a good-natured way): “Is bioinformatics real? I give the same data to two different bioinformaticians and get completely different answers!” Often, it is is in the subtle form of: “are you going to validate that in the lab?” - as if validating it another way would not itself be valid.

If you are a bioinformatician and are asked a question like that, the correct answer is: it’s as real as [insert appropriate “wet” discipline of choice]. For bioinformatics is science and like all science it can be done well, or it can be done badly. It can generate meaningful results, or meaningless results.

If you want to get meaningful results, you have to treat it like a science, rather than a “black box” of magic. What do I mean by that? Here are my not-quite-buzzfeed-worthy, “8 shocking ways that bioinformatics is just like bench science”:

1. Experience and Training. You wouldn’t hand someone a wet lab protocol for, say, Southern blots, give them a key to your lab and say, “off you go” without first giving them some training and, preferably, the opportunity learn from someone who already knows the procedure. If you do, expect bad results. Bioinformatics is no different. Just because a two year old can work a computer these days, that does not mean that bioinformatics is easy. A two year can also press “Start” on a PCR machine.

2. Optimising your workflow. If you were doing a PCR, you wouldn’t just find a random paper you like that also did a PCR, copy the Mg²⁺ concentration etc. and then bung it in PCR machine and run the default cycle. Likewise, you should not just stick your data into a bioinformatics program and automatically expect it to do the right thing. Just as to be a good molecular biologist, you need to be (or know) someone who knows a bit of chemistry to understand what’s going on, to be a good bioinformatician, you need to be (or know) someone who knows a bit of molecular biology (and chemistry! and sometimes physics) to understand (a) the data you are putting into a program/workflow, and (b) what the best way to process that data is. If you make the wrong assumptions of your data, you will get the wrong answer. (And if different people make different assumptions, they will probably get different answers.) Computers just do what they are told - don’t blame them if you tell them to do the wrong thing. (It is also important not to get “target fixated” on perfect optimisation; just like for bench science, the performance of your bioinformatics workflow only needs to be as good as your experiment/question demands.)

3. Planning. You wouldn’t start a bench experiment without planning it first. Just because bioinformatics is not time-dependent, that doesn’t mean that you shouldn’t plan your analysis before you start. Know what your final output is going to be and work backwards. Making decisions as you go along is a great way to make bad decisions. Sure, have a play to work out how things work but then go back and do it properly from beginning to end.

4. Lab notes. You wouldn’t just stick a tube labelled “20/8/15 mouse 3 PCR” in the freezer and expect to remember what it was and how it was made 3 months later. Instead, you would (hopefully!) keep a meticulous record of primers and reaction conditions etc. in your lab book. Bioinformatics needs the same record-keeping mentality. Program version numbers, dates and settings are important. Write them down. You will almost certainly end up running an analysis more than once, and it won’t always be the last run that you end up using. You do not want publications to be held up because you are having to re-run your bioinformatics just to work out what settings you settled on.

5. Labelling. Even with a well kept lab book, you wouldn’t store samples or extracted DNA in tubes labelled “tube 1”, “tube 2” etc. for every experiment. If someone rearranges your freezer - or there is an emergency freezer swap following power/equipment failure - you could quickly get muddled up. Likewise, don’t call your files things like “sequence.fasta”. You’re just asking to accidentally analyse the wrong data. Include multiple failsafes so that if you enter the wrong directory, for example, your file names won’t be found. (A pet hate of mine is bioinformatics software that outputs the same generic file names each time it is run for lazy scripting.)

6. Reproducibility. Bioinformatics is - or should be - extremely reproducible in a trivial way. If you put the same data into the same program with the same settings, you should get the same answer. In this sense, it should have the edge over bench work - you do not need to repeat experiments. Right? Well, not really. Just because it should be consistent in how it goes wrong, you cannot be sure that a bioinformatics tool is not getting confused by some subtle nuance or peculiarity of your data. Try with another tool that does the same job, or change a setting that should make no difference, and check that you get qualitatively the same answer. (Better still, try changing a setting that should make a predictable difference and make sure that it does.) Just as you can get a misleading lab result if you mislabel your tubes or add the wrong buffer, you can get a misleading bioinformatics result if you mislabel your data or use the wrong parameter settings.

7. Validation. Bioinformatics often receives a certain amount of flak that it is not “real” and everything needs to be validated. This is true, up to a point. The forgotten point is that nothing is real and everything needs to be validated. In the lab, you rarely actually measure or observe something directly - you are inferring reality from things you can measure (e.g. fluorescence) based on what you think you know about the system (e.g. what you’ve labelled) and certain assumptions (e.g. lack of off-target binding). You then have to perform additional experiments - and/or bioinformatic analysis of your data - to test that your assumptions appear to be good and that there are not alternative explanations for your observations. Bioinformatics is no different. NO different. You make assumptions and you make inferences based on observed outputs. These assumptions and inferences need to be tested. This might be by “validation” in the lab. It might be by independent analysis of other data. The only reason the former is more common is that one often needs to generate new data, which clearly bioinformatics cannot do. However, if the data already exists, there is no reason why bioinformatics cannot be used to validate other bioinformatics, or even bench experiments.

8. Limits. Regrettably, bioinformatics is not a magic wand. (Sadly, we are not bioinformagicians.) It cannot correct poor experimental design. It cannot overcome a lack of statistical power. Just like at the bench, if you design an experiment poorly, include confounding variables or overlook covariates, you might not be measuring what you think and/or you might not have any signal from your analysis. It is tempting to think that bioinformatics is more limited that bench science because we cannot collect our own data, but this would be wrong. Bench data is the raw material on which bioinformatics is performed. We can collect new data from other data - much of sequence analysis is doing just this. Of course, if our particular study focus of interest has no data, we need to generate it. But if you want to study the affect of a certain drug on a certain cell line and either/both do not exist, you have to generate that too.

So, what can we do about it? Bioinformaticians have to take some of the responsibility, largely because we are the ones that write software that perpetuates the myth that understanding parameters is not important. What do I mean by that? Well, often the documentation or “help” for bioinformatics tools is poorly written and poorly maintained - if it exists at all. When it does exist, it is usually written with expert users in mind. The novice is flooded with parameters and does not know which ones are important, or when. One solution is to write a series of protocols in the same vein as bench protocols, highlighting when one might want to change certain parameters - and which parameters are most important. (I am no saint in this department, sadly. If nothing else, this post has made me more determined to do better.)

The bottom line is quite simple, though:

Bioinformatics is science. Full stop. It is no better than other science. It is no worse than other science. People do it right. People do it wrong. However, if you are worried that it’s not real, the chances are that either you are doing it wrong, or you have deluded yourself about the “reality” of observations from bench science.

WTF, Britain?!

This could be an audioblog post today, in the form of The Bugle, episode 292, as it sums up my feelings about the recent UK General Election. And that feeling is:

What The F#@k, Britain‽

Hopefully, the Labour Party will now get someone decent in charge. I can’t help but agree with Andy Zaltzman’s reading of the situation: people had a last minute change of heart on the basis that they could not imagine Ed Miliband as Prime Minister.

Following the LibDem coalition shenanigans, all three major parties have now shown that they cannot be trusted to keep promises in power. Therefore, you cannot really be sure what policies you will get, whoever is voted in. On the other hand, one thing you can be sure of is who will be PM, at least to start with. However odious the Tory policies may be, David Cameron can at least hold his own on the international stage. Ed Miliband, on the other hand, is embarrassing to watch on any stage.

In an ideal world, politics would be all about policies. (Which is probably why so many people were too ashamed to admit to the pollsters that they were going to vote Tory.) Sadly, this is not an ideal world. When it comes to a leader, it’s not just the ideas that matter. Personality counts. Charisma counts. With Miliband, Labour had someone who had all three. Then, for reasons that remain a mystery to me, they elected his brother as leader. Hopefully, the country won’t suffer too much as a result.

My other hope is that Lib Dem supporters will stop punishing the party for one bad mistake on tuition fees. I know that they let people down, but no more than Labour or the Conservatives have done in the past. 27 of their lost seats went to the Tories. Really, people?

At least Nigel Farage will be departing along with Nick and Ed, even though that’s only because the UK electoral system is so unrepresentative. With any luck, UKIP will now wither and die. (I'm not feeling lucky.)

The British Humanist Association Voting Guide

Having moved overseas, I’m no longer registered to vote in the UK election. This is probably just as well, as I’m not sure that I really want any of the politicians on offer. However, they are the only politicians on offer, and one of them is going to lead the country. Therefore, if you’re eligible to vote then, as the British Humanist Association said in a recent email:

However you vote, just make sure you vote!

Democracy is an important value for humanists.

Democracy is a vital part of good politics: the enterprise of free individuals having their say in how they want their society governed. In the UK, general elections for the Westminster Parliament are an opportunity for citizens to exercise their democratic freedoms. After all, democracies function at their best when as many of us as possible make use of the right to vote.

Of course, you’ll read up on all the different issues and weigh up the ones which matter most to you. But whoever you decide to support – or however you feel about the state of politics in Britain – we would urge you to go out and vote for the vision of our future you believe in on Thursday 7 May.

If you are still undecided, here’s the BHA’s guide to what the parties stand for with respect to some important humanist issues:

Despite their cowardly u-turn on tuition fees after the last election, I think that the Libdems would still have my vote. I’m not sure that I trust them but then I don’t trust the others either, more’s the pity. The Greens would be a close second, I guess. No prizes for guessing who I would not be voting for.

You can’t vote for what you will actually get, but you can vote for what you actually stand for.

I'm sorry sensitive types but hate speech *is* still free speech

There appears to be a worrying trend spreading through supposedly liberal circles: the notion that free speech should only be free when it doesn’t offend anyone. This quickly morphs into a notion that “hate speech” does not count as free speech and should therefore be censored at will. It’s nonsense and it’s dangerous.

There are certain places where one can and should be expected to be sheltered (as much as possible) from overtly offensive material, which constitutes harassment or bullying. These include workplaces and schools and are the reason behind equality and diversity laws. In essence, there are places that cannot (or should not) be avoided. A functional and free society does well to protect people in these places.

There are other places - the media, events, debates, private homes etc. - that can easily be avoided. In these places, anything goes when it comes to ideas that can be expressed. If you propagate hostile, bigoted or offensive ideas then you expose yourself as someone who is hostile, bigoted or offensive. However, those offended have no right to stop you and it is dangerous to give people the authority to do so.

Ironically, it is frequently a call to protect “oppressed minorities” that nominally lies behind calls for censorship. Just as secularism is the only true protection for religious freedom (even if it reduces religious privilege), freedom of expression is the only true protection for minority groups, even if it subjects them to occasional offence. Once there is precedent to censor due to offence, the door is open for the majority to silence the minority whenever they disagree.

Not only is it dangerous, it’s unworkable. After all, who gets to decide what’s sufficiently sensitive to be censored? Pretty much every idea is offensive to someone, including lots of really important stuff. Evolution, climate change, sexual equality, homeopathy: you name it, someone will be offended by your views on it. So what should we do? Never criticise any idea, no matter how bad you think it is? Unless you want to live under a dictatorship, this is no way for society to function.

I sometimes wonder if free speech suffers from the same thing as vaccination. In modern democracies, we’ve got pretty good at it and so the dangers of not having it are getting forgotten. Rather than look back at how crappy things were - or look to other countries where the poor and oppressed are far less fortunate - come people focus on the relatively rare times when things go horribly wrong and then brand the whole exercise as dangerous. Those who cry "hate speech" too quickly are the anti-vaxxers of free thinking.

Free Speech at Universities

The free speech versus hate speech issue is particularly tricky at universities, I think. This is because a university is a microcosm of the real world. There are parts of it which must be inclusive and “safe”, namely lectures (excluding lectures about certain ideologies), assessments and university policies. They should be places where everyone is welcome and no one is discriminated against. However, universities are also melting pots of cultures and ideas, and places for people to develop and challenge (and sometimes change) their thoughts and beliefs.

As long as their views are not being officially endorsed by the university, individual students (or staff) or groups should be free to declare and discuss any idea, however controversial or potentially offensive. This includes cartoons of Mohammad, or anything else that might really upset certain people.

If you are offended, it is your responsibility to remove yourself from the situation and/or grow a thicker skin; it is not the university (or society)'s responsibility to remove the situation from you. Only if you cannot (fairly) remove yourself from the situation, should the authorities step in: and this is precisely what equality and non-discrimination laws are for.

The way to combat bad/offensive idea is by expressing - and explaining - your opposition, not by trying to shut them up. Who knows, you might even convince them to self-censor or even change their mind altogether, which is surely a much better outcome all round.

Lack of religious discrimination should start with schools

A modern society has to be a secular one. A secular society is not an atheist society; it is a society in which no one gains undue favour or faces discrimination due to their religious beliefs - or lack thereof.

According to the British Humanist Association:

1.2 million school places in England and Wales are prioritised for young people whose parents are of a particular religion, which is more than the total number of places at grammar schools and private schools combined. The law permits ‘faith’ schools to discriminate in all sorts of ways, including in admissions and employment, which has been shown to contribute to social segregation in communities up and down the country.

Religious discrimination is bad enough. What’s even worse, is that some schools seem to be using their ability to select students to discriminate against students from poorer socio-economic backgrounds. It’s not clear whether this is direct or indirect discrimination but given the general negative correlation between wealth and religiosity, it is hard to see how it could be accidental. Either way, it’s clearly not good.

To combat this discrimination, the Fair Admissions Campaign has been established.

Are you facing the prospect of your child being unable to gain admittance to your local school, because of religious selection? Or have you had to game the system in order to get them in? Are you happy to live in a society in which children are discriminated against on these grounds, while parents feel compelled to behave in this manner?

This situation is clearly unfair, and that’s what we’re here to challenge. We are a new campaign that is supported by a wide coalition of individuals and national and local organisations, aiming to tackle the single issue of religious selection in school admissions.

Happily, many organisations - including religious ones - are supporting this campaign. Religious selection as a basis for education has to end.

Religions already have tax-exempt institutions in which they can try to influence the minds of the innocent. They do not need schools as well. If you live in the UK, please support the campaign.

The power of positive incentives for healthy behaviour

There’s no real secret to a long and healthy life: eat a balanced diet with plenty of fresh fruit and veg (but eat your fruit, don’t drink it), However, despite the fact that we all know this deep down, knowing it and doing it are two different things.

Unfortunately, most of the messages we get, and tactics used to modify behaviour, focus on getting us to avoid the stuff we are not supposed to do. Cigarette and alcohol is restricted, taxed and comes with warning labels. Tasty unhealthy foods have “traffic lights” telling you how much bad stuff there is in there (sugar, salt, fat) and what it corresponds to as a percentage of your daily recommendation. There is regular talk of whether there should be a sugar tax or a fat tax.

If you are anything like me, these negative messages are only of so much use. I don’t smoke, and never have (and never will), so that one is easy to obey. The other stuff, however, is generally at its most appealing when my will power is also at its lowest. When I eat unhealthy food it is usually because it scores high on combined taste/convenience, not because I have consciously sought it out.

A tax would probably help in this respect, but what would really help would be something to encourage eating of good stuff, which tends to have the double whammy of being expensive and more effort to cook.

Exercise is the same. We all know we should do it but it’s not always easy to find the motivation. One step (no pun intended) is to know how much you are doing, just as one step to a healthy diet is labelling food. But this only goes so far.

For example, I got a FitBit for Christmas, which was great for seeing how much general exercise I was getting. I walk to work and back so thought that I was probably doing OK. However, my daily step counts for January and February paint a different picture:

The good week in February was our holiday in Tasmania, which featured quite a lot of walking. This included, I still did not have a single week where I hit the 10k goal every day. (Although I was better than the 3.5k-5k average.)

Then came March:

The difference? I’d like to say that I just decided to be more active. I have taken up running again more seriously, which is part of the answer - but only a small part. The main difference is this:

That extra incentive was enough to actually cause a change in behaviour. There weren’t actually that many times that I needed to pick up extra steps at the end of the day - about four times I went for a short evening stroll - but I did change my behaviour to make more trips to the shops on foot and things like that and routinely hit the 10,000 step target. It also served as extra motivation for running.

The annoying thing is obviously 28th March when I lost track of time and midnight came before I’d made the target. It was enough to miss out on the $100 (although I should get $10 credit for 10 consecutive days) - and make me rather cross with myself - but not enough to avoid developing the habit. And, at the end of the day, I think it’s really all about building habits. The incentive has run out but I still went for a stroll on Wednesday to get the extra 700 steps before bed. (Today is a very rainy day off work, which will be the real test!)

The best way to avoid the bad stuff is to replace it with good habits. Rather than taxing sugar or fat, I think that it would be much better to subsidise fresh fruit and veg. Or, if you are going to tax sugar and fat, then use the revenue to subsidise the good stuff. Or give out vouchers for it. Anything, really, to give us more carrots (literally!) and fewer sticks.

OMICS Group strike again with more scam conference spam

I am always wary when I receive an email that begins something to the effect of:

Dear Colleague,

The purpose of this letter is to solicit your gracious presence as a Speaker at the upcoming 5th World Congress on Cancer Therapy on September 28-30, 2015 which is going to be held in Atlanta, USA.

Soliciting my gracious presence smacked of an OMICS Group “predatory” conference invitation. The rest of the email went on:

The aim of this conference is to learn and share knowledge in cancer research. Leading World cancer researchers, Public health professionals, scientists, academic scientists, World Breast Surgeons, Medical and Surgical Oncologists, Radiologists, Researchers, Healthcare professionals, Industry researchers, Nurses, Scholars, Decision makers, Students and other professionals gather in Atlanta to speak at our conference.

Exceptional Benefits

All accepted abstracts will be published in the respective Journals
Each abstract will receive a DOI provided by Cross Ref
Certification by the organizing committee
Global Exposure to your Research
Best Poster Competitions and Young Researcher Competitions
The Career Guidance Workshops to the Graduates Doctorates and Post-Doctoral Fellows
Networking with Experts across the globe

For more details on scientific sessions and abstract submission, please Click Here

In closing, we would be pleased and honored if you would consent to be our speaker at our Conference.

I will call you in a week or so to follow up on this.

Regards,
Isaac Bruce
Cancer Therapy 2015
2360 Corporate Circle
Suite 400 Henderson
NV 89074-7722, USA
cancertherapy@conferenceseries.com

The thing I find most curious is that there is not direct reference to OMICS Group anywhere in this information: they don’t even name the “respective Journals”, which are presumably OMICS journals as with their other conferences. The address and even the email address are equally opaque.

If you do “Click Here” then you go to an abstract submission page with the “OMICS International” logo and some OMICS Group references/email addresses but even here they opt not to use an omicsgroup.com URL.

This does not strike me as the behaviour of an organisation that is proud of their brand. Indeed, I suspect that they know that their brand is toxic thanks to their reputation for predatory journals and conferences and thus try to lure people to submit an abstract (with a hefty $899 registration fee) before they realise their mistake.

The only other clue was the line hidden at the bottom in small font:

You are subscribed to OMICS Group as XXX. If you do not wish to receive any further communications, please click here.

Suffice it to say that I clicked there.

Aussie vs British/Irish Fish ’n’ Chips

We celebrated the start of the Australia Day long weekend by driving out to Brighton le Sands on Botany Bay for some fish and chips on the beach after work on Friday. I grew up in a seaside holiday town, so I am no stranger to fish and chips. Here, then, are my reflections after a year and a bit in Oz. It boils down to this:

In the UK and Ireland, it’s all about the chips. In Australia, it’s all about the fish.

Chips. Aussies can’t do chips. Well, OK, that’s a little unfair - and they often produce something considerably superior to “fries” - but they cannot do chips as well as the Brits and Irish. There is a reason that “chippy” or “chipper” are common affectionate slang for fish and chip shops - you cannot beat chips from a good chippy. Big, fat, slightly greasy chips with salt and vinegar. Yum. It may not be the most healthy thing but it’s one of the few food items that I really miss.

Indeed, the rest of the fayre on offer is somewhat secondary and fish are only one of a number of different accompaniments for your chips. Pies, kebabs, scampi, burgers and all sorts of unhealthy items like battered sausage (or nowadays, a battered anything) are on offer.

The best chips ever? Well, Leo Burdock in Dublin stakes a good claim on that one.

That's not a chip...

That's a chip!

Fish. As indicated, the average British or Irish fish and chip shop does not focus so much on the fish, and there are usually only 3 or 4 different types of fish available (cod, haddock and some kind of flat fish such as plaice or sole being most common, I think) in addition to scampi. In Australia, the choice of fish can be quite overwhelming, and will include several other kinds of seafood (calamari, prawns, oysters etc.).

On Friday, for example, we went to Ocean Heart Seafood who offered five kinds of fish plus other seafood, grilled (barbecued) or battered and fried.

Conclusion. The overal verdict, therefore, is a draw. If you fancy chips, then Australia’s not the place. (Although the wdespread availability of chicken salt does go some way in terms of compensation.) However, if you want a good selection of really fresh, tasty fish, I think Australia is the winner. (Unless, I suspect, you are away from the coast - but more that 85% of Aussies live within 50km of the coast.)

Advance Australia Fair

Today is Australia Day, so I though I would write a post celebrating the attitude of Australia. Whilst the nation has undoubtedly done some terrible things in its not-too-distant history, and has its fair share of bigots, one of the things that I really like about Australia is the way that optimism and inclusiveness are promoted as part of the national identity.

Recognising its foundation and continued growth/development at the hands of immigrants, it manages this without (in my eyes) the excessive patriotism of some other countries one could mention. There is a pride to be Australian without the insecurity of thinking/implying that any non-Australian must be inferior.

This is captured in one of my favourite things about Australia the nation, which is the national anthem, “Advance Australia Fair”. There are a couple of things I like about this. First, the lyrics of the song itself:

Verse 1 Australians all let us rejoice, For we are young and free; We’ve golden soil and wealth for toil; Our home is girt by sea; Our land abounds in nature’s gifts Of beauty rich and rare; In history’s page, let every stage Advance Australia Fair. In joyful strains then let us sing, Advance Australia Fair.

Verse 2 Beneath our radiant Southern Cross We’ll toil with hearts and hands; To make this Commonwealth of ours Renowned of all the lands; For those who’ve come across the seas We’ve boundless plains to share; With courage let us all combine To Advance Australia Fair. In joyful strains then let us sing, Advance Australia Fair.

OK, so the reality might be a little different, but as something aspirational you can’t do much better than: “For those who’ve come across the seas, we’ve boundless plains to share; with courage let us all combine to Advance Australia Fair.”

It certainly beats lines about killing and/or being killed by ancient foes, who are now your close neighbours (or even fellow countrymen). Admittedly, Australia’s federation as a nation was a blood-free independence (and they’ve not yet done away with the monarchy completely) but it’s still decidedly up-beat and lacking in über-nationalism.

The second thing I like about it is the fact that, whilst performed in 1878, it only became the official national anthem in 1984, supplanting the fusty and outdated God Save the Queen. As merits the national anthem of a modern democracy, it was chosen by plebiscite (i.e. non-binding referendum) - something that I think should be at the heart of a lot more political decisions in the digital age.

You don’t have to be stuck in the past. In my opinion, a national anthem should reflect modern ideals. After all, it’s supposed to be something to identify with. I’d love if it the UK replaced God Save the Queen with something more secular and democratic (even if it does contain the classic line, “Frustrate their knavish tricks”). I’m sure that the anthems of a few other nations could do with a bit of a spruce up too.

Well done, Australia.

Antibiotics really matter and need more research funding

Last year, I went down with tonsillitis on New Year’s Eve. The timing sucked a bit but I guess there are no good times for such things to happen. However, I was/am lucky: lucky because I live in an age where antibiotics are available and still work.

As a scientist, I often get frustrated about science funding. Firstly, there’s not enough of it (compared to other endeavours of less benefit to both society and the economy) but secondly, a lot of it goes to the wrong places, namely human diseases such as cancer. Don’t get me wrong: I’d love to see cancer cured. It’s just that there are bigger fish to fry, and global crises looming that would make diseases of old age such as cancer and Alzheimer’s a bit of a moot point.

An obvious need of greater funding is climate change, thrown into the spotlight again (as if it were needed) by the confirmation that 2014 was the the warmest year on record. Another is the development of new antibiotics.

Antibiotic resistance is a big problem and one that is currently only getting worse. We are heading for a “post antibiotic world”, which is a really scary thought. Indeed, some scientists have argued that antibiotic resistance is a bigger problem than climate change because we have the technology to combat climate change, we just lack the political will. We do not yet have the technical solution to the impending “antibiotic apocalypse”, hence the real need to throw money at research into solutions.

The annoying thing is that this is not a problem that has snuck up on us. In an editorial from 1997 entitled “Antibiotic Armageddon”, Calvin Kunin from The Ohio State University wrote:

“The advances of the antimicrobial era are being dissipated by the emergence and spread of resistant microorganisms, the inevitable consequence of intense use of antibiotics in humans over the past 50 years. The process is accelerating in the community as well as in hospitals and is a problem worldwide. The attrition of older drugs is sustained by the selective effects of new and more expensive drugs developed to overcome resistance. Novel compounds will no doubt be discovered, but their demise is inevitable. It is just a matter of time until resistant pyogenic organisms join the opportunistic microbes as major threats to humans.”

…

“[The] long-term outlook for control of antibiotic resistance is bleak. There are simply too many physicians prescribing antibiotics casually and too many people buying antibiotics without a prescription in developing countries. There is only a thin red line of infectious diseases practitioners who have dedicated themselves to rational therapy and control of hospital infections. The issues need to be presented forcefully to the medical community and the public. Third-party payers must get the message that these programs can save lives as well as money.”

Sadly, if these words were written today, I don’t think anyone would argue the point; not much has changed. And that’s without even mentioning the big problems caused by the long-running over-use of antibiotics is agriculture.

Things are not without hope. Earlier this month, a Nature paper by Lin et al. reported the discovery of a novel class of antibiotic from a screen of 10,000 bacterial strains, following the development of novel method to grow hitherto uncultured bacteria:

“Antibiotic resistance is spreading faster than the introduction of new compounds into clinical practice, causing a public health crisis. Most antibiotics were produced by screening soil microorganisms, but this limited resource of cultivable bacteria was overmined by the 1960s. Synthetic approaches to produce antibiotics have been unable to replace this platform. Uncultured bacteria make up approximately 99% of all species in external environments, and are an untapped source of new antibiotics. We developed several methods to grow uncultured organisms by cultivation in situ or by using specific growth factors. Here we report a new antibiotic that we term teixobactin, discovered in a screen of uncultured bacteria. Teixobactin inhibits cell wall synthesis by binding to a highly conserved motif of lipid II (precursor of peptidoglycan) and lipid III (precursor of cell wall teichoic acid). We did not obtain any mutants of Staphylococcus aureus or Mycobacterium tuberculosis resistant to teixobactin. The properties of this compound suggest a path towards developing antibiotics that are likely to avoid development of resistance.”

Personally, I remain skeptical about claims that teixobactin is resistance-proof. It may not be easy but I am sure the bugs will stumble across a way to evade or destroy the toxin and evolve resistance. Nonetheless, the message is clear: there are new antibiotics out there to be found. This one was found in the backyard of one of the researchers! Bacteria have been killing each other for millions, maybe billions, of years and so the global diversity in nature is likely to be massive. We just need the ingenuity and funding to find them.

References

Farrar J & Woolhouse M (2014). Policy: An intergovernmental panel on antimicrobial resistance. Nature 509:555–557

Kunin CM (1997). Antibiotic Armageddon. Clinical Infectious Diseases 25:240–1

Lin LL et al. (2015). A new antibiotic kills pathogens without detectable resistance. Nature doi:10.1038/nature14098

Do we need a bioinformatics dead links database?

Keith Bradnam on his ACGT blog has recently highlighted the irksome issue of “link rot” - the unfortunate but all-to-common scenario in which a publication points to a URL that ceases to exist after an oft-too-brief time has elapsed. (In severe cases, before the paper is even published!)

Personally, I think that journals need to take a bigger responsibility in maintaining the integrity of their publications. Surely it is not beyond a big publishing house to have a bot that systematically checks their published links once a week and reports and errors? Authors could be notified and/or online manuscripts updated. In severe cases where the URL is critical to the paper, such as databases and webservers, lack of repair could even lead to retraction.

The problem goes beyond publications, however. For (sometimes mysterious) reasons of their own, even established biological resources quite often change their URLs too. For example, Pfam embeds the Wikipedia entry for a domain into their pages. I was browsing the globin page last week and clicked on a link to see the entry in Interpro, only to be greeted with:

Sorry, the requested URL has changed

The requested URL: http://www.ebi.ac.uk/interpro/IEntry/ac=IPR002338

has moved to

/interpro/entry/IPR002338;jsessionid=BB50E35E3DD96F6C83B7AD432B8E2E2A

You will automatically be redirected to the correct URL in a few seconds. Please update your bookmarks.

It redirected OK but I wonder how long it will be before that redirect itself disappears… and how many Wikipedia articles and database cross-references run the risk of breaking.

Perhaps we need a database where bioinformaticians can report, track, update and hopefully fix all these rotten links? In the meantime, if anyone spots any in my own webpages or papers, please let me know!