All biology is computational biology – 28 days later

Almost a month has passed since I published an opinion piece called “All biology is computational biology” in PLoS Biology.

In my paper, I envisioned a biology that explicitly and clearly acknowledges how much it has changed over the last 20 years, how much its questions have changed, and how much the practice of doing biology has changed. I envisioned a biology that gives credit broadly and fairly to everybody who contributed to key insights – regardless of what tools they used.

As intended, my paper provoked many responses from the community, and in the following you find my thoughts on some particularly interesting comments.

Well, that will cause some eye-rolling: All biology is computational biology!

I met Emma Ganley from PLOS Biology at the #scidata16 conference last year, and shortly afterwards she invited me to contribute to the PLOS Biology collection Research Matters:

In this series, we ask leading scientists in their respective fields to explain clearly and engagingly for a lay audience why the research carried out in their laboratories – and those of their collaborators and their colleagues – matters.

It wasn’t immediately clear to me, what I should write about. I tend to label myself a cancer researcher nowadays, but cancer research does not need any explanation why it matters – unfortunate as that is.

At the same time, I am a computational biologist – and here I thought was a much bigger need to explain why it matters. The question is not so much why computational biology and bioinformatics are useful (nobody seems to question that it’s handy to have the geeks around) but why is it biological research, rather than just a support and service activity.

Science is devoid of significant human and social elements, they say I said.

Every citation is a good citation, right? So I was pleased to see that even the little pamphlet I wrote about my lab last year has a couple of citations now (ok, one is a self citation, please don’t tell anyone).

“You are not working for me; I am working with you” is what I said back then.

And my paper got cited here: “Are Leadership and Management Essential for Good Research? An Interview Study of Genetic Researchers” by Alison L. Antes, Adelina Mart and James M. DuBois in the Journal of Empirical Research on Human Research Ethics.

Leadership in Science – a topic I am definitely interested in.

Let’s see where and how they cite me ..

So exciting!

If I don’t get it, you should be concerned.

The latest post at Shit My Reviewers Say is “My first concern is that I don’t get it.”

And the obvious response is illustrated by a picture saying “Your problems with me are not my problems, those are your problems.“

What can you do as an author if the reviewer is just too stupid to understand your ingenuity?

But … and this is a big but … there are areas of research where I would use that reviewer’s comment myself. If, say, you are writing about probabilistic models in cancer genomics and I can’t make any sense of what you are saying, it is your problem, not mine.

Here is an example. The ABSOLUTE paper on “Absolute quantification of somatic DNA alterations in human cancer”.

I am a research parasite. Got a problem with that?

In case you wondered what’s wrong with biomedical research, just read this editorial on data sharing by Longo and Drazen in the New England Journal of Medicine, a leading journal in the field. What you will find is a desperate attempt to take data hostage and to enforce co-authorships for people who didn’t make any intellectual contributions.

But let’s take it one step at a time. What did Longo and Drazen actually say? They think there are major problems with sharing data fully, timely and openly.

“Superstar professors with massive research groups are bad for science.” I agree.

‘My professor demands to be listed as an author on many of my papers’ writes an anonymous scientist in the Guardian.

[T]here’s one instance where it’s acceptable for scientists to lie: when fraudulently claiming authorship of a paper.

Too often, researchers attach their names to reports when they have contributed nothing at all to the work.

The problem gets worse the higher up the academic ladder you go.

I think this is completely true.

The reasons are manifold:

Technocrats versus scientists – the managerial mindset in UK elite universities

You must have heard about the death of Prof Stefan Grimm, who apparently had been bullied by his departmental line managers at Imperial College London.

In case you have missed it, you can read the whole sad story at DC’ science: Publish and perish at Imperial College London: the death of Stefan Grimm.

ICL will of course claim that bullying is not endemic and this was a very sad but isolated case.

Evidence-based decision making in academic research

However, rather helpfully, a Mr John T Green has written a paper about the managerial mindset at ICL: Evidence-based decision making in academic research: The “Snowball” effect.

The paper appeared in 2013 in a journal called The Academic Executive Brief – welcome to the Dark Side!

Replication of results in statistics and biology

“Do differences between biology and statistics explain some of our diverging attitudes regarding criticism and replication of scientific claims?” asks Andrew Gelman on his blog.

I was not very impressed with the post or the comments it received. Here is what I posted as a response:

Don’t believe the petabytes! Against Big Data Empiricism

The data never speak for themselves; and even Big Data doesn’t change that.

“The business of Big Data, which involves collecting large amounts of data and then searching it for patterns and new revelations, is the result of cheap storage, abundant sensors and new software. It has become a multibillion-dollar industry in less than a decade,”

writes Quentin Hardy at NYtimes.com. Big Data is everywhere, even in medicine. Just have a look at Atul Butte‘s presentation at TEDMED2012:

“Who needs the scientific method? Vast stores of available data and outsourced research are simply waiting for the right questions,” claims Atul Butte.

On systems biology and bullshit

Clarity and lucidity are key strengths of scientists and writers. Jargon and cliches can make the best paper unreadable. This is why science writer Carl Zimmer keeps an index of banned words his students should avoid.

One of the words on the index is ‘breakthrough,’ which is overused, because the person reporting it doesn’t bother to think about how big the step forward really is. Using such cliches shows sloppy thinking and lack of scrutiny. This is why Zimmer bans ‘breakthrough‘ “unless you are covering Principia Mathematica”, in which case you are fine, regardless of whether you refer to Whitehead and Russell or Newton.

Not only science writers need to avoid cliches and enrich their texts for content – ‘real’ scientists also often use fancy buzz words with far too much levity. Just think of these three (in no particular order) that you can hear in almost every systems biology talk:

1. Integrated,
2. Network,
3. System.

‘For now failed’ — cheating German ex-minister threatens with comeback

Rapid rise, steepest fall! Karl Theodor Maria Nikolaus Johann Jacob Philipp Franz Joseph Sylvester Freiherr von und zu Guttenberg was German minister of defence until March 2011, when his PhD thesis was proven to be riddled with plagiarism.

Emotions ran high this year in Germany.

So beautiful, it’s almost science

In today’s Guardian I read about a new Turner biography written by James Hamilton.

Joseph Mallord William Turner (1775-1851) is famous for his energetic land- and seascapes. And what’s more..

..fresh research suggests JMW Turner’s work was also rooted in groundbreaking scientific theories.

Well, sure, why not? It seems Turner had many scientists as friends and it’s not surprising at all that some of the things they have told him may have made it into his paintings.

But now here comes the greatest compliment you can make an artist:

Hamilton said Turner’s sun was more than art – it was almost experimental science.

Wow! Your art is so great, it’s almost science. Almost!

What hubris!

Florian

Duty Calls

A pretty famous comic from xkcd is called ‘Duty Calls’:

1> Are you coming to bed?

2> I can’t. This is important.

1> What?

2> Someone is wrong on the internet!

Who doesn’t know that feeling? Ok, most people, I’d guess. But ‘Duty Calls’ will be my category for all the stuff that I write being upset about something I read on the web.

I guess I will be able to monitor my mental status by how quickly it fills up.

The first example of a Call For Duty is my reaction to an article I recently read in PLoS Biology.

Feyerabend and the tyranny of science

In October 2011 PLoS Biology, a top biology journal, tried something new – it took a deeper look at the boundary between biology and philosophy:

“Does the cultural divide between science and the humanities, first articulated by C. P. Snow over 50 years ago, still exist between biology and philosophy? In a mini experiment to find out, we asked a philosopher and biologist to review the recent English translation of Tyranny of Science, by 20th century philosopher Paul Feyerabend, perhaps best known for rejecting the claim that science is a singular discipline unified by common methods and concepts.”

What a nice idea! The philosopher is Ian J Kidd from Durham in the UK, who does research on Feyerabend and other philosophers of science, while the biologist is Axel Meyer from Konstanz in Germany, who studies diversity in fish. And Feyerabend (1924-1994) is a very good choice, because he is notorious as a polemic writer and not known for holding back his opinions. If there is any divide of any kind anywhere, Feyerabend will be right in the thick of it.