Blog to subreddit – Join r/FutureBio

Hello friends,

It’s been a long time. Well, a reaally long time. Mostly I haven’t been posting here because I’ve been too busy with the live action version of TXL – The Genomics Salon here at UW. Check out genomicsalon.wordpress to find out more.

But I’m missing the online world. However, I really want to stop just critiquing the status quo and start envisaging what the future could look like. So if you’ve enjoyed reading the posts in this blog then I encourage you to head over to http://www.reddit.com/r/FutureBio/ and join the discussion there!

Orlando

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My opinoins are a matter of fact!

If you’ve read a few posts on this blog you might notice that I like to preface a lot of statements with ‘I have experienced’ or ‘it seems to me that’. This is not just filler, its a reminder that any statement I make is merely an opinion informed by the limited experiences I have accrued during my time in the scientific world. Often I suspect that these impressions are representative, but I have no basis for claiming so. This is how most of us form our opinions on most things most of the time.

Obviously, the scientific method stands in stark opposition to that approach. It forces you to actively disbelieve first impressions and anecdotes. It forces you to measure the world and see if those measurements match a well-thought through assessment of what they ought to be if your hypothesis is true and not if it is false (you try to disprove your own opinions). The scientific method has been the most persuasive approach to defining truth that humans have ever invented. It is largely so persuasive because it underpins engineering and has given us all the wonders of modern life. Conclusions drawn from the scientific method carry gravitas.

It seems to me that many scientists believe that because in their professional context they utilize the scientific method all of their opinions ought to carry similar gravitas and be presented in a similar form.  Take a recent review piece from Nature Plants with the provocative title: Is modern wheat bad for health?  written by researchers at a prominent crop research centre in the UK. The first figure, unceremoniously stolen is apparently proof that people are concerned about the health impacts of wheat. It is titled Increased interest in the impact of wheat on health over the past two decades shown by internet search hits.

This is problematic. Leaving aside the fact that google was only started in 1998, the metric being measured is searches for Wheat/Gluten + Intolerance/Sensitivity relative to searches for terms related to four common cancers. This is thus a complex metric and its hard to say how much this tells us about peoples health concerns. It also says nothing about any actual health impact (as recognized in the text of the article there has been little research into that).

I’m singling out this graph because I just read that article and its fresh in my mind, not because I think the authors did something egregious. It’s just an example of trying to quantify an impression about the world and dress it up in the imperious robes of science.

Maybe I’m being too harsh. Isn’t this just the result of the data rich world we live in. Probably. But I think thats a danger.

Data is not the scientific method. Data must be framed within the context of hypotheses and they must be very carefully vetted. Most scientists know that you can generate useless data ad infinitum if the set up of the experiment was not well constructed.

I have often heard scientists lamenting that politicians act contrary to ‘the science’ when what they mean is that they acted contrary to ‘what scientists felt was the correct course of action informed by both their research, the opinoins of their colleagues and their general world view’. There is nothing shameful about having opinoins and recognizing them as such, and opinoins will always be the basis of political decisions at a very fundamental level. Whilst I would love to see governments employing the scientific method more frequently and with more rigor than they currently do, the decisions they take must always rest on some basic principles on what is right or wrong.

So if you are a scientist, next time you hear a colleague talking about anything beyond their immediate research see for yourself if they try to impart the gravitas of the scientific method onto all of their opinoins.

Maybe I’m totally wrong on this. I could be. I’m just telling you how it seems to me.

Pseudoquantification.png

Confessions of a workaholic

I think it’s wrong that postdocs consistently work evenings and weekends and generally far more hours than they are paid for. I think it makes life much harder for postdocs with young children who simply cannot work those hours. Disproportionately these are women. Devotion to science is also a way to keep women out of the lab in practice. The PI will obviously hire the postdoc who consistently works overtime for free.

Even worse there is a culture that honours working crazy hours. It proves your devotion. I instinctively find myself repelled by the idea of getting sucked into that mindset and being part of some smug culture that views academic scientist as an exceptional career path only for those of true faith, it feels a little culty.

Beyond that as someone who has had two, mercifully mild work induced breakdowns I am well aware that working long hours can end up being counterproductive.

And yet…

I love it.

I love getting totally sucked into work, wrapping my whole brain around it and staying till midnight staring at a computer screen or pipette in hand working towards the next experiment. And try as I might I can’t seem to kick the habit.

And worse than that, I can’t seem to shake the nagging suspicion that as much as I think a career in academic science should come with things like job security, work-life balance and accountable management structures, I also think there is something just a little exceptional about it. Should we embrace our devotions as good monks, or is this a sickness that needs to be cured?

What do you think? Anyone else prepared to step into the confession booth?

Introducing the TXL website – we need you!

Today TXL just got bigger and better – introducing the TXL website 

This will be an opportunity to expand the scope and content of what TXL has been till now. Trying to include more interviews and humour alongside the more standard short-essay style posts. And more importantly a way to get more people involved.

Interested in having your opinions heard or contributing your skills in software design or illustration? Then drop me a line – delangeo@gmail.com

Peace and Love,

Orlando

Science in a moral muddle

This post has been brewing in my drafts far too long so I decided to let it free.

I recently (not so recently anymore) listened to a BBC radio4 programme that enraged me far beyond my usual curmudgeonly old man level. It was an episode of the Moral maze asking the question – is science morally neutral.

As anyone who has had to write a scientific paper knows, the very first thing you have to do after interesting your topic broadly is to precisely define some of the key terms/concepts you will be addressing and to lay out the current status quo in terms of our understanding of the issue at hand, before moving on to make your arguments. The BBC programme went straight from broadly introducing science and morality to launching arguments, and the result was an unhelpful mess.

Let’s start where they should have, with the definitions. No definition was offered of the discussion’s two main themes – science and morality. Taking science first, there’s a traditional definition that seemed to be generally accepted in the BBC discussion. This particular abstract concept was of science as the study of the natural world in order to improve our understanding of it. This seemed to be accepted by the whole panel without challenge. I wonder if anyone reading this, even those from the natural sciences, could say that such a model is a good descriptor of the current practice of science. I am aware of research being carried out that fits that bill. I suggest, however, that most research carried out these days has the stated purpose of improving understanding or knowledge to address a stated problem. Natural science, defined as research of the natural world carried out using the scientific method, is about growing crops, preventing climate disasters, curing diseases or making new materials. No this doesn’t preclude curiosity for its own sake, but it channels it in a particular direction. That’s the reality of science today, and it requires important moral decisions. To implicitly define science as the pure pursuit of knowledge, which some but not all of the panel on the programme did, is to beg the question.

Morality as a concept was also unchallenged. Yet the discussion at hand ranged from scientific misconduct to robot armies, from dodgy emissions data to the interpretation of clinical trials. Yes morality is involved in all these areas but in different ways, and its important to differentiate these. Scientific misconduct is about integrity. Interpretation of clinical trials is about how to disseminate information in order to prevent harm to the public. Robot armies and other such future apocalyptic scenarios are about unintended consequences (does possible future harm make it immoral to pursue present benefit).

So much for science and morality, what about the scientist? The scientist was at sometimes the brilliant academic in an ivory-tower and at other times anybody who dons a labcoat. Techincians involved in VW emissions testing, were addressed in the same way as Copernicus charting the cosmos. This topic of who is an insider and who is an outsider is one that continually intrigues me and one I have addressed on this blog before. In the discussion of scientific morality it is of great practical importance. Suggestions were made of how to regulate the morality of scientists, such as an oath made by researchers or better oversight from funding bodies. Such measures will only reach the traditional core of academic science. Scientists within Industry would have free rein, as would engineers/plant breeders/pharmaceuticals companies i.e. the people who turn scientific knowledge into tangible outputs that affect our everyday lives. Arguably those involved in translational work (going from knowledge to product) deserve greater oversight. It was even acknowledged again and again in the programme that science was morally neutral but its applications were not.

After skipping the definitions they also skipped the discussion of the status quo. There was much spoken in the programme about the need for funding agencies to make moral decisions for scientists by deciding what to fund, without addressing the ways that funding agencies already do this. Governments impose strict moral standards by law in some cases: animal testing, human clinical and psychological trials, use of stem-cells, human cloning. There also are examples of scientists self-regulating on moral issues, and imposing moratoria on certain research (Molecular cloning at Asilomar, CRISPR more recently). There are already multiple different ways that moral decisions are implemented to restrain/channel what scientists do, which was for the most part (not completely, in fairness) ignored in the programme. I might be offending too fields at once here, but I felt the programme took a more classical History and Philosophy of Science approach that asked the big picture question about whether it is conceptually logical that science is morally netural. I think the Science and Technology Studies approach of studying what scientists actually do in order to address the why and how questions would have been more useful.

So they brushed over the status quo of regulation. They also seemed to largely skip probably the single most relevant discussion point – the actual moral impacts of research. A couple of examples were brought up again and again, namely falsified emissions testing and the impact of disseminating bad science that can’t be repeated, if its in the field of public health. Both of these are really bad examples, that are about 1) Industrial standards regulation or 2) Science communication. Far more relevant would have been to take examples of academic research and follow through to it’s moral consequences. Look at some particular research, ask who the stakeholders are and how they will be affected. What vision of future agriculture and rural lifestyles are promoted by our plant science, what vision of human health from our biomedical research? How does biomedcial research define health and disease and what are the moral implications of that? What has been the moral impact of the internet (a more direct product of basic research than most of our major technologies)? What is the morality of spending $13.25 billion on the large hadron collider? Was it morally neutral for Henrietta Lack to have her cells taken without permission to be used in research labs around the world? No such questions were asked. Instead the panelists wrung their hands about whether super robots will destroy us all, which whilst really interesting in itself is impossible to answer and thus not very helpful to move the discussion forward.

Sticking to the big picture, conceptual, approach would have been all well and good except that specific ‘remedies’ for the very loosely defined problem were proposed. One ‘witness’ (provider of expert testimony’) insisted that scientists should be self-governing on moral issues because they will use the scientific method to address moral questions (lay people, one is to assume from the tone of the witness, simply fling their feces into random patterns and divine from these what path they should take in life). Now I have sat in a lot of discussions with scientists about politics, religion, economics etc., and I can vouch for the fact that most people who use the scientific method for their work do not extend the approach to every opinion they have in life. Scientists are humans who, like other humans, are swayed by emotions and by their peers in powerful ways. That’s before you even get to the question of how you could use the scientific method to answer moral questions, even if you were inclined to. I think taking a slightly more Marxist view would be helpful here. Remember scientists are a societal group with common interests that they are pursuing. Scientists want to do what they love and they want money for it. To imagine that such self-interest is irrelevant in moral discussions seems pretty naive.

I won’t go on much longer for fear of this rant descending into verbal diarrhoea. To summarise, I think that in this case a topic I deeply care was butchered. If they had more clearly defined terms and laid out the status quo I believe that the only realistic answer to the question they wanted to address would be that science is not morally neutral. The fact that governments, funding agencies and scientists themselves act to constrain/direct science on moral grounds would support this. Any cursory glance at research carried out today and in the last hundred years would also show that science has moral implications. I’m not just ranting for the sake of it (though I do love a rant), I also believe very strongly that the public is not just entitled but is required to be part of debate on moral issues within research. We scientists need non-scientists to temper and guide us, and we need them because they are the majority of the world and the whole world will be impacted by what we do, if we are lucky. I have a particular idea about engaging non-scientists in citizen panels/juries, as used in Canada and the US state of Orgeon to guide political decision making. But that’s something I’ll return to at a later date. For now I’ll end with a plea: let’s not shroud science in a fog of mystery and pretend it is a morally neutral pursuit of toga-clad natural philosophers; science is drenched in moral implication and the important question is what we do about it.

P.S.

In defence of the BBC: I subsequently heard a really nice programme on misconduct from them – http://www.bbc.co.uk/programmes/b072jdqm . I generally think the there is a lot of great science programming on the BBC, in particular The Life Scientific, Inside Science and the science episodes of In Our Time (and I have to mention More or Less, falling as it does within what one might call ‘the scientific world view’). So this is not an attack on Radio4 in general, just on this really shitty programme in particular.

 

 

The Biologist is dead, long live the Bioengineer!

It’s been a long time since I last posted here. The most obvious and relevant reason is that in that period I have finished my PhD and moved to the West Coast of America to start a postdoc position. I’m now working at the University of Washington in Seattle. What’s more shocking, I am now working under the aegis of the Electrical Engineering department. Quite a change from the comforting bosom of the Centre for Plant Molecular Biology in Tuebingen. Yes that’s right, I have found myself in the land of the Engineers. This is no coincidence. I actively sought this position out so that I could immerse myself in the heady world of Synthetic Biology, which is a many-headed beast but the head I most relate to is that of the discipline where Biology and Engineering meet.

While I’ve had much to do learning the ropes here, I have also had time to think. And the particular thought I wanted to share today is very much inspired by my experiences over the last few months. Namely, is it still meaningful to distinguish between scientists and engineers? In theory the scientist discovers information and principles about the natural world and the engineer applies these to solve human problems. Methodologically a scientist uses the scientific method of hypothesis testing and theory building, while the engineer uses design-build-test cycles to arrive at a finished product. While the theoretical divide still exists conceptually it is no longer a good way to differentiate between the work done by academics in different faculties. Chemistry and Physics have long involved very strong applied components that merge seamlessly with the fundamental (Materials science, chemical engineering permeate academic research). This is also increasingly the case with Biology where funding favors the applied; I’m thinking in particular of Biomedical science and crop science. Till now I have the impression that such work has been carried out by trained research scientists learning on the fly how to do real-world problem solving. But increasingly, trained engineers and trained research scientists are working together. Now one academic department may encompass research falling within the theoretical remit of science and engineering.

And of course on the practical level the two are becoming very blurred. Scientists rely on engineers to design the latest hi-tech tools they use. They are also learning from engineering how to model systems mathematically as a way of learning about them. In the era of big data every scientist may need to be a bit of an engineer.

The narrative that I’m threading here is that Engineering is encroaching more and more into the sciences, and particularly into Biology, where most research in the future, if not already, will be applied and most researchers will use the methods of engineering. I’m not decrying this one bit, I think its quite natural. Biology is really complicated and its taken a long time to lay down the fundamentals. But now we’re at a point where the level of detail and predictability are at a point that Engineering as a discipline, one that thrives on precision, can actually get involved. It’s not all hand-waving anymore, and I for one think that’s something to be welcomed. The Biologist is dead, long live the Bioengineer!

(Not quite, I rather think that the total sum of Biological research will increase with the added stuff coming from more bioengineering. So how about long live the Biologists AND the Bioengineer!)

 

 

 

 

A position on PeerJ

On sitting down to scrutinise the PeerJ Q&A session on Reddit I was ready to employ my cynicism to its fullest. Surely flash in the pan, reactionary, buzzword-laden and naive would all be terms I could employ in my summary of the session and of PeerJ itself. Yet after reading all the comments and concordant responses from PeerJ founders Jason Hoyt and Pete Binfield I found myself rather sympathetic to their approach.

In a nutshell PeerJ is a cheap, open-acess peer reviewed publication outlet and preprint archive for Biology, with a more recent Computer Science site. The J stands for Journal but also, through its abbreviation, stands for doing Journals differently. Altmetrics, open peer review and no novelty requirement, are some of the forward thinking approaches they take. Publish everything that’s scientifically sound and make it machine readable to allow collated information on comments, social media shares and citations to guide what gains prominence in a given field. Don’t rely on Science or Nature to tell you what’s hot, let the wisdom of scientific communities acting together determine what’s hot. And take an inclusive view of this community by making publications free at the point of access and acceptably priced at the point of publication. Hopefully you can see that none of the specifics of their publication method are unique or radical, yet overall they represent a new approach to scientific publishing. They form part of a spectrum of non-traditional approaches alongside other journals such as PLoS, eLife and F1000.

There are three interesting points that emerged from the thread on PeerJ, two specific to that journal and one of more general relevance to communication within the scientific community:

  • How to get the price of open access down
  • The rise of open peer review
  • The vexing problem of robust and professional post publication peer review

How to get the price of open access down

Most open access journals charge around $2000 per article, and apparently this is a reasonable reflection of publication costs (asserted in the Reddit thread). PeerJ charges $700 per article. They also other a more unusual membership model. Become a member with a one off payment of $99, and you can publish one article per year. Caveat, all authors must be members, so thats $99 per author, but only once. PeerJ claim they achieve their low prices in 4 ways: using cloud storage to minimise costs, being online only from the start minimising costs by not needing to prop up an inefficient print format, accepting more articles than most outlets so getting higher revenues, and finally by being generally nimble and efficient. It may be that enthusiasm and determination have been helping them get by for their first few years (they started in 2012). Maybe they’ve just been burning through their million dollars of starter funding. At any rate it will be very interesting to see if they can maintain their low prices and what this will do to other open access online journals.

The rise of open peer review

One can publish a pre-print on PeerJ without peer review, but in order to get a normal article published you must go through peer review from two experts in the field. In this respect PeerJ are quite conformist. However, authors have the option to open up the entire peer review history of their article. And peer reviewers can choose if they would like their names to be made open. According to the PeerJ co-founders 80% of authors opt to open up their peer review history. PeerJ are not the only ones offering this feature. Elite open access journal eLife also does so for example. To clarify the term ‘Open peer review’ covers a range of approaches: publishing reviewer names, reviewer comments, allowing authors to know reviewer identities during review, and also an open public peer review (see this article for further discussion). The 80% figure relates only to opening up reviewer comments at the point of publication. To me this model seems to answer the growing demand for greater transparency in the review process without throwing the baby out with the bathwater and dispensing with peer review by selected experts. It’s hard to argue why the comments shouldn’t be published. Whether the names of the reviewers are opened up is another question. I think opening up reviewer names would be a positive step, encouraging people to take their duties as a referee more seriously allowing shaming of shirkers and praise of professionalism. It’s controversial of course in that it may lead to science feuds. Though scientists seem to have no trouble feuding at the already (want proof – check out this acerbic PubPeer thread). At any rate I suspect that open reviewer comments, named or not, will become ever more common and adopted by established journals, not just championed by new ones.

Post publication peer review (PPPR)

PPPR can mean two quite different things. One form means publish straight away after an initial QC, and then let people comment as a form of peer review. This is the approach of F1000Research and ScienceOpen. I’m frankly troubled by this approach since I know from experience that taking on board reviewer comments can be a really helpful part of producing a mature manuscript. The other PPPR is simply comments on already peer reviewed articles, to complement not replace the initial referee process. According to the PeerJ co-founders they’ve really been trying to encourage people to post comments and questions to little avail. Others such as PLoS have a prominent link to the comments section of every article in their header bar, but you’ll mostly find ‘0 reader comments’ to greet your hopeful click on that button. Surely it’s a good thing to have scientists from around the world discussing the merits of articles and posing questions to authors in the open for all to read. Debate is a key part of the scientific endeavour, to help us better understand research and draw the correct conclusions. We all do it within our working groups, and at conferences. Do we just need to get used to doing it online. It may be something that needs to build momentum. Why post a comment when you suspect no one will read it or reply. One platform where online discussion is vigorous is PubPeer (see here for my thoughts on PubPeer). Unfortunately PubPeer seems to be mostly orientated at attacking suspected fraudsters, not being used for more general debate. Praise of good studies is a key part of the scientific discussion but I suspect such entries are few and far between on PubPeer, but maybe with time they’ll come. It may indeed be best to put all our comments on one platform to link up as many people as possible. Another model would be to use online platforms to simply create larger communities, online journal clubs where thousands of researchers take a different paper each week to focus their comments on, for good or bad. I wonder if such platforms already exist?

I think I’ll leave my musings on PeerJ there for now. It’s a new platform, and growing, with backing from plenty of well established researchers and institutions, so definitely one to watch for all those interested in the future of academic publishing.