• There will be some activity over the coming months to tie in with the first Kindle book, Challenging Cancer. We’re also going to be working on forthcoming Kindle books, which will cover topics such as renewable energies, ageing, and how scientists view the world.
• The New Optimists Forum is something we’re really looking forward to – a series of unconference-style gatherings where we bring together scientists to talk about viable approaches to deal with challenges which we will face in our near future. The first Forum theme is the prevalent topic of Food & Cities.
• There’s also a book in the pipeline about stem cell research, covering epigenetics and how our environments reprogramme the human genome.

I needed illumination. I thought I’d get it in Chapter 11. Its title ‘Using information stored in DNA‘ suggested this is where it’d be. Into the third page, however, I knew I was just as mystified as ever by any relationship between what I’d already learned and my own daily existence — yours, too, for that matter, let alone that of the zillion creatures great and small that infest this sceptr’d isle and the rest of the planet.

Chapter 11 is all about DNA, mRNA, tRNA . . . And I can’t do that any more, take in lots of seemingly unrelated stuff; my mind balks, just empties itself of meaning. So what, I asked myself, is the conceptual framework of all this, something I can hang all this DNA, mRNA, tRNA stuff upon? What’s the over-arching concept I’m simply missing?

And now for an aside about a book I’ve just read; bear with me please, it’s relevant. It’s Ian Stewart’s Mathematics of Life: Unlocking the secrets of existence. I’m a big fan of this man; he writes with such wonderful clarity about difficult-to-understand stuff.

His basic tenet in this eye-opening book is that there’s a sixth scientific revolution about how scientists think about life  — the first being the invention of microscope, the second the systematic classification of the planet’s living creatures, the third the theory of evolution, the fourth the discovery of the gene and the fifth the discovery of the structure of DNA.

The sixth revolution is, he says, a contentious one. Mathematics.

Not contentious for me personally. Ian Stewart’s account of a series of lectures John von Neumann gave in 1948 have revolutionised the way I can now approach Chapter 11 and thereby my understanding (cf failed rote learning) of DNA, RNA et al. And happy coincidence, that was the year my particular make-a-human-DNA-instruction kit was first made, alongside that of my twin.  At that auspicious time, von Neumann proposed a thought experiment:

“Imagine a programmable robot living in a warehouse with spare parts, which it can manipulate. It also has a tape containing instructions. The instructions tell it to wander round the warehouse and build a copy of itself by picking up all the parts required — except for the tape. Finally it makes a duplicate of the tape and inserts this into the copy.”

There are problems with this description. The robot has to be able to copy the tape, hence replication is built in from the start, as Ian goes on to explain.

Von Neumann’s point was that in this scenario, neither the robot alone, nor its program, can replicate. Only the combined system does that. The program replicates the robot; the robot replicates the program. This division of roles was a key insight, because it got round what had previously seemed to be an insurmountable logical obstacle to a self-replicating device.”

(Without this division of roles, a self-replicating device is what Ian illuminatingly calls a ‘Russian doll”; i.e. the device must contain a representation itself and inside that representation must be a representation  . . . and inside the representation is nested a representation . . . “the doll has to become smaller than the smallest fundamental particle”.)

“Von Neumann’s proposal for the architecture of his device avoided the Russian doll objection. It did so by interpreting the same physical object — the program on the tape — in two conceptually distinct ways. In one, the program consisted of instructions, to be obeyed. In the other, it consisted of symbols, to be copied. In one, a piece of paper with ‘put the kettle on’ causes a kettle to be boiled. In the other, it leads to a second piece of paper bearing the message ‘put the kettle on’.”

“Now the program can replicate the robot when the robot obeys the instructions, and the robot can replicate the programme by copying it but not obeying the instructions.”

Thank you, Ian. You’ve given me enough in these few paragraphs of yours for the conceptual framework I need. Time for another coffee, time to return to Chapter 11 . . . and for a very different journey through the same words.

And that’s exactly what New Optimist Andreas Hornung is about to get. The European Bioenergy Research Institute (EBRI), where he’s the boss, is part of Aston University. They’ve got the go-ahead for £16.5M investment in labs and a small-scale industrial power plant which will convert biomass (sewage, sludge, algae, wood and agricultural waste et al) into electricity for thee and me, using a revolutionary new process that is carbon-negative; i.e. takes carbon out of the system.

Even more exciting than that is the prospect that Birmingham has a “thermal ring” of such power plants around the city. Like many urban environments, we’re energy dependent, waste prolific. Supplies of power, taken for granted for a couple of generations, are looking increasingly vulnerable.

Just as Joseph Chamberlain had the foresight to provide the city with long-term supplies of water, so has our generation the opportunity to to do what’s needed for the long term supply of power — and, while the while, using the energy-rich ‘waste’ we create to make it.

In 1774 Samuel Boswell said I shall never forget Mr Boulton’s expression to me, I sell here, Sir, what all the world desires to have — Power.

Here’s Andreas talking about the research that already goes on at the EBRI:

But Jackie Chappell is not alone in her discoveries that parrots can think, and think in complex ways. Let me, by way of a starter, introduce you to grey parrots called Alex, Griffin and (wait for it) Einstein. (See examples of the trio’s behaviour on YouTube.) 

They’ve engaged in many a complex communication with a researcher, Irene Pepperberg. (She’s perhaps the most famous of bird-cognition people, a Brandeis psychology prof, also teaches at Harvard, has shown that parrots can think and use ‘language’.)

Jackie is far closer to home, a step away from Brum’s Old Joe. When I met with her and her colleagues, she talked about an intriguing experiment she wanted to do to test just how thoughtful parrots could be.

Some parrots are tool-users. How would a parrot behave, she was asking, with a stick weighted so so its centre of gravity were in an unexpected place? Carefully placed sensors would inform her of every tiny movement of the parrot’s tongue and claws.

Measurable evidence is what Jackie is after. She starts with the idea that her birds can think ahead, can weigh the odds both metaphorically and literally.

But, she asks herself, is she anthropomorphising? Is she seeing what she wants to see?

Typical scientist that she is, she’s suspicious of what’s in her mind. And wants to set up an experiment where she might be proved wrong.

Jackie Chappell and Juliet Coates, the latter doing a turn at the CASC Conference later this week, were already there when I arrived to talk to them about next steps with The New Optimists. And thereby got myself a front row seat on an intriguing discussion about: Can plants get cancer?

They can, I learned, get located growths. But secondaries, no, it seems not. Their cells mechanisms are more far plastic than ours, more stem-cell like, able to switch functionality much more readily than ours.

And plant scientists have a good understanding of how some of these mechanisms work which will prove valuable to medics in their exploration of how cancers happen in us.

Why are plant cells more plastic than those of animals? Well, they need to be. Plants can’t escape from the vagaries of their environment, and unable to run from predators, whether fleet-of-foot herbivores or the (literally) sluggish. So they have ways of either beating the predator through toxins, thorns and the like or difficult-to-eat cell walls  . . . and ways of safe  regrowth after being partially eaten.

If you google the question, you get millions of hits . . . here’s the Naked Scientist’s response.

note: Here is our video interview with Juliet Coates talking about plant diversity.

We saw too how our minds can be developed in remarkable ways. We watched a blind man using echo-location to cycle safely. And for someone like myself who is frequently lost, seeing someone wearing a device which enabled him to learn how to respond to the earth’s magnetic field to get around was truly remarkable.

Watch it while you can.

Balancing the outlook of the science world with the perspective of a caring mum, it’s a very thought-provoking piece covering fears about what might await future generations.

For more on climate change, see Andreas Hornung’s essay about problems faced worldwide and the potential for biomass residue to be used as an energy source.

Flooding costs in the region of £1 billion a year to clean up and it’s likely to get worse too;  a recent Parliamentary report suggested annual flood damage could cost £27 billion annually by 2080.

Water management is of growing concern to many, and New Optimist, Coventry’s Susanne Charlesworth is a leading authority. She has novel ideas on how the UK’s aging sewerage infrastructure could cope with the increasing demands being made on it.

She heads a team looking at the potential of SUDS (sustainable drainage systems). This is a deceptively simple approach to dealing with waste water, one new to the UK though in use in the States for some time.

When it comes to traditional drainage, the idea is fairly simple: pipe everything from cities as soon and as fast as possible. But this way of doing things can have hazardous knock-on effects. Collecting run-off from hard paving and roofing can increase the risk of flooding, plus this surface water run-off is often seriously polluted. Also by diverting rainfall to piped systems, ground water depletion becomes more likely.

“SUDS” by contrast are made up of a series of devices and techniques which either allow water to infiltrate or be detained; either way, these devices encourage the water to remain at source and to dissipate slowly; examples include swales (often traditional flood plains), also permeable paving and green roofs to mimic the natural drainage of a site and reduce the speed of run-off.

It’s one idea of many, for all sorts of imaginative things can be done with storm water. As blog The Dirt reports, in Illinois, Hoerr Schaudt Landscape Architects have completed work on The Circle.

The Circle’s a sustainable roundabout that cleanses – through filtration bogs, ultra violet sanitizers, and a “structural cell system” – and recirculates storm water into a public fountain providing community green space and making a fairly decent roundabout at the same time!

Susanne’s chapter in the New Optimists examines how ideas like these can become a vital part of our urban infrastructure and, at the same time, provide lots of wildlife habitats. She concludes

In the future, I see cities as blue and green rather than grey and brown. I see them as attractive and pleasant places to live, cool and clean and in a fit state to hand on the future generations.

Her contribution to The New Optimists is important, cutting edge and fascinating to read.

She knows this because as a senior lecturer in environmental science she researches “the spatial pattern and dispersal of plant species within the urban mosaic of remnant and emerging habitat fragments.”

Which means she knows a great deal about the importance of places like Selly Oak brownfield site, where she joined us with botanists Ian Trueman and Mike Poulton to tell us a bit about her work.

Lucy, Mike and Ian were quite hard to get to sit down. The sun was shining and there was an abundance of distracting flora and fauna in every direction. What we learned however was fascinating.

Urban brownfield sites, she told us, are surprisingly impressive in terms of biodiversity, especially in terms of insect species and their microhabitats. Why? Because the disturbance which makes these sites look so unmanicured creates short-lived habitats which have become rare in city surroundings.

Dirt Bikers Rule

Ian even told us that entomologists by all accounts have a soft spot for dirt bikers, for by keeping such sites open, churning up the soil and building their jumps they’re actually making for all sorts of insects a rather nice, if noisy, habitat.

Lucy’s research seems incredibly topical, with the Guardian last week launching a campaign, “Piece by Piece” to protect the UK’s biodiversity. Yet as several bloggers have noted that the planning issues surround brownfield and greenfield sites are far from simple.

And although wildlife habitat design, rather than the “accident” that brownfields provide, remains a compelling subject, changing Environmental Impact Assessment regulations make it no mean feat to support such habitats.

Perhaps, as Lucy writes in the New Optimists, brown roofs are the answer.

Meanwhile it seems important to remember that, as pointed outby this conservation blog:

Our wastelands, old industrial sites, rail embankments, roadside verges and gardens are… so beneficial to wildlife that they are bolstering and in some cases actually supporting the populations of species that would perhaps otherwise be danger of undergoing serious declines.

So take care what you tidy!

If only, as Ian Stewart reminded us in the 2009 Lunar Society Annual Lecture, it were zero percent who believed in evolution!

For the theory of evolution is not a belief system. I was reminded of this when following one of John Brockman’s tweets (@edge) to the hugely enjoyable series of brickbats between Jerry Coyne (who’s written the book Why Evolution is True) and Massimo Pigiliucci.

The debate is important, even without the engaging vitriol and neat turn of phrase (very neat in Jerry Coyne’s case). Not because there’s a right or a wrong, and right must win. Nor because one party is telling a “truth” and the other lying and the “truth” must out. But because out of such debate we may see that it’s inappropriate as well as unproductive to see “science downgraded to just another belief system”. (I’m quoting from Keith Richards’ Introduction to The New Optimists.)

It’s a pity Jerry Coyne used the word ‘true’ in the title of his book; evolution is no more ‘true’ that the incidence of webbed toes in my family (a Mendelian explanation fits the evidence there) or the ‘look’ of my great-grandmama playing hit and miss across the faces in the family album (no-one, not even the finest of scientists, has a clue as to how).

Let me quote further from Keith’s Introduction, and note the warning inherent in these words:

There are shifts in mood, attitude and policy that are drawing science into new alignments which may have profound consequences for all of us, and in the public arena the sound of something different and altogether more worrying: a disturbing categorisation of science and religion as alternative belief systems. This first surfaced in the protests of creationists but is currently most strident in the climate debate, where words like religion, agnostic and believer are bandied about. If we are not to be misled by such talk, there has never been a more important time to listen to the voice of science and the ideal that it represents.

As the contributions in this collection demonstrate, scientists have different views about issues related to global warming, as they have different views of most things. But what they all agree on, what they are committed to, is doing science. For them, it’s not a question of whether or not they happen to believe in their findings – it’s whether they got the science right.

That’s not how most people see science. Science, as any daily newspaper will tell you, is about discoveries, facts, finding the truth and changing the world. For professional scientists, living down the wilful distortions and extravagant promises made on their behalf by the popular press is an occupational necessity, but seeing science downgraded to just another belief system is harder to swallow. Scientists, like the rest of us, have plenty of beliefs, but the pursuit of science does not allow the luxury of indulging them at the expense of proper procedure.

Watching Juliet Coates take us around her lab, catching the enthusiasm she has for her work and its importance in furthering our understanding of plant life seems far removed from the arguments about creationism that are hurled at scientists working in the States. Nonetheless, whether in the States or in Timbuctoo, evolution is no more “true” than belief in fairies or (Terry Pratchett’s) small gods. There is, however, infinitely more evidence for the former.