ARGH! How to give your journal a bad reputation

Received on 21 February 2017:

Dear Dr. Richard J Edwards,

Good Morning…..!

We are in shortfall of one article for successful release of Volume 3, Issue 2. Is it possible for you to support us with your transcript for this issue before 28th February? If this is a short notice please do send 2 page opinion or mini review, we hope 2 page article isn’t time taken for eminent like you.

We are confident that you are always will be there to support us.

Await your response.

Sincerely,
Brittney Reeves
Advanced Research in Gastroenterology & Hepatology (ARGH)

Begging for a two-page article in a week from someone who doesn’t even work in the field… ARGH indeed!

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.

---

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.

Thank YOU, PLOS ONE!

There are many flaws with the peer review system but it remains the best system we have for ensuring a certain degree of quality control prior to publication. One of the ways that the system could be improved is better recognition - and therefore motivation - for reviewers.

Ideally, there would be some form of payment, but I find it hard to see this happening any time soon. (It is difficult enough to get funds to publish papers - getting funds to get papers reviewed when they might well end up getting rejected is going to be way harder.)

The next best thing is some kind of reward or recognition. Some journals give discounted publication fees to reviewers, which is a great idea. Another great idea has just been put into action by PLOS ONE*: public recognition for reviewers:

On behalf of PLOS and the PLOS ONE editorial team, I would like to thank you for participating in the peer review process this past year at PLOS ONE.

We know there are many claims on your time and expertise and we very much appreciate your valuable input in 2015. With your help, we have continued to publish an influential, lively and highly accessed Open Access journal. Simply put, we could not do it without you and the thousands of other volunteers for PLOS ONE and the other PLOS journals who graciously contributed time reviewing manuscripts.

A public “Thank You” to our 2015 reviewers – including you – was published earlier this week.

(2016) PLOS ONE 2015 Reviewer Thank You. PLoS ONE 11(2): e0150341. doi:10.1371/journal.pone.0150341

Your name is listed in the Supporting Information file associated with the article. I hope that you will be able to use this letter, along with the article citation, to claim the credit and recognition you deserve within your institution for supporting PLOS ONE and Open Access publishing.

The article itself is short but sweet:

PLOS and the PLOS ONE editorial team would like to express our gratitude to all those individuals who participated in the peer review process of submissions to PLOS ONE over this past year. During 2015 PLOS ONE published over 28,000 research articles. This would not have been possible without the contribution of more than 76,000 reviewers from around the world and a wide range of disciplines.

The names of our 2015 PLOS ONE reviewers are listed in S1–S5 Reviewer Lists. Thank you to all our reviewers for generously sharing your time, insight and expertise with PLOS ONE authors in the evaluation of their work. Your efforts are a key reason for PLOS ONE’s success as an innovative and influential publication.

It’s nice to be appreciated. One more reason to be a fan of PLOS ONE. (Which I am, despite those who look down their noses at the journal because of its “scientifically rigorous research, regardless of novelty” policy.)

*The other PLOS journals did it to but I did not review anything for them this year.

Is this the shortest abstract ever?

I’m currently writing a new program as part of a comparative genome analysis, which has the working title of “Snapper”. Unusually (but not uniquely) for me, this is not an acronym, but is instead a simple contraction of “SNP Mapper”.

Before doing too much, it is always wise to check for existing tools with the same name, especially if they might do similar things. A quick Google search for “Snapper bioinformatics” threw up this paper:

• Kolesov G, Mewes HW & Frishman D (2002). SNAPper: gene order predicts gene function. Bioinformatics 18(7):1017-9.

The abstract:

SNAPper is a network service for predicting gene function based on the conservation of gene order.

AVAILABILITY:
The SNAPper server is available at http://pedant.gsf.de/snapper. SNAPper-based functional predictions will soon be offered as part of the PEDANT genome analysis server http://pedant.gsf.de.

I know that Bioinformatics application notes are pretty concise - the idea is that the described software has the documentation you need - but that has to be one of the shortest abstracts that I have ever seen!

SNAPper itself is not an acronym, although the SNAP part is: Similarity Neighbourhood APproach. For such a common acronym as “SNAP”, that one needs some work, I think.

PEDANT, on the other hand, is a full ORCA-worthy acronym: Protein Extraction, Description and ANalysis Tool. It reminds me a bit of a defunct classic of my own, PIRATE: Protein Identification, References, Annotation and Tissue Extraction (or something like that, lost in the mists of time) that was basically just a parser for Uniprot entries that tabulated certain data, after I discovered that a PhD student in the department had spent several days copying and pasting data from Uniprot into Excel. Happy days!

My number one exam tip

Answer the question! (I’ve said it before but some things are worth repeating.)

Click here for more exam tips.

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!)

A tale of two conferences - #ABACBS2015 and #AGTA15

Two weeks ago, I attended the awesome double-header of ABACBS2015 and AGTA15. In some ways they were chalk and cheese - ABACBS was cheap and cheerful, where as AGTA was expensive and (therefore) exclusive - but both were great and highlighted some of the very best features of successful academic conferences.

As part of the ABACBS2015 organising committee, I needed to collect my thoughts for a debrief, so I thought I’d got down some thoughts here. (Thanks to grant writing, the post itself got a little delayed!) As with biology itself, most decisions are trade offs and the following comparison is not to criticise - I just find it interesting. As with the awesome ABiC14 conference last year, I mainly want to document good practice for future reference. (Some of these will no doubt be repeats of my ABiC14 thoughts!)

Size. Both conferences were, for me, the perfect size - around 180-190 people. This is enough to give the conference a good buzz and ensure that there are sufficient interesting people to listen to and posters to visit. Critically, though, it was small enough that you could find and speak to the people you wanted to. (Even if I didn’t fully get the chance at ABACBS2015 because I was busy, and managed to miss some people at AGTA15 because time ran out!)

Venue. ABACBS2015 was run on a budget and we were very fortunate to have the Garvan Institute provide a free venue for the conference. The Garvan lecture theatre is lovely, with a great AV system and comfy seats. The only negative for a conference of that size - and we got close to our 200 person limit - is that the space outside the theatre for breaks and posters does get a bit cramped. In contrast, AGTA15 was held in the Crowne Plaza at Hunter Valley, which is a pretty luxury hotel in the wine region of New South Wales. It took me a while to warm to the main conference setup, with seats around tables in a large, wide room with a screen each side of (and a long way from) the podium. However, the “trade exhibition” space where the breaks, lunch and posters were, was excellent. I am big fan of having the posters up all the time and in the same place as the breaks.

Location. ABACBS was held in the city centre at a research institute. This kept the costs down and made it easy to get to. (We did not organise accommodation.) It also made it easy to escape from, which might have affected evening social numbers. AGTA was out in the sticks, which made it harder to get to and may have put some people off attending - it essentially added another day to the length of the conference. The plus side of this was that everything was on one site and it was not so easy to disappear or go home, and so most people were around most of the time, I think. (Although there was the temptation of wine tasting on the doorstep!)

Goodie bags. I’m pleased to say that both conferences went down the reusable shopping bag route (pick above). Being budget, we got UNSW to sponsor us with some canvas bags for ABACBS. (Complete with the scary statistic that plastic bags take 15-1000 years to break down.) AGTA was (a) a bit more upmarket and (b) in wine country, so they provided wine coolbags!

Trade exhibition. We binfies are a cheap lot - and I don’t mean tacky or miserly, I mean that we don’t need a lot of money to do great things. As a result, it is hard to attract trade sponsors: we just don’t spend (or often even have!) any money! Genomics is clearly a different matter, as you literally cannot do it without lots of expensive kit. The AGTA trade exhibit was therefore pretty big and bustling. Again, putting it with the food and posters made for some great…

…Breaks. Breaks really do make or break a conference. One of the few criticisms of ABACBS2015 was that the breaks were a bit too short - we were somewhat hemmed in for time because we needed to leave people enough time to get to AGTA in the afternoon of the second day. We also tended to over-run a little, because people would be enjoying the breaks and take a bit of time to filter back into the theatre for the talks. My advice for conference planners: (1) make all breaks 5-10 minutes longer than you think they should be (e.g. 40 minutes for coffee and over an hour for lunch); (2) build in some dummy time into the program to soak up delays; (3) Make sure you have a bell or something to signal that the next session is starting! Being a more leisurely multi-day conference, AGTA had nice long breaks, including a session off for posters etc. after lunch. Lots of opportunities for mingling and looking at posters.

Invited speakers. Both conferences had outstanding invited speakers that gave really interesting talks. I know some of the binfie crowd would have enjoyed a bit more about the methodology in ABACBS2015 - and we should perhaps brief our speakers a little better in future - but personally I was blown away by the quality of the science presented. Both fields are rapidly changing as technology opens up opportunities and there is some really cool stuff going on out there! AGTA in particular seemed to have a lot of invited speakers, talking about really cool stuff - possibly part of the reason it's so expensive. (It must be said: the quality of the selected abstracts was good too!)

Gender Equality. Both conferences did pretty well on the gender front, I think. ABACBS2015 in particular nailed it, with a 50% split of invited speakers and over 50% female speakers overall! (The latter wasn’t deliberate as such - there are just loads of good female bioinformaticians in Australia who submitted interesting abstracts!)

Twitter. (And #confBingo.) I have mixed feeling about live tweeting at conferences. This year, I decided to throw myself in a bit more and, on balance, I feel that I got more out of it than I missed. It is true that sometimes I missed something a speaker was saying because of a tangential Twitter conversation (such as #JediKelpie) - but I also learnt stuff and picked up on things that I had missed thanks to the Twitter feed. The #confBingo thread was also quite entertaining a fun, and helped networking and building community spirit, which is what a lot of a good conference is ultimately about.

Coffee. Unfortunately, we were unable to attract the barista sponsor from ABiC14 to sponsor ABACBS2015. AGTA did have a sponsored barista, though. Roche (I think) gave out three tickets with registration for the trade exhibit barista. Not quite as good as unlimited but it hit the spot. My other top conference coffee tip: bring a reusable cup! It' so much easier/safer if you want to take coffee into the talks and generally cuts down on spills - and refills! (Next year, I am hoping for ABACBS Keep Cups in the goodie bags!)

Overall, I had a lot of fun helping with the conference organisation - and would recommend it - and even more fun attending. Australia has some great science going on and a really strong/vibrant bioinformatics community, and I am proud to be part of it.

OMICS Group conferences are still to be avoided at all costs

Regrettably, my most popular post of the week is pretty much always: OMICS Group Conferences - Sham or Scam? (Either way, don’t go to one!) [I’d much rather it was one of the evolution posts - maybe Artificial Selection versus Natural Selection.]

A few weeks back, I was contacted by an ABC journalist doing an investigation of OMICS Group conferences, which have been trying to break into the Australian market. The show, Predatory publishers criticised for ‘unethical, unprincipled’ tactics, is fully available (complete with transcript) and an interesting, disturbing and upsetting in equal measure.

In the end, I declined to do an on-the-record interview - as another anonymous academic on the show said:

“Having been duped, it is somewhat embarrassing and you don’t really want to wave that around too much on national radio. Yes, I don’t want to be known as someone who was so easily drawn in.”

Nevertheless, I am still glad that I wrote the post. Predatory publishers and conferences are a scourge on academia and need to be exposed. Hopefully, Hagar Cohen’s ABC show will help. (They seem to know their brand is toxic and now avoid using it in emails - but they are still easy to spot!)

Good news! WHO calls for results from all trials to be reported

A bit belated but good news worth sharing nonetheless. From Ian Bushfield at Sense About Science, and as reported in Science and other media sites:

For the first time ever, the World Health Organisation (WHO) has taken a position on clinical trial results reporting, and it’s a very strong position! The WHO now says that researchers have a clear ethical duty to publicly report the results of all clinical trials. Significantly, the WHO has stressed the need to make results from previously hidden trials available. Ben Goldacre said, “This is a very positive, clear statement from WHO, and it is very welcome.” Ilaria Passarani from the European Consumer Organisation BEUC called it “a landmark move for consumers.” It is the position we and hundreds of you wrote to the WHO last autumn urging them to adopt. Well done everyone!

You can read more about the WHO’s statement and responses to it on the AllTrials website.

Further reading: Goldacre B (2005): How to Get All Trials Reported: Audit, Better Data, and Individual Accountability. PLoS Medicine 12(4): e1001821.

Yet more OMICS Group spam full of vacuous rubbish

Despite unsubscribing from a mailing list that I never subscribed to, OMICS Group keep sending me pointless emails to crappy conferences. Today it was “Biodiversity-2015”:

Biodiversity-2015 is specifically premeditated with a unifying axiom providing pulpit to widen the imminent scientific creations. The main theme of the conference is “Share and Enhance Ecological & Geological Conservation research” which covers a broad array of vitally key sessions.

“Biodiversity-2015 is specifically premeditated with a unifying axiom providing pulpit to widen the imminent scientific creations.” Wow! Someone had been over-using their random vacuous crap generator.

Again, no explicit mention of OMICS Group as the organiser was made, although this one did mention “accepted abstracts will be published in the respective OMICS Group Journals”. (For free - they’re so generous!)

At the end of the email, they tell me to:

Have a Great Day Doctor!!

Well, with two exclamation marks, do I have any choice?! What would have made a greater day would have been (a) not receiving the email in the first place*, and (b) having the “To unsubscribe click here” line at the end of the email actually contain a hyperlink. Instead, the “click here” was just text in a different colour!

*I’m not being entirely honest with (a) - I think my day was brightened a little by “specifically premeditated with a unifying axiom providing pulpit to widen the imminent scientific creations”!

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.

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!

Every conference should be like ABiC 2014 (#ABiC14)

Last weekend, I attended the inaugural Australian Bioinformatics Conference (ABiC 2014) in Melbourne. (Twitter tag #ABiC14 so as not to be confused with the ABIC Foundation conference in California.) I’ve been to quite a few conferences in my time, including a fair few bioinformatics conferences. The latter (in my experience) are often quite dull affairs - good for meeting people and “networking” but not so good for interesting science beyond the invited keynote speakers.

Happily, ABiC14 went far beyond expectations. I signed up because it is important for me as a relative newbie to meet more Australian bioinformaticians. This was accomplished but was only the start of the positive experience of this conference. In fact, the conference was so good that I thought it worth posting its successful attributes/decisions as a model for future conferences (and reminder to myself should I organise one).

Here then, in approximate chronological order, are my top take-home quality attributes of ABiC 2014:

Organisation. The conference website was well organised and clear prior to the meeting. The program outline was available in good time, enabling planning, with abstracts etc. available in a single PDF. The only real improvement I can think of would be to have a printed program (just the outline, not full abstracts) provided upon arrival. However, because there were no last minute changes to the program, this turned out to be a moot point.

Coffee. Science in general, and bioinformatics specifically, is fuelled by coffee. The Aussies do coffee well and ABiC 2014 had the genius idea of a sponsored barista who made a decent cup of fresh coffee to order. I took advantage of this on arrival, which really set me up for the morning session and got the whole thing off to a great start.

Venue. The Royal Children’s Hospital was a great venue. Access by public transport was easy. The lecture theatre was comfortable and a good size. Eduroam provided free WiFi access (even if HTTP sites were unavailable for some reason). Coffee breaks, lunch, and poster sessions were near to the lecture theatre and promoted mingling.

Size. I’m not sure what the final number of delegates at ABiC 2014 was but for me it was the perfect number. (I would guess around 180+/-.) There were enough people for some interesting diversity, presentations and posters but not too many to actually get to chat to people and visit all the interesting posters.

Interesting Science! This is clearly one of the most important aspects of a good conference but sadly one that is often not achieved by a bioinformatics meeting (beyond the keynotes). I think there were several contributing factors to this. First, there were not too many talks and no parallel sessions. There were twenty talks in total, in six sessions of 3-4 talks of 10-50 mins each. Each session kicked off with an invited speaker. By keeping the quantity down, the quality of the talks - and stamina of the audience - was maintained at a very high level. I was expecting to “zone out” and struggle to maintain concentration a few times but I found my attention captured by each speaker. Talk quality was further enhanced by…

No published conference proceedings. Because of the large computer science community within bioinformatics, a lot of bioinformatics conferences have the submitted work published as papers in conference proceedings or a journal special issue. Even when the journal is a good one, this massively decreases the likelihood of getting interesting science, which will normally be either (a) published in a higher impact biology or general science journal, or (b) not yet be ready for publication. As a result, talks tend to be more technical and specialist… and boring. ABiC 2104 avoided this trap.

Food. You don’t go to a conference for the food but having tasty snacks at the breaks and at lunch does add to a general vibe of happiness and satisfaction.

Beer. Scientists and computer geeks are not always the most extrovert of individuals, and a little something to grease the wheels of social interaction never goes amiss. The ABiC committee went as far as to establish the beverage categories of choice with a pre-conference questionnaire. They gained extra brownie points from me for the presence of Fat Yak among the offerings.

Posters. This is largely a composite of the above points but the poster session was one of the better ones I have attended. For a start, the posters were up for the entire conference. It really bugs me when conferences do not do this and it all comes down to choice of venue - so well done ABiC for selecting a venue with this capacity. Furthermore, the poster location had great access - being a wide corridor - and was between the auditorium and the morning/afternoon drinks and snacks, maximising quality exposure. Furthermore, restricting the number of talks saved lots of interesting science for the posters!

Conference Dinner. If you are lucky, the conference dinner will be one of the best networking points of a conference, as your table represents a fairly captive audience with whom you have to interact. Nevertheless, conferences are generally charged to grants and researchers are on a budget, so it is frustrating to be forced to spend a load of cash on a meal that rarely lives up to the expectation of the price tag. ABiC 2014 took a pragmatic solution of booking out a restaurant and bar, and everyone paying for their own meal and drinks ordered off a standard single course menu. It worked really well. The food was good (but not excessive) as was the company. There was only one course but you never need more than that when there are morning and afternoon snacks in the breaks.

Timing. As far as I could tell, the talks generally seemed to stick to time, so coffee/lunch breaks were not truncated. Again, by keeping the number of talks (and talks per sessions) low, this was easier to achieve. Nonetheless, it's still something that is not achieved by all conferences. (I remember one conference in which my talk started 5 minutes after it was supposed to finish!)

Twitter. I’m a bit sporadic on Twitter at the best of times and not entirely convinced that live tweeting in a conference is not generally more of a distraction than a benefit - for those present, at least. However, I did enjoy having the #ABiC14 twitter feed open during the meeting and felt that it added to the sense of community. Of course, the aforementioned interest of the talks (and the smallish size of the meeting) limited the distraction.

As of the end of ABiC 2014, there was no plan for an ABiC 2015. I, for one, really hope that there is one - and that the organisers are able to stick to the same model.

How (not) to apply for a PhD

As with most academics, I get a fair a number of unsolicited enquiries about possible PhD placements. Unfortunately, a number of these appear to be from students who are receiving little or no advice regarding how to go about making an application.

Every now and then, an application stands out from the bunch for being particularly good or bad. A while back, I received one of the latter, which made me so sad that I thought I would turn my response into a post. What made it particularly tragic was that it was from a student who had received government funding to study abroad, and was therefore in a fairly strong position.

The email (name redacted) was as follows:

On [DATE] "XXX baby" <XXX@yahoo.com> wrote:

Subject: Hello doctor

My name is XXX, I finished M.Sc. degree in XXX University in Iraq at (2012), I have obtained a fund from the Iraqi government to study PHD in Microbiology in the Ustralia.

I had opportunity to be a student of Iraq and My interests are about Bacteriology and Immunity in general and I really hope to get your kind acceptance to pursue my PHD under your supervision in University of UNSW.

Kindly find attached my C.V please which I hope it gives detailed overview about me

Thank you very much

The CV was then attached as several JPEGs of scanned pages. Unusual attachments plus a username of “XXX baby” and subject line of “Hello doctor” meant that this one almost went straight in the bin as spam. Given the number of typos and other errors, it might have been better if it had.

I’ve had some others that were almost as bad, including one that started “Hello Sir !” and proceeded to end every sentence with an exclamation mark! Yes! Every sentence! No! That’s not a good idea!

Lest I get misunderstood, I must stress that the point here is not to be mean to these students. The issue is that they are clearly not getting the advice they need, especially given the fact that they are writing in their second (plus) language and applying to academics with a different culture.

Here then, is my advice/guidance for those wanting to make an unsolicited application for a PhD studentship (though most points still apply if a project is being advertised). I get many applications from overseas students. If I am even to consider you as a potential student then you need to impress me. The following impress me:

Professionalism. Send a well structured email, with a sensible subject such as “PhD enquiry” and a CV (if attached) that is provided as a single sensibly named PDF (or docx), i.e. your name and “CV” feature somewhere in there.

Genuine Interest. Personalise your message and provide some indication that you really know who I am. “Dear Sir” indicates a blanket mailshot to all and sundry and is thus destined for the bin. Knowing who I am is not enough, though. I also want an indication that you know and understand at least something of the research that goes on in my lab. Referencing degree subjects or research experience that match neither my background nor research focus indicates poor research/understanding. A PhD is long, hard graft and I need to know that you have genuine interest or everyone’s time will be wasted.

A clear CV. Your CV should have relevant skills and metrics highlighted. If you are from overseas, remember that I probably do not know what your grades mean, so place them in context. What proportion of students get those grades/medals etc.? This is a research post, so describe some of your research projects and your role in them. When it comes to CVs, evidence is the name of the game. Don’t just list skills and positive attributes: provide examples.

Motivation/Enthusiasm. Good grades are not enough and academic ability will only get you so far in a PhD. Motivation and enthusiasm are critical. As well as a CV that stresses relevant achievements, include a personal statement that convinces me that you want to do a PhD (with me) for the right reasons, and are likely to see it through.

Ask questions. This is basically genuine interest + motivation/enthusiasm but worth stating in its own right as intelligent questions are the evidence of those things. It's your PhD and your life - you should care about what you might be doing. The caveat is this: do not ask a question that is answered by ten minutes of reading my lab's webpages and/or paper abstracts.

Good communication skills. If English is not your first language, get your emails proof-read by someone with good English. Exclamation points after every sentence indicates that communication will be tricky, as does failure to appropriately understand/respond to emails. I am not going to think you are not keen if you take a few days to give a measured response. I am going to think that communication may be insurmountably difficult if I get a speedy response that is riddled with errors.

Funding. Unless you are applying for a specific funded project, you will need to secure your own funding. A clear indication of a funding plan is therefore crucial. If you already have funding, this is good. Better still, would be to detail exactly what that funding covers (i.e. duration? fees AND living expenses? any attached conditions?) and to indicate how the funding was won and how competitive it was. Winning a competitive scholarship is one way to impress. Even better, provide evidence in the form of an official notification of funding etc.

References. Ultimately, it is very tricky to assess a student from a CV and covering letter alone. Again, evidence is the name of the game. Provide two or more faculty members or professional scientists who can provide an academic reference. These should have institution email addresses, not personal gmail/yahoo addresses, as anyone can create these and they will carry less weight.

Fail to hit most of these points and your application is in the bin. (I now have a generic response that I send out to generic applications.) This may seem harsh but there is a lot at stake and it is important to get a good fit between student, supervisor and project; a poor student/fit is a net drain on lab productivity.

A PhD is not something to embark upon lightly. It will consume many years of your life and will quite possibly determine the direction of the rest of your professional life. A PhD application should be made with all of the research, care and attention to detail that this implies.

STAP retractions are both a failing and a triumph of science

It was looking inevitable and this week two high profile Nature articles on “STAP” (stimulus-triggered acquisition of pluripotency) stem cells were finally retracted in Nature:

Several critical errors have been found in our Article and Letter (http://dx.doi.org/10.1038/nature12969), which led to an in-depth investigation by the RIKEN Institute. The RIKEN investigation committee has categorized some of the errors as misconduct (see Supplementary Data 1 and Supplementary Data 2). Additional errors identified by the authors that are not discussed in RIKEN’s report are listed below.

...

We apologize for the mistakes included in the Article and Letter. These multiple errors impair the credibility of the study as a whole and we are unable to say without doubt whether the STAP-SC phenomenon is real. Ongoing studies are investigating this phenomenon afresh, but given the extensive nature of the errors currently found, we consider it appropriate to retract both papers.

Nature cover the retractions in an editorial, “STAP retracted”, which runs with the tagline,

“Two retractions highlight long-standing issues of trust and sloppiness that must be addressed.”

You can get a sense of those issues from the retraction statement and the editorial, which concludes:

“we and the referees could not have detected the problems that fatally undermined the papers. The referees’ rigorous reports quite rightly took on trust what was presented in the papers.”

They also highlight “sloppiness” in science, manifest as a “growth in the number of corrections reported in journals in recent years”. (Something not helped, in my opinion, by high profile journals such as Science and Nature burying so much of the important methods in Supplementary Data, which is rarely reviewed or edited as critically as material in the main text body.)

You can read more about those issues in the editorial and elsewhere, such as the Faculty of 1000 blog. The STAP papers, their initial irreproducibility and eventual retraction highlight potential failings of the current scientific system, which places far too much emphasis on output quantity and impact rather than (true) quality and integrity.

However, they also highlight the tremendous success of the scientific system.

The fact is, the experiments were repeated, the failure to reproduce results was documented, suspicions were raised and investigations made. Science works because, ultimately, you cannot fake it. Whatever data you make up, whatever results you misinterpret, whatever sloppiness leads to “conclusions [that] seem misleadingly robust”, the truth will out eventually. You cannot hoodwink nature.

And that is why science remains far and away the best (probably only) method we have for establishing the truth about reality. The system maybe flawed, it may waste money and it may lead poor unsuspecting suckers chasing wild geese, but eventually it will self-correct. So, whilst I would never put my trust in individual scientists (unless they have earnt it) or results, and I remain skeptical of every new claim, I still emphatically trust science itself.

Prof Bryan Clarke (1932-2014)

I was sad to read a post on the Evolution Directory (Evoldir) by my PhD supervisor, John Brookfield, that Professor Bryan Clarke died last month. Bryan founded the Genetics Department (later Institute and now Centre for Genetics and Genomics) at the University of Nottingham , where I did both my undergrad degree and PhD. He and retired when I was still an undergrad but, as Emeritus Professor, he was still heavily involved in the department for the rest of my time there.

Although I did not know Bryan well, he always had time for students and was an inspirational character - and that was before the Frozen Ark project was launched. I was particularly impressed by the way that he managed to combine ground-breaking basic science with regular visits to Pacific island paradise!

With permission, I have repeated John’s post below:

It is with great sadness that we have to report to the evolution community the death of Professor Bryan Clarke FRS on Thursday, the 27th February 2014.

Bryan Clarke was a leader in our understanding of the process of evolution for more than four decades. He made fundamental contributions, both empirical and theoretical, particularly in elucidating the forces that maintain genetic variation in populations, and in throwing light on the process of speciation.

Bryan was born on the 24th June 1932, and, following service in the Royal Air Force, was educated at Magdalen College Oxford, from where he received both his BA in 1956 and DPhil in 1961. From 1959 to 1971 he worked at the University of Edinburgh, starting as Assistant Lecturer and rising to a Readership. In 1971 he was the Foundation Professor at the new Department of Genetics at the University of Nottingham, and remained until 1997, when he became Professor Emeritus.

The Darwinian theory of evolution by natural selection identifies genetic differences in populations - polymorphisms, as the key to evolutionary change. It is of fundamental interest whether polymorphisms are affected by natural selection, or solely by genetic drift. Bryan’s research focussed on polymorphisms in snails, including members of the genus Cepaea, the shells of which vary greatly in colour and in their banding patterns. While some had naively suggested that this variation might have no effect on the organisms’ fitness, earlier experiments and observations, from Cain and Sheppard in particular, had demonstrated that these variants were indeed subject to natural selection. But, if there is selection operating on this genetic variation, why does the population not come to consist of only a single, best-adapted, type? The answer is that selection can, in some circumstances, maintain variation rather than destroying it. One mechanism for the maintenance of genetic variation is heterozygote advantage, which explains, for example, the high frequency of the allele causing sickle cell anaemia. Bryan knew that the patterns of inheritance of the polymorphisms in Cepaea could not be explained by heterozygote advantage. Rather, he was able to demonstrate that these are maintained by a different mechanism, frequency-dependent selection, in which the fitness of genetic types increases if their frequencies in the population diminish, thereby creating a stable equilibrium in which multiple genetic types are maintained. His studies of frequency-dependent selection were able to demonstrate the near-ubiquity of this phenomenon when visible polymorphisms are studied in wild populations, and also showed the selective agents which brought this about. The frequencies of polymorphic variants in snails can vary greatly in space, without any obvious environmental correlates. An important and influential step in the understanding of such “area effects” came from Bryan’s models of morph-ratio clines in his 1966 American Naturalist paper.

Studies of visible polymorphisms were augmented, from the 1960s, by the study of polymorphisms in the amino acid sequences in proteins, investigated initially through electrophoretic detection of differences in the electric change on enzyme molecules. As with the visual polymorphisms in Cepaea, some assumed that the changes were invisible to natural selection. Bryan Clarke advocated the view that a large proportion of the changes were indeed subject to natural selection and demonstrated experimental support for this view, particularly for variants in the enzyme alcohol dehydrogenase in Drosophila melanogaster. The study of selection acting on polymorphic differences in amino acid sequences is a direct way to obtain evidence about whether the long-term evolution of the amino acid sequences of proteins is shaped by natural selection. Some believe that protein evolution is almost completely dominated by random forces in which the successful variants were so not because of the advantages they gave to their bearers, but as a result of genetic drift. Bryan Clarke was one of the main advocates of the view that a large part of the evolutionary changes in the amino acid sequences of proteins were indeed driven by Darwinian natural selection, a view that results from large-scale DNA sequencing are confirming in many species.

Bryan Clarke also played a large part in developing our understanding of the process through which species form. He carried out a long-term study of species of the land snail Partula on the South Pacific island of Moorea and neighbouring islands. He appreciated that, in the early stages of speciation, matings between members of populations undergoing speciation do not stop instantly- some hybridisation persists. Species stay distinct notwithstanding there being some gene flow between them. Thus, selectively important genetic differences between species, such as those determining form, colour and behaviour, are maintained as distinct and recognisable features, while the low levels of gene flow resulting from hybridisation allow genetic differences which are not selectively important to randomise themselves between the hybridising forms. These phenomena have been documented in Partula, where less important differences have been shown to be shared between species which live in the same geographic location. The ability to study these early events results from the choice of the Partula species, where speciation has been “caught in the act”. Increasingly, similar phenomena are now being documented in patterns of DNA sequence diversity in other species studied at these early stages.

Through these diverse achievements at the cutting-edge of understanding of the process of evolutionary change, Bryan Clarke was a great mentor and role-model for younger scientists in evolutionary genetics, and supervised more than thirty research students, at least six of whom are now professors. He was a co-founder of the very successful Population Genetics Group, a meeting for population geneticists from the UK and Europe that has been running for almost fifty years.

He was co-founder and trustee of the charity “The Frozen Ark”, which preserves, in the form of DNA and cell lines, the genetic material of endangered animals, to allow future scientific study.

Honours and awards for Professor Clarke reflected his outstanding role in modern evolutionary genetics. He was elected a Fellow of the Royal Society in 1982, became an International Member of the American Philosophical Society in 2003, and a Foreign Honorary Member of the American Academy of Arts and Sciences in 2004. Medals and awards include the Linnean Medal for Zoology in 2003, the Darwin-Wallace Medal of the Linnean Society in 2008, and the Royal Society’s Darwin Medal in 2010.

Bryan leaves his wife Ann, his son Peter and daughter Alex.

Picture from Bryan Clark's obituary in The Telegraph.

UNSW Biological Sciences makes the Top 50 in QS World Rankings

I’m deep in grant- and lecture-writing at the moment (hence the lack of posts) but the QS World University rankings are out for 2013/2014 and UNSW is ranked 50^th in Biological Sciences. Obviously, I haven’t been there long enough to have contributed to this but still good news and worth a mention! Overall, UNSW was ranked 52^nd.

Pretty good result for the University of Southampton at 86 too. (U. Sydney is 38^th but you can’t have everything! :op)

OMICS Group Conferences - Sham or Scam? (Either way, don't go to one!)

I want to preface this post by saying that it’s been one of the harder ones to decide whether to write. On the one hand, it feels a little unprofessional and self-sabotaging to criticise a conference at which one was an invited speaker. On the other hand, my recent experience of an OMICS Group conference was so poor that I feel compelled to warn others. One thing I want to make clear from the outset, however, is that I do not want to denigrate any of the speakers; despite the shortcomings of the conference itself, there was nothing wrong with the contributions of those in attendance. (I wish I could say the same of the OMICS Group organisers.)

Earlier this year, I was invited to speak at the OMICS Group 3rd International Conference of Proteomics and Bioinformatics, held in Philadelphia earlier this month. It sounded like it would be a fairly big conference - the topic was broad, the website listed 24 conference organisers (including scientists from renowned Universities), eleven thematic tracks and venue pictures featuring a conference room of reasonable size set up for a talk. Although I am not generally a fan of massive conferences, it is good to present at one; I recognised a couple of names of confirmed presenters, one of whom was a friend, and after weighing up the costs I decided to accept the invitation. With hindsight, I was rather naïve and/or gullible in accepting the invite. The conference website, it seems, is very misleading - it lists four front-page “Renowned speakers”, for example, of whom only two actually spoke at the conference. At the time, though, I had no particular reason to be wary.

There were a few bad signs before even turning up to the conference, included poor information regarding the speaker guidelines and even the hotel in which the conference was taking place. The big one that worried me most was the timetabling of the conference when the full scientific programme was finally released. Despite 11 “tracks”, the conference was organised into a single stream. This is not so bad in itself - parallel sessions often cause problems of clashing talks of interest; the issue was that the resulting programme was so crammed full, there were hardly any breaks.

As anyone who has been to conferences knows, many of the most productive parts of the conference are the conversations over coffee, lunch and evening refreshments. This conference had scheduled two 15 minute coffee breaks and 40 minutes for lunch in the context of days of 9-6 talks. A one hour “cocktail” (beer and wine) session was listed for each day but there was no conference dinner or other activity to promote extended interaction. Not only was I worried about the lack of interactions - particularly for someone a bit introverted like me who is a bit slow to warm up - from past experience, there was a chance that talks would over-run to the point that breaks would disappear and/or it would take longer than the coffee break to get everyone out of the auditorium and lined up for coffee.

(As it happens, concerns about breaks were ill-founded. The reason for this is that the disorganisation of the conference at the event and the alarming no-show rate of speakers meant that we often ended up with extra time for breaks. The exception to this was Day 1 but I’m getting ahead of myself and will come back to that.)

Despite these warning signs, I really wasn’t ready for the shambles that was to come. Having had breakfast on Monday in the wrong room due to lack of information, I went to the conference suite to register and make my way to the conference room. The conference pack itself set the scene for the conference, being mostly advetising for OMICS Group activities with precious little regard for the science. (No lists of attendees, or places to write notes that I could see.) This was then reflected in the venue.

For one thing, it was tiny. I mean tiny. The venue image that I previously interpreted as the one of several parallel sessions turned out to be twice the size of the venue for the entire conference. This is partly because the room had been divided and the other half was being used for another OMICS conference. (There were three in the hotel plus one or two other meetings not organised by the OMICS Group.)

Not only was it tiny but the layout was awful - half a dozen large round tables surrounded by ten or so chairs each. Given that there were 52 speakers on the programme plus four keynote speakers and one workshop presenter, this was not encouraging. A conference with 24 listed of conference organisers having not much more than double that number of participants tells you that there is a problem somewhere. The biggest thing in the room was the banner advertising the OMICS Group and its sponsors.

Things did not get any better once the conference began. The schedule included a rather intriguing 30 minute(!) slot for an "opening ceremony", which again added to the pre-conference illusion of grandeur. In reality, it was five minute introduction by an unfortunate member of the keynote forum who seemed to have been volunteered for the role not long before. Furthermore, the absence of formal organisation was such that agreeing to this role seemed to land him with the unenviable task of essentially organising and managing the rest of the speaker lineup for the rest of the conference. To add insult to injury, this was someone who was not even on the organising committee.

The rest of the day was odd, bordering on farce. Things started OK. Thanks to the “opening ceremony”, we were running ahead of schedule. One of the keynote speakers had substituted a junior member of their lab in their place - a good move, I now see - but the keynotes were generally interesting and I was beginning to think “maybe this won’t be so bad”. At that point, the conference organisers made their only detectable organisational intervention - the group photo.

Quite why you want a photo showing how embarrassingly tiny your broad International conference is, I don’t know, but they did - enough to not only obliterate our time cushion but (thanks to some comically bad preparation and organisation by the photographer) also eat into the scientific schedule. This for me summed up the whole endeavour: science taking second place to OMICS Group publicity. The photo is now up on the website and reproduced below. I count 48 people. There were 57 listed speakers. (I will come back to that!) Remember, this is for a conference with an alleged 24 organisers!

I now suspect that essentially everyone at the conference had been invited to speak and that the “organising committee” had no role in the organisation or speaker lineup - indeed, I wonder if they all even know that they are being listed as organisers. Nevertheless, after a now-delayed coffee, things picked up again with some interesting talks, although there had clearly been little or no instruction (and sometimes little thought) regarding the technicalities of getting talks ready and computers switched over etc.. (There wasn’t even a clicker for advancing slides - I had to use my own!) Thanks to a few hiccups compounding the photographic nonsense earlier, we were late for our 40 minute lunch break.

Lunch. This should be one of the best times in any conference - a time to discuss the science of the morning and look at what’s on offer in the afternoon. After a couple of interesting talks, I was looking forward to a bit of discussion. Instead, lunch was a buffet affair on the mezzanine floor, shared by all the conferences and with insufficient tables and seating to be able to sit even with the two or three people you were just chatting to in the lift. On one occasion, I stood up to get a coffee after lunch and found my seat taken by members of another conference before I could return to it. Later, we were even asked to leave our table to make room for the next conference when I was still eating. (On that occasion, we were still well within the allotted lunch time on the programme.) The food itself was pretty nice but lunch, thanks to shoddy organisation, was one of the worst conference lunch experiences I have had.

The rest of the conference bumbled along in much the same vein. I’ve been at a few conferences where the schedule has been re-jigged slightly on the day but never before have I been at a conference where speakers were AWOL and nobody appeared to know. Before each talk, there was a hopeful appeal to the audience for the speaker to come forth and show themselves - or, as in a few cases, not. The first couple of times, I thought it a bit rude to just not show up but I fear that the real reason might be a bit more sinister - the OMICS Group, it seems, have a reputation for not refunding people who decide to pull-out of their activities; given the small size, I would not be surprised if they kept those that withdraw on their programme. As far as I can tell, the OMICS Group simply do not care if conference is a disaster, as long as they can spin it as a success. The packed programme quite possibly exists only to maximise the number of names they can associate with their conference for some credibility.

One of the saddest things - and one of the reasons for this post - is that a little more research on my part would have warned me off. The Scholarly Open Access blog had an article from January this year: OMICS Goes from “Predatory Publishing” to “Predatory Meetings”. (My wife emailed me the link at the meeting but I wasn’t brave enough to read it until at the airport to come home!) The title says it all really but some of the content within resonated with me quite strongly.

Now new evidence has surfaced revealing that OMICS, which is also in the business of organizing scientific conferences, has been 1) using the names of scientists, oftentimes without their permission, to invite participants to their meetings, 2) promoting their meetings by giving them names that are deceptively similar to other well-established meetings that have been held for years by scientific societies, and 3) refusing to refund registration fees, even if their meetings are cancelled.

First, OMICS implies that its editorial board members are conference organizers by placing their names and photographs on their conference web pages, and by sending email invitations to their meetings which are “signed” by members of the editorial boards. However, many of these people never agreed to be meeting organizers, and some have never even agreed to be become OMICS editorial board members.

The rest of the post - and the comments (to which I have now added) - do not make comfortable reading. The author ends by saying:

I strongly recommend, in the strongest terms possible, that all scholars from all countries avoid doing business in any way with the OMICS Group. Do not submit papers. Do not agree to serve on their editorial boards. Do not register for or attend their conferences.

I find myself having to agree. Despite the small size, lack of focus and crappy organisation, I did actually get some useful outcomes from the conference but these were despite the efforts of the organisers rather than because of them. Some of the science and individual presentations were of good quality but this was the worst scientific conference that I have attended by a long stretch - and I let them know as much in my feedback form! (Of course, visiting the conference website now shows a bunch of supportive quotes of praise, making it look like an unmitigated success. Either these individuals were at a different conference to me, have not experienced a good conference, or are way too polite.)

The whole thing left me feeling a little violated, to be honest. The delusions of grandeur portrayed by my “Certificate of Recognition” does nothing to ease this sense:

OMICS Publishing Group and Editor (s) … enjoy special privilege to felicitate [me] for his/her phenomenal and worthy oral presentation…

Even worse is what happens if you click “View More” following the “Renowned Speakers” on the front page. Another page is opened listing 42 “Executive Editors”. I am dismayed to find myself listed among them. I am not sure what qualifies someone for the list - as far as I can tell, not all those listed spoke at the conference and not all of the conference speakers are listed - but I want to make it quite clear that I have made no executive and/or editorial contribution to the OMICS Group. I have contacted them about this error, so hopefully it will be rectified. (I am not holding my breath.)

I am not sure whether they are fraudsters but, either way, I also strongly advise boycotting OMICS Group activities on the basis that they are scientifically bankrupt beyond anything that individual attending scientists bring to that activity. It is possible that I was just unlucky. Given the Scholarly Open Access comments and the apparent lack of embarrassment - and total lack of apologies - at the utter shambles that was the OMICS Group 3rd International Conference of Proteomics and Bioinformatics, I highly doubt it. For this reason, I feel the need to warn others.

Conferences are not cheap, so save your money and use it to go to a conference organised by scientists, for scientists, with science and not money/prestige/publicity as the primary motivator. Based on my experience, this will not be one organised by the OMICS Group.

There is one other thing I have learnt from this experience: if you are invited to present at a conference, do your homework.

[NB. I have made the OMICS Group aware of my thoughts and concerns. I will update this page in the light of any responses.]

[Update 4/12/13: Although OMICS Group never responded to any of my emails, it appears that they have modified their conference homepage and I am no longer listed as an “Executive Editor”. Doubly so, in fact, as they have corrected the title to read “Renowned Speakers” instead and removed me from the list!]

[Update 18/8/15: ABC have a recent exposé of predatory publishers (including OMICS), which is worth a read or listen.]

The best exam (and coursework) tip ever!

I'm heavily in the middle of exam and coursework marking, hence the distinct paucity of posts, but I felt compelled to revisit a similar post from last year with the number one best exam tip of all time:

Answer the Question!
There is an equivalent for coursework too:

Follow the Instructions!
As examiners, we're not out to trip you up but we can only give credit for relevant material. (More exam tips here.)

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PS. If someone knows why all my post titles have gone wonky, I'd love to know! Blogger, what have you done?!