If you can't take the heat...

In what follows I am keen not to name names and point out that these comments are not aimed particularly at The University of Manchester.

There has been a lot of speculation about what is going to happen to the UK research budget in coming months. Regardless of who gets in after the election it looks like we're in for cuts, it's really about the magnitude of these.

I've been thinking a lot about ways of getting extra money into research (see other funding posts). One that particularly strikes me at the moment is that there are a lot of PIs who can only be described as utter shite.

Softly softly catchee monkey, or the Long Tail of Academic Research

Here is a snippet from another document on alternative ways to fund academic research.

...I am particularly interested in developing the massively underexploited economy around basic research. In my opinion universities have focussed too heavily on commercialising only those innovations that generate large payoffs. Yet along the way research often generates many smaller developments of lesser commercial value that typically are not exploited. It is upon many small profits (in ‘the long tail’) that companies such as Amazon are built. Universities need to make more of their smaller developments. Working up new approaches to funding research is one of the activities of our growing band of Hartlibians.

Figure 1. A monkey with a long tail (photographed by Peter Maas)

Biological Engineering

 

This is a short piece on Biological Engineering ripped from another document I am writing.

 

‘We are now starting the century of biology’ - Craig Venter
‘This is a century of Biology. Physics has had its good time, but now, it’s going to be Biology’ - E.O. Wilson

It is said that Biology will lead the technology of the 21st Century. Behind this assertion are a set of new technologies and ideas that define the emerging field of Synthetic Biology, which essentially treats Biology as a problem of Engineering.

Synthetic Biology considers how biological machines can be made through genetic modification. An example would be expression of genes encoding arsenic-sensing and fluorescent proteins to create a new machine for detecting arsenic contamination. This has been possible for some time, but key to Synthetic Biology is that the biological parts and mechanisms by which parts are coupled are now being standardised and catalogued, so new biological machines can more easily be assembled. It is now rather simple (and with little background knowledge) to assemble parts from ever-growing catalogues into novel biological machines. Moreover, tools to simulate these machines emerging from Systems Biology allow their behaviour to be explored and tested computationally prior to assembly. Through these mechanisms Synthetic Biology provides the capacity to engineer novel biological machines. Future biological machines might include organisms able to rapidly and cheaply synthesise drugs or biofuels from basic raw materials, crops that produce pesticides appropriate to the pests that threaten them, new paints and fabrics, and very many other applications not yet anticipated.

 

A friend of mine even suggests that we might one day build tunnels like the Channel Tunnel that are supported by biological material grown inside, making going through "something like passing through a colon". Nice.

While there is much excitement around Synthetic Biology I do not believe all Biological Engineering will rely upon intelligent design (without capitals). Biology has previously been able to meet its needs through evolution. By the judicious application of appropriate selection pressure in the laboratory evolution can be directed towards desired endpoints. For certain problems this might require less insight and be more efficiently realised than designed solutions. Future Biological Engineering will likely come to exploit a combination of Synthetic Biology and directed evolution.

The coming century may well be one of Biology, but Biology thus far has mostly been concerned with understanding Life’s origins and operation. It is in its new form, as a discipline of Engineering, that Biology’s increased importance will be realised.

Convergent Evolution: Musk Ox versus Takin

I like examples of convergent/parallel* evolution (where evolution has arrived independently at analogous solutions).

The takin (1) and musk ox (2) appear basically rather similar. Takin live in the Eastern Himalayas and musk ox in the Arctic. Analysis of a mitochondrial gene (cytochrome B) suggests that the takin and musk ox are separated by around nine million years on the molecular clock (see the data here), so it appears unlikely the physical similarity is due to a common ancestor but is convergent.

*Convergent or parallel?

Thoughts on Windmills

The other day I met up with the artist who created the Tilted Windmills outside Selfridges in Manchester. Tilted Windmills - do you see what he's done there? Very good. A delightful moment amidst the mundane. I wish we could capture some of the magic of science - research has become rather prosaic for my liking.

The power of Academia Past was that it had fantastically quixotic tendencies. Looking a hundred years ahead or taking a sideways leap nobody expected is precisely what academia is for. Modern academic science only tends to pursue basic research with predictable results. Where we can anticipate the answer is it particularly worth looking for? I suppose yes, sometimes, but always? Should we be so relentlessly pragmatic?

Even the practical answer to this is No. The foundations laid by basic research now are built upon by applications in the future. Moreover, I think unexpected and deeply profound insights are unlikely under our current cautious, incremental model. One cannot crawl across a gorge, only leap.

Science is an inherently delightful subject in which the uniquely human trait of immense and boundless curiosity is manifest in its most reliable (objective) form. The pursuit of knowledge purely for it's own sake might appear quixotic but it is what the human animal does. I think basic research - where we seek answer to questions without knowing why - is often justifiable simply because exploration is good, new knowledge is good, understanding is good.

For me this combination of factors defines curiosity: explore, learn, understand. While I appreciate the many good practical reasons for applied science, it is where these processes elegantly combine to give new and profound insights that I find my lonely impulse of delight. I am sure that Science is shot through with such moments, but it can seem unrelentingly mundane in practice and I lose sight of them. I'd like more delightful moments of science magic amidst the mundane.

The Economic Case for Independent Research

Here I explore the idea that universities do not always offer the best value-for-money in research and look at whether independent researchers might sometimes be a better alternative.

According to the CBI “the UK is now seen as the most expensive place in the world to fund a post-doctoral researcher”[1]. A major factor in this is that research grants once only supported direct research costs but now also include a very large component to cover the operating and development costs of research institutions to support their long-term sustainability. In combination with increased economic pressures and changing research methods this has driven up the cost of research.

Metabolic Gothic

 

The detailed and non-repeating ornamentation of metabolic wallcharts (a full version of which can be seen here) reminds me of Gothic cathedrals, like the Cathedral of Notre-Dame, Reims.

After a bit of flipping and chopping, here's a nice depiction of what I mean.

Blogging knowledge with Knowledgeblog.org

My former office-mate Duncan Hull (EBI), and current Ondex colleagues Robert Stevens (Manchester) and Phil Lord (Newcastle), are contributing to a new book all about ontologies that is being written, reviewed and edited through a standard Wordpress blog.

The advantages of scientific publishing in this way are many and obvious. Most importantly, it is fast, authors retain control of manuscripts, peer review is out in the open, and (my favourite) you needn't post the entire content to the blog but can keep it on your own blog and bring in the ad revenue. Carry on like this and we're in real danger of developing an economy around the knowledge exchange that is scientific research, rather than persisting with this absurd and unsustainable lab-coated philanthropy.

This very strongly relates to the initial idea around which the Hartlibian Group was formed and I hope it grows into something that is widely accepted and indexed by the major scholarly search engines.