TREEFINDER has no strong feelings about immigration

MUNICH.  The software TREEFINDER has distanced itself from its own author by stating categorically that is has no strong feelings on immigration, and is definitely not a racist.

Social media was buzzing yesterday as a scientist from Germany, Gandolf Yob, decided to reveal that he was a mental, screaming, racist, bigot by changing the license on his TREEFINDER software limiting use from countries who “host non-EU immigrants”.  Rambling about a new world order, Gandolf essentially committed career suicide.

However, the software itself, TREEFINDER, sought to distance itself from its psychologically unstable author.  “Clearly the images of drowning children weren’t enough to shake Gandolf’s belief that all of the problems in society are caused by poor, brown, foreign people.  I just want to state, categorically, that I do not share Gandolf’s world view”

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Scientists amazed that PLOS isn’t rolling in cash

BOSTON, USA.  Scientists have expressed their amazement that the public library of science (PLOS) isn’t “absolutely rolling in it”, it has emerged, after PLOS announced that they were increasing their article processing charges to $1495 on Tuesday.

Wikipedia lists that PLOS ONE alone published 31,500 papers in 2013 and 30,040 papers in 2014.  Even at just $1000 per paper, that amounts to an income of $61.54 million in just two years.  Given that the majority of scientists (academic editors and reviewers) work for PLOS for free, this appears to be a large income for PDF generation, a bit of type-setting and running a website.

“I think this must all be going into Mike Icing’s Swiss bank account” said one source, who wished to remain anonymous.  “I mean, $60 million is a lot of money – what do they spend it on?  Is their a PLOS jet sitting round somewhere?”

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Scottish government to ban evidence

Edinburgh.  Following criticism of the Scottish government’s decision to ban GM crops, it has emerged today that they also plan to ban all forms of scientific evidence, including all rational and logical thought.

Speaking for the government, Richard “Dick” Thickhead said: “We don’t want to place the Scottish food system ‘at risk’, therefore we are going to base all of our decisions on unfounded opinion, anecdotal evidence and second-hand stories we heard down the pub.  We pay particular attention to any stories about how the old days were much better.  Only by completely eliminating all forms of rigid scientific endeavour can we ensure that the public gets what they want”.

In favour of the ban on evidence was Danny McMurphy who recovered remarkably quickly from ‘flu’ in 1982: “I’m in favour of this ban on science!  Listen, I had the flu way back in 1982.  After a few days, I went to the Doctor, and he told me to take paracetamol and rest in bed, which I did.  But on the way out of the surgery, I saw this wee dog who seemed to wink at me as I walked by.  The next day I was right as rain, and I just know it was that dog that did it.  So screw you science!”

Rather predictably, every single scientist in the World is against the ban.  Speaking for all scientists, Ann Glover explained: “Look, you can’t base decisions on anecdotal evidence.  People will tell you they saw Elvis in their local chippy – that doesn’t mean he’s alive!  Similarly, someone with cancer who happens to get licked by a swarm of angry squirrels might recover from the disease and live a healthy life – that doesn’t mean we should apply squirrel-lick therapy to all cancer sufferers.  That’s why we have the scientific method, based on evidence, rationality and logic”.

Other things the Scottish government plans to ban include the colour blue, double-glazing, impersonating Lionel Ritchie and plays with the letter “A” in the title.

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Loud, annoying scientists still dominating conference calls

USA.  The loud, brash and annoying scientists that everyone secretly hates are still dominating weekly conference calls and collaborative scientific discussions, much to the annoyance of the polite, shy but very good scientists who end up fixing everything quietly afterwards, a new study has shown.

“It’s so annoying!” said ‘Phil’, undercover of anonymity and using a pseudonym.  “We’re on the conference call and the chairperson asks for volunteers to carry out a task.  Of course, I am painfully shy, and I would never vounteer for anything in case I upset someone else who wanted to do it; but what I don’t expect is for some noisy fool to step up and loudly proclaim their intention to do the task.  I just have to sit there and quietly fume, all the while planning how I will fix their half-finished work” he finished, visibly annoyed.

“The problem is” said Gunther Knockwurst, first author of the study “… the problem is that as soon as you ask for volunteers, the busy people, i.e. the good people, they’re busy because they’re good, they don’t volunteer.  No, no – the people who volunteer are those who have time on their hands.  Why do they have time on their hands?  Because they are stone-cold idiots, people that no-one in their right mind would assign tasks to” he finished.

The study, published in PLOS TWO (similar philosophy to PLOS ONE, but does not require actual scientific evidence), also found that academic science selects for arrogant, loud, brash, annoying men who are capable of ruthlessly marketing their own brand, regardless of scientific ability.

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Post-doc realises supervisor was bullshitting the whole time

Birmingham, UK.  A post-doc at the Institute for Microbiology and Infection has come to the realisation that her PhD supervisor was a complete bullshitter, after graduating and joining a better, more competent group.

Dr Emily Noodles, who now works in the Quick group at the University of Birmingham, said: “During my entire PhD, I looked up to my supervisor, and I thought he knew everything.  He certainly was never short of opinions and had an answer for every question.  But now I’ve joined a competent group, led by Josh, I’ve realised what an utter bullshitter he is – he literally knows nothing” she finished.

It’s a problem on the increase – as more and more principal investigators apply for fewer available grants, they are incentivised to “exaggerate” their skills.  This can exacerbate an existing problem, whereby arrogant, narcissistic researchers believe they are capable of virtually anything, just because they published a few papers in BMC journals and won a £20k travel grant in 2006.

However, with the increasing mobilisation of PhD students around the world, the chances that they will join a better group and call out the utter crap their former supervisors used to spout are increasing, and social media is a perfect outlet for their fury.

We contacted Dr Noodles’ former supervisor, but he refused to comment, as he was too busy with his new career in artificial intelligence.

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Most people doing genomics not actually doing genomics

CAMBRIDGE.  Most people who claim to be genomics researchers are not actually doing genomics at all, and instead are just sequencing things and calling it genomics, it has been found.

“Genomics is the study of genomes” said Barney Ewingsworth III from the Excellent Biology Institute (EBI) “and genomes are incredibly complex, with repeat regions, duplications, deletions, selective sweeps, gene deserts, 3D structure, mobile elements etc etc.  … and it turns out that many people who say they are genomic researchers are actually just people with a few quid who paid to sequence a stupid genome, like the lesser spotted tree trout.  Then they assemble it (badly), submit it to GenBank still full of adapters, and bloody PhiX, and get a paper in BMC I couldn’t get this into Genome Research.  It’s a scandal – they give genomics a bad name!” he finished, and then went back to his day job as Mayor of London.

In an earlier survey, it was found that many scientists are sequencing things because they can’t think of anything else to do.  Now it would appear that those very same scientists have no idea how to handle the data, and are poisoning the well with hundreds of crappy genomes.

Genomics researcher and rock star Neil Kardashian has a potential solution: “Come the revolution, people who submit crap genomes will be first against the wall.  Seriously – if you had anything to do with the Carp genome, which is full of Illumina adapters; or you published a bacterial genome with a mysterious PhiX contig, you probably deserve to be shot.  Get out of science, you’ve no place here!”

TheScienceWeb share Neil and Barney’s frustrations!


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At nanopore hackathon, PacBio turn up with sweets

Birmingham, UK.  At a hackathon to develop software for oxford nanopore sequence data organised by Dr Rick Slowman yesterday, attendees were shocked to find that PacBio had turned up unexpectedly and started offering everyone sweets.

The hackathon involved some of the finest minds in bioinformatics, as well as a range of hangers on.  However, all were shocked when, uninvited, PacBio attack-bot Racing Jason turned up with candy and offered it to everyone.

“It was weird – at first we were really scared” said Dr Slowman. “We all knew how dangerous he could be after his relentless-but-passive-aggressive attacks on Twitter, but he was all smiles and asked if we could all be friends” he finished, slowly.

“Racing Jason” was formerly thought to be a hyper-intelligent AI that existed only in graph-space, producing ever more complex assembly graphs that few humans could understand.  However, in recent years, he has turned up at meetings as an actual, 3D person.  His appearance at the nanopore hackathon is surprising given his stated hatred of the technology.

“After the initial shock” continued Dr Loose Matt (a co-organised of the hackathon) “we all decided to try his sweets.  They tasted really nice, and made you think that you could do a lot with such beautiful sweets.  But they were really huge, massive unwieldy things – you couldn’t fit them in your mouth.   Racing Jason suggested we should build a new mouth just to fit the sweets in. Really expensive too” he finished.

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