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The Age of Quantum Biology

12/29/2014

2014 was a fine year for popular science with books that opened up new vistas cogently and elegantly for a large audience. Several made a huge impact on me but Jim Al-Khalili and Johnjoe McFadden’s Life on the Edge: The Coming of Age of Quantum Biology administered the biggest shock. I’ve never really got on with matters quantum and comforted myself in my ignorance with the lazy assumption, often quoted, that quantum phenomena are only applicable to their tiny realm: we live in the big, wide world and can ignore its counterintuitive findings, not only in daily life but in other sciences, especially biological science.

There is now a wealth of evidence, expertly and entertainingly marshal led by Al-Khali and McFadden, showing that it is precisely in living processes that quantum effects are seen. In popularising this revolutionary idea they have the advantage that quantum mechanics seems to be involved with many familiar and beautiful aspects of nature and to provide answers to some of the greatest mysteries. A list: the homing of robins and monarch butterflies; the rapid metamorphosis of a tadpole into a frog; how do our rather few olfactory genes cope with so many identifiable odours? how does photosynthesis capture light at almost 100% efficiency; how does DNA replicate so faithfully? Quantum phenomena seem to be implicated in all of these. It is early days but we are going to have to get used to the fact that we really do live in a quantum world.

I Am Almost Completely Beside Myself With Praise for this Book

12/19/2014

Most years there’s no doubt about what is my novel of the year. Last year it was John Williams’ Stoner (an oldie of course but new to most of us). This year it is Karen Joy Fowler’s We Are All Completely beside Ourselves. Writing about it is difficult because of its key plot twist but there’s plenty more. Fowler’s novel reads like a memoir, the protagonist’s voice pitch perfect: witty and often heartbreaking. Without giving anything away, the psychology of human nature could be said to be its theme and it is true both to scientific psychology and the subjective version that fiction has always traded in. It’s a book you will never forget and a book that starts or re-ignites countless debates about the human animal’s place in the world.

Age of Silver

12/19/2014

I was out of the country when Horace Silver died in June this year and when I got back no-one told me. So I only discovered a few weeks ago. Reading the obituaries I was struck by the fact that the key songs they mentioned were not my favourites: the highlight was on the funk numbers like Sister Sadie. For me Silver was one of the greatest jazz composers, up there with Mingus, and the funk numbers, with their simple, derivative riffs, weren’t his strongest suit.

I have regrets about Horace Silver: when I discovered jazz as a student in the ’60s I was in thrall to guitarists and hardly at all listened to Miles, Coltrane, Monk or any of the great innovators. Wes Montgomery was my hero (and still is) but I missed the golden age of jazz: I was there but not there.

So my first Silver pieces were Ecaroh (Wes Montgomery) and Nica’s Dream (Kenny Burrell and Jack McDuff). The latter exercised a special fascination for me: it’s perfectly formed structure; its indefinable quality: part Latin, part bebop. And some characteristic Silver chords which I later discovered to be minor 9ths.

Why I didn’t explore the Silver song book then I will never know but it took another 30 years. When I did, I set myself to work out the harmonies of Nica’s Dream and recorded it myself on computer. And I starting buying Horace Silver albums.

I’m not a completist in anything but I’ve now heard enough Silver to pick a top 10, so here goes:

Pretty Eyes

Song to my Father

Nica’s Dream

Peace

Melancholy Mood

Calcutta Cutie

Lonely Woman

Cape Verdean Blues

Ecaroh

Lonely Woman

Silver’s music is sui generis. He is the master of structure: during the solos you always know where you are in the chord sequence – none of the blur that much up-temp bop creates. He runs serpentine melodies over simple pedal chords, as in Pretty Eyes and Calcutta Cutie; minor 9ths and augmented fifths create much of the appeal of his most famous piece, Song for my Father. He is a whole pattern book of jazz resources. To make a surprising comparison, he is like Frank Zappa in writing instantly recognisable music that could be by no one else and which combines a wide range of elements: in Silver’s case: swing-era sax voicings, Latin, Afro, bebop, and a taste of his father’s Cape Verde Islands.

Arrival of the Fittest

12/9/2014

In a fine year for science writing one book stands out for me: Andreas Wagner’s Arrival of the Fittest. Not too many people are watching the unfolding drama as evolution’s secrets are prised out at an ever increasing rate but for those who are Wagner offers a step change.

There have been many step changes over the 61 years since Watson and Crick’s DNA structure of 1953. For me the most dramatic was the discovery of the hox genes – the genes that parcel up the body into regions, creating limbs, for instance. At last some of the mystery of how biological form is created was dispelled.

A new science, Evolutionary Developmental Biology came into being in the 1980s. But despite many insights into the process of gene regulation and body building – especially in the fruitfly, whose body-sculpting genes are known in some detail – the mystery remained of how truly novel forms come into being. A new model car or aeroplane can be built from scratch – de novo. But all living things have to stay viable whilst genetic novelties emerge that eventually result in modified organs or an entirely new way of life. It is this that has provoked endless sterile debate since Darwin, with sceptics muttering about the likelihood of assembling a 747 in a gale.

Andreas Wagner points out the difficulty of understanding the complexity of gene interactions on the basis of isolated examples: “No list of examples, however long, could tell us how innovation through regulation is even possible”. Instead he shows how the complex circuits that link gene regulation are extremely robust: so robust that countless mutated genes can produce the same end result. Genes code for proteins and there are some examples of proteins that have the same 3D structure and the same function but in which every single amino acid has been replaced by a totally different one. As Wagner points out: this brings a whiff of Platonism back into biology after a very long absence. There do seem to Platonic forms of genes and proteins which the living tissue approximates to in its endless genetic dance of mutation, duplication and rearrangement.

Wagner has provided the answer to what the book jacket calls ”Evolution’s Greatest Puzzle”. There are countless linked pathways through this genetic maze, which means that a bodily organ or a physiological function can change gradually over time without ever losing its fitness. The process is a little like those puzzles in which one word turns into another via many steps, all of which must also be viable words. Of course, some genetic changes are lethal – we have always known this – but what is new is the knowledge of this remarkable robustness of multicellular creatures to genetic tinkering. We know, empirically, without ever looking at the DNA that this must be so: life forms do go extinct, but, on the whole, they are remarkably tenacious. But they also contain the possibility of novelty, which again we have known as an observable fact but now we know how it is done.

The Age of Quantum Biology

I Am Almost Completely Beside Myself With Praise for this Book

Age of Silver

Arrival of the Fittest

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