Some hard facts about science, money and evaluations

The most fun experiments are those that generate a lot of noise and heat. So why not ask a scientist about her latest grant application? Or about the reports she has been asked to write describing the results of her research? These simple questions will likely result in spectacular fulminations at the evil minions of government agencies, the incompetent idiots that call themselves university leaders, or the ill-will of society and the universe in general.

Scientists want to get on with their work. They hate the bureaucratic drudgery of writing grant applications and reports. Who can blame them? Every day spent on grant writing is a day less for real work. The worst part is that most grant applications fail. For example, the Swedish governmental science grants agency VR received a total of 222 applications in the field of natural sciences and technology in the round of 2016. The results were announced 23 Feb 2017. A total of 18 (eighteen) applications were successful. That’s 8%. The rest, 92 %, were written in vain. From discussions in the media, it is clear that this is a general phenomenon in most of the world. Who can say that scientists should not hate this system?
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Har statistik inga fördomar?

I papperstidningen använde Dagens Nyheters ledarredaktion 17 januari 2017 rubriken ”Statistik är ingen fördom”. På nätet blev rubriken istället ”Rätt att granska brottslingars nationalitet”. Den konkreta frågan som diskuteras är huruvida Brottsförebyggande rådet (Brå) bör samla in statistik om brottslingars ursprungsland eller inte. Principfrågan handlar om vilken statistik som skall anses relevant när en viss samhällsfråga diskuteras. Kan själva valet av statistik styra vilka slutsatser som dras politiskt?

Dagens Nyheters ledare skriver:

Själva sakfrågan då: Är det rätt eller fel att låta Brå göra analyser där gärningsmäns födelseland är en av de faktorer som tas med? Naturligtvis är det rätt. Statistik är sällan fördomsfull. Vill vi begränsa kriminaliteten är en början att samla in så mycket fakta som möjligt om brotten, och dit hör vilken bakgrund den har som begår dem.

Notera att ordet ”sällan” används. Det kan alltså trots allt finnas fall då det är fördomsfullt? ”Så mycket fakta som möjligt” samlas in, tycker DN. Nja, knappast. Det finns en gräns för hur mycket fakta man orkar samla in. Det finns fakta som man skulle kunna samla, men som ingen skulle betrakta som relevant. Till exempel hur många fåglar som fanns i närheten av brottsplatsen. Eller färgen på husen intill. Bara för att ta ett par ytterst triviala exempel.
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How an embryo develops: The miracle of self-organization

The development of an organism such as a plant or a human being has always been a source of fascination. How can a small seed give rise to a giant tree? How can an egg cell combined with a sperm cell develop via the embryo into the complex structures of the human body? In a recent book ”Life Unfolding. How the human body creates itself”, Jamie A. Davies, professor at the University of Edinburgh, describes the current scientific understanding of this miraculous process.

One possible solution to the fundamental problem of an organism’s development is the teleological one. Teleology is the idea that a purpose is the driver of a process. This idea is associated with Aristotle, the great Greek philosopher, who, according to the Stanford Encyclopedia of Philosophy (SEP) ”is properly recognized as the originator of the scientific study of life.” Aristotle’s argument was that the development of an organism is fundamentally teleological; the goal of the process is to produce a functional adult organism. The final cause, as he called it, is the driving force of the process. The SEP describes his view thus:

[…] parts and the processes that produce them [organisms] do not necessitate the outcome; on the contrary, the outcome necessitates that the developmental processes bring about the parts that are necessary for the organism to live its life, and do so in a temporally and spatially coordinated manner.

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A researcher’s view of data handling for life science

Given the current mess of data handling in life science (or bioscience, as it is also called) which I described in a previous article, what should be done? Let us begin with a few words from one of the gurus:

You have to start with the customer experience and work backwards to the technology.

Steve Jobs, quoted here.

We should start by defining what the needs are. What does the scientist, the research group, want in terms of data storage and handling? What do they need in order to pursue successful life science? What other goals for data storage in Swedish science are there? How can we promote approaches to data handling that facilitate Open Science?

This text is not a final text or treatise. It’s a snapshot of my thinking on the subject. Serious policy and design specifications must of course be crafted through debate and input from various experts. There is now an initiative at the Science for Life Laboratory, where I work, to discuss these issues. I have written this as a starting point for the discussion, in the hope that it may be useful for SciLifeLab and for others.
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Is there a philosophy of biology?

Having just read the book ”Philosophy of Biology” by Peter Godfrey-Smith (who is Distinguished Professor of Philosophy at the City University of New York Graduate Center), I am left wondering if there is such a thing as a philosophy of biology. The book is well-written, and it discusses a number of fundamental phenomena in biology quite well. I did learn some new things, and the discussion does explain some issues very well. I cannot find any errors or misunderstandings of significance, except for one statement, discussed later.

Yet, I cannot say that I would know how to respond if anyone now asked me what philosophy of biology is actually being proposed in the book.
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Mötesplats Open Access 2016: Open Science needs infrastructure

The two-day conference Mötesplats Open Access 2016 MOA2016 was held 26-27 April 2016 in Stockholm, Sweden. It was arranged by Kungliga Biblioteket together with Stockholm University. My conclusion is that the conference showed that there are severe deficiencies in the policies and infrastructure required for Open Science, even if the idea of Open Access is fairly well established in Sweden.

I will not review the entire conference. The presentations are available here and the Powerpoint slides are available here. Instead, I will discuss the main unsolved issues that I think the conference brought into focus.
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Open Science: challenges for life science

I have created a page Open Science with links to interesting discussions and information about Open Science, especially issues related to life science (bioscience). I hope to add more links to the page as I find them. I may also discuss some of them in this forum. Please feel free to send me tips.

The latest addition to the page is a very good recent article in The Economist about the emergence of bioRxiv, the pre-print server for life science. Publication of research in life science is currently under stress for many reasons. As the article in The Economist discusses, the delay between submission and publication of an article in life science may cause real damage. The peer review system is showing serious signs of dysfunction. Too many publications present results that cannot be replicated.

The Open Science movement is gathering momentum, in part as a response to these issues. Many challenges and issues lie ahead, and we are in for a very interesting time. Science, especially life science, must find new ways of doing things. Data storage and publication is one of these issues. The web is obviously already the medium of choice for scientific publication, and we need to leverage its advantages. I intend to write more about these issues in the near future.

I have published an opinion piece on Open Science in the Swedish newspaper Dagens Nyheter

I have published an opinion piece in an on-going debate in the culture section of the main Swedish daily newspaper Dagens Nyheter (in Swedish, of course): Vetenskapens problem handlar inte om fusk (”The problems of science are not about cheating”), 6 April 2016.

It’s a response to Roland Paulsen who wrote Studier i rent nonsens (approx. ”Nonsensical research”) 30 March 2016. I do not so much attack Paulsen as use his article as starting point.

The issues with errors abounding in science is part and parcel of science in progress, I maintain. We need to focus more on how to weed out errors as we progress, rather than worry mainly about cheating and sloppiness. Open Science is the way forward, and institutions as well as attitudes need to change to allow this. In particular, an infrastructure that allows scientists to work easily with and for Open Science needs to be developed.

Read more in my previous two posts: The mess in bioscience data handling and What is important, and what is not, for bioscience data handling.

The mess in bioscience data handling

Science is a social activity relying on knowledge sharing, reproducibility, reanalysis and extension of previous work. The movement towards Open Access publication and Open Science sharing of data and analysis protocols can be seen as a natural development of these ideals. Large data sets are essential to many scientific investigations and are sometimes the product of an investigation. The biosciences have fairly recently started producing large data sets. There are several well-funded international efforts maintaining focused bioscience data sets, such as genomes at Ensembl, protein sequence data at UniProt, and many others.

Bioscience researchers are performing more Big Data experiments, but the various infrastructures available at the group, department, university and national levels are unable to cope. The situation for individual research groups is basically a mess. Various ad hoc solutions are being implemented, ultimately leading to a patchwork of systems that is becoming increasingly difficult for anyone to navigate. This also makes proper implementation of Open Science extremely hard, if not impossible.
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