Making predictions: The future of biology

Amye Kenall 5 Aug 2014

Its hard to make predictions, especially about the Future.
Yogi Berra (via Titus Brown)

What will biology look like in the year 2039? In July I attended the Bioinformatics Open
Source Conference (BOSC), a friendly community of open source advocates, where I heard
bioinformatician Titus Brown deliver his thoughts on this in his talk, A History of
Bioinformatics (in the Year 2039).
Good for my jet lag and a great start to BOSC. Talks about the future often focus on data
size. Titus pointed to one such talk by Mike Schatz of Cold Spring Harbor: The next 10
years of quantitative biology. (Also check out the latest big data Cold Spring Harbor
meeting, whose abstract deadline is August 22nd.) Sequencing data is growing at the rate of
3x per year. Several people, including Titus and Mike, even point to automa

ted data collectiondrones scanning the

bottom of oceans and sequencing the air of all major cities.
As neuroinformatics takes off with theHuman Brain Project, which expects to generate
yottobytes of data, and the increase of the use of big data imaging in areas like zoology,
genomics will not be the only area of the biological sciences facing a data tsunami.
Titus, however, focused on a far less talked about aspect of this data tsunami: our inability
to make anything of it. While our ability to gather data increases, our ability to use
computational tools to draw conclusions from the data is sparse at best.
Although the easy-to-use computational tools might prove useful in the short term, they
cannot substitute for true understanding. But perhaps it is this black box problemas it is

exposed that such tools actually embody quite a few assumptions leading to errorsthat
will lead to the biggest revolution of biology.
In Titus history, it takes some time to register this as a problem. Funders are slow to
recognise the importance of funding computational training. But they do. Slowly but surely,
the term bioinformatics disappears, to be replaced with biologist, as all biologists
become computationally competent.
Training from such initiatives as @softwarecarpentry expand into @datacarpentry and
@modelscarpentry. Before that happens, sweatshops of bioinformatics grad students
processing the never-ending deluge of data flourish.
The biggest mistake proves to be withholding coffee. One step too far. As the sweatshops
become unbearable, the great migration of the brightest of these data scientists to California
begins. The Bay Area is transformed. Meanwhile, the peer review system becomes even
more strained and those who are left revolt. The new rules to science are founded:
1.
2.
3.

All of the data and source code has to be provided for any computational part of a
biology paper.
Methods and full methods sections need to included in review.
If an unpublished method was used in analysis of new data, a separate and thorough
description and analysis must be made available at the time of peer review.
Open science becomes valued across the community in the midst of the mess that is left.
Scientists begin to realise it is not the access to data that is the bottleneck, but
theanalysis of it. A new strategy of sandbagging competitors with data emerges. Titus
points to quite a few possible developments, and I highly recommend watching which you
can view below.
But here I want to turn to a more serious point I found particularly interesting. With the data
deluge, one problem that surfaces is biologys hypothesis-driven, rather than data
exploration-driven, tradition. Indeed, this is how, from my perspective across the sciences, I
see research changing most. As data becomes a resource existing in large explorable
quantities from the startie, not after collection of specimens, analysis, etcmore and
more scientists will turn to data exploration as a starting point. Questions rather than
hypotheses will guide science.
This is in line with another point Titus makes: Prepare for poverty. Winter is coming. We
need to maximise our resources. The obvious answer to that is to open up data for reuse,
but in line with this research needs to become smarter. Doing more with less. Data
exploration, to make the most of longer more expensive experiments and analyses, is part
of that.