Penguin recently sent me their reissue, as a Pension Modern Classic, of Arthur Koestler’s The Sleepwalkers. His book entranced me when I read it as the age of 23. It was a formative influence in my developing understanding of the culture of science. I also devoured Koestler’s Ghost in the Machine  and that inspired a burgeoning interest in biology which has never left me. Over the year though I came to see that Koestler’s attempt to justify anti-scientific paranormal cults seriously dented his credibility as a historian of science. Nevertheless, his books had been catalyst and I remain grateful.

But now the reissued  Sleepwalkers come with an Introduction by John Gray in which he praises Koestler for showing that great science does not proceed by “scientific method” and attacks Richard Dawkins and other scientific proselytizers s for advocating “If only we apply scientific method to our problems, the world can be immeasurably improved”.

This is seriously misleading. Dawkins and others are not suggested that the masses should practice “scientific method” but that they should pay heed to scientific evidence. Dawkins’ book The Evidence for Evolution is a good example.

Non scientists will never be able to devise research strategies to find the nature of dark matter or to synthesis a drug that can overcome bacterial resistance to antibiotics. Ordinary people do though possess the ability to understand and respect evidence. That is why juries are composed of 12 such people.

Dawkins in particular and many others like him are concerned about the 40% or so of Americans who consistently deny the facts of evolution and the even greater percentage who deny anthropogenic global warming. You don’t have to be able to sequence a genome to recognise that the remarkable base-for-DNA-base similarity between the human and the chimp genome is telling us something. Or that every organism on earth, from a bacterium to us uses the same genetic code and the same metabolic machinery.

The road to a great discovery may be an error-strewn drunkard’s walk but the result is a piece of elegant machinery that everyone ought to be able to understand. Read James Watson’s The Double Helix and compare the sordid tale of personal rivalry, arrant sexism, error and skulduggery with the beautiful image of the DNA double helix and the wonderful single page paper describing the structure in Nature.

John Gray’s confusion of scientific method and evidence is deeply damaging to the human understanding of science and to the progress of humankind generally.

The ability of fish to survive in subzero Arctic waters is due to a whole range of antifreeze proteins (AFPs). First  investigated in the 1950s many have now been characterized. The magic ingredient is a protein that binds to ice and prevents its growth. It works entirely differently to human-engineered antifreeze agents such as ethylene glycol and in much lower concentrations.

Antifreeze proteins have now been found also in plants and are one of nature’s neatest tricks. But where did they come from? AFPS are a classic case of evolution of new functions by gene duplication.  The original gene continues in its old function; the copy mutates and finds a new role. The AFPs in some fishes such as eelpouts, ocean pouts, and wolffishes are similar to an old enzyme present in most creatures from bacteria through vertebrates that catalyze intracellular synthesis of sialic acids. AFPs have evolved independently in different fishes from different genes.

In a recent paper in Science, researchers at Queen’s University, Kingston, Canada, describe the structure of the AFP from the winter flounder. The two helices of its polypeptide chains corral around 400 water molecules in a kind of cage structure. The water molecules also spill out of the overall molecule and certain sites on the protein orientate ice crystals which form within the cell. Crystal growth is halted before it can freeze the cell.

The fact that a protein can be fashioned, full of water, to create an antifreeze compound, from a gene derived from a much more humble biochemical housekeeping gene, demonstrates once again the astonishing versatility of proteins. DNA gets all the hype but it is just a string of letters. Life’s machinery – its chemical engineering – is protein-based. Proteins can gown into exquisite structures by self assembly, such as a bird’s feather, or ferry oxygen around the body in haemoglobin, or power the muscles of Usain Bolt, or regulate the body’s burning of sugar (insulin), or speed up the body’s vital chemical reactions by almost a billion billion times. Proteins, by human engineering standards, seem miraculous.

We consume AFPs regularly in the fish we eat (and some plants too). Engineered AFPs could have many uses. The first is fairly trivial – they are used to control ice crystal growth in ice cream – but in future, nature’s antifreeze proteins will almost certainly find more profound applications.

Science, 2014, 343, pp. 795-98

I have finally got round to reading Steve Jones’ 2007 book Coral. I was attracted to it long ago because I’ve always had a vague hankering to know more about coral reefs (likewise I am always meaning to read Darwin’s pioneering book on the subject but have yet to do so). If I‘d known that the book was about far more than coral I would have dived in long ago.

Coral is subtitled  A Pessimist in Paradise and Jones is the Prince of Pessimism. The book is in fact a memento mori  for the planet and humankind as well as coral: the bleached bones of dead coral serving as the contemplated skull under Jones’s gaze.

Steve Jones is a genius who can spin seamless moralities and lugubrious commentaries on human vanity, greed and ugliness whilst all the while informing us of the life of our planet in the clearest terms. Under his gaze, the fornications of Captain Cook’s crew in Tahiti, the absurdities of economic bubbles (coral has been one such, like diamonds and tulips), Eternal Reefs Incorporated of Decatur, who will “arrange for human ashes to be cast into concrete balls and used as the foundations for new coral reefs”,  are all as one.

Jones is an effortless aphorist, turning what in other hands would be dry facts concerning economics, ecology and  ageing into literature: “money is the memory of past bargains”;”Gods, in general, gain immortality through celibacy rather than starvation”.

Corals are symbiotic organisms and Jones generalizes his discussion of self-interest  and mutualism in nature and human economics until a whole pattern of sex and death and ageing has been woven from the forces of decay – whether of genes or reef-building animals – and the strategies that oppose them. Jones is a master essayist of an almost 17th century kind but his message is wholly of our time, which he believes to be apocalyptically geological rather than merely historical.

Sean B. Carroll, Endless Forms Most Beautiful (Quercus)

For a very long time many people acted as if the mystery of life was solved: DNA carries the code; it makes proteins; proteins do all the work in the body; QED. But this, although the essential underpinning of the mechanism of life, did not explain how organisms developed their form a single egg and how novel types of organism had evolved. Enter the science of evolutionary developmental biology: Eva Devon for short. 

Although the master pattern gene, the hox genes, were discovered in the early ‘80s and Evo-Devo developed rapidly form that breakthrough, Sean Carroll’s book in 2005 was the first to bring the new knowledge to a wider readership. Carroll is one of the leading researchers in the field and brings a broad passion for natural history to bear on the subject. Pioneers of molecule biology were often utterly disdainful of organismic biology and ecology (Edward O. Wilson has recounted his battles with James Watson at Harvard in the 1950s) but Carroll’s passion extends to the history of biology as well as the cutting edge. His title comes from Darwin and he has Darwin’s passion for nature in the round.

Endless Forms show how the hox genes sketch out body plans and how, for instance, shifting hox gene can create a snake skeleton  of 200-400 vertebrae from the standard pattern of no more than 33 in human beings.  Besides showing the way for the future, Evo Devo highlighted the relevance of some previously neglected work such as that of William Bateson who had explored large-scale mutations: work that decades of the Modern Synthesis orthodoxy  of only tiny incremental changes in evolution had sidelined.

Endless Forms satisfies our artistic urge to know where the zebra’s stripes, the butterfly’s eyespots, the human form, really come from. The answers aren’t just-so stories, but the truth about life on earth.

Melange Adultere de Tout

Having very recently tweeted that “Life, we have discovered, is modular, with functions bolted on to existing ones” I stumble on confirmation of just how this process works in a paper on horizontal gene transfer (HGT) in Science magazine. HGT is one way in which large chunks of genetic material are incorporated into a different organism. In the Science paper the organism is the flowering shrub Amborella trichopoda, believed to be one of the earliest flowering plants.

Amborella is found only on the Polynesian archipelago of New Caledonia. Its genome was sequenced in an attempt to understand the evolution of flowering plants. Amborella, it seems, has practised HGT on an enormous scale. The HGT concerns its mitochondria, the energy producing organelles in every cell of multicellular organisms. Of course, this arrangement itself, which gave rise to all multicellular creatures, was a result of the most important act of HGT ever: the engulfment of the proto-mitochondria by other cells, where they eventually settled down to their role  as universal energy providers.

The mitochondria of Amborella show multiple transfers of genetic material from a variety of algae, mosses, and other flowering plants. In some case, whole mitochondrial genomes have been engulfed. In this case, the foreign genetic material seems to be inactive, with no function, but in some crucial cases HGT has provided important new functions, the most striking being the syncytin gene active in the human placenta, which derives from a retrovirus gene.

How did Amborella  acquire its hitchhikers? Perhaps in the simplest way. Algae and mosses often festoon the plants. It is thought that genetic material is incorporated when the plants sustain wounds.

Science, 2013, Vol 342, pp. 1468-73

Nick Lane, Life Ascending: The Ten Great Inventions of Evolution (Profile)

Our knowledge of evolution is filling in rapidly, thanks to a plethora of new techniques that enable a multi-pincer attack. Nick Lane is a biochemist, which gives him a different slant on a question that is usually considering entirely in terms of replicating molecules, ie DNA. The question of the evolution of life is not just a matter of reproduction and natural selection: the life process itself, bodies able to maintain them by the intake of energy is equally important. There has to be some energetically viable entity that can reproduce.

Lane thrillingly recounts Mike Russell’s theory that life evolved in the cold deep ocean where hot currents poured out from the churning mantle beneath. Biochemists have discovered that some of the essentially energetic reactions that now occurs in every cell are already present in these hot and cold chemical reactions in the deep ocean. This suggests that there are three requirements for life:

1)      Cellular structures to contain the living material (this is the easy bit: such “cells” easily self-assemble from  fatty substances

2)      The aforementioned energy reactions that enable metabolism and  motion

3)      Self-replicating substances that can take over the running of the cell and its contents and allow the cell to reproduce itself.

Life, we have discovered, is modular, with functions bolted on to existing ones. There is no reason to suppose that the very beginning was any different: these three processes combining to create the cell, which could then undergo Darwinian evolution as we know it.

Lane’s 10 inventions are: the first life itself; DNA; photosynthesis; The Complex Cell; Sex; Movement; Sight; Hot Blood; Consciousness; Death. This single book will set the reader off on many exciting trails. What was once mostly speculation is now becoming hard science.

At end of year the papers publish their lists of Books of the Year and highlights from the forthcoming year’s catalogues. There is a wood-for-the trees problem here. A single year often contains no truly great books. But the last few years have seen some truly mind-expanding popular science books. Our knowledge of life on earth is growing so rapidly and the picture that is emerging is so at odds with our lazy received viewpoints, it’s not going too far to claim that these books are essential reading if there is to be a future not entirely horrific.  This is the raw list. Over the next few weeks I’ll post commentaries on each book.

David Deutsch, The Beginning of Infinity (Penguin)

Nick Lane, Life Ascending: The Ten Great Inventions of Evolution (Profile)

Sean B. Carroll, Endless Forms Most Beautiful (Quercus)

Philip Ball, Shapes (OUP)

Richard Wrangham, Catching Fire (Profile)

Steven Mithen, After the Ice, Phoenix

Gregory Cochran and Henry Harpending, the 10,000 Year Explosion (Basic Books)

Guy Deutscher, the Unfolding of Language (Arrow)

Jared Diamond, Guns, Germs and Steel (Vintage

Daron Acemoglu and James A. Robinson, Why Nations Fail (Profile)

Ian Morris, Why the West Rules – For Now (Profile)

Wolfgang Behringer, a Cultural History of Climate (Polity Press)

Bill McGuire, Waking the Giant: How a changing climate triggers earthquakes, tsunamis and volcanoes (OUP)

As a recent convert to Geological obsession I have  been entranced by Iain Stewart’s BBC2 series Rise of the Continents. So many questions I’d never even asked are answered. Why, for instance, is Antarctica a waste of ice and snow but Australia tropical desert?  Until 200 million years ago they were joined as part of the single earth landmass Pangaea, and covered in lush Glossopteris forest.  When they sundered, the Antarctic island, surrounded by ocean, began to chill. Wind currents stirred ocean currents to circulate around the continent rather than trade with the warmer waters coming from the tropics. I haven’t worked out yet quite why Australia became tropical desert. Obviously it was always moving north, getting warmer and, drying out, so desertification presumably became unstoppable.  Australia, in any case, is still moving and will eventually crash into Asia, unleashing a new mountain range and becoming tropically lush again

Speaking of mountain ranges, I didn’t know that New York sits on the eroded base of a mountain range once of Himalayan dimensions, produced when South America collided with North. A good base on which to build skyscrapers.

For those who can access BBC iPlayer, I can’t recommend this series too highly.

Understanding form is probably the biggest problem in biology. OK, many would argue that the brain is the one. But let’s not quibble. If we can just about understand how single-celled life evolved, working out how we acquire our limbs, eye, noses, mouths is a way beyond that in terms of complexity. But we know a lot. Why do pretty well all higher creatures have 5 digits? A gene called sonic hedgehog is largely responsible. But it used to be thought that the gene operates on the basis of a concentration gradient. It runs from thumb to little finger then runs out of steam (polydactyl though is sometimes seen).

But a report in Science back in December (only just arrived in the British Library after supply problems) shows that Alan Turing’s reaction–diffusion process may be involved. This was proposed in 1952, a year before DNA let alone genome biology and for a long time was regarded with suspicion by biologists. But it is very much back in the frame now. Turing’s mechanism was originally devised to explain stripes and spots but if you think about it, digits are stripes: digit, no digit, digit, no digit . . . It has long been known that the hand begins as a one-piece and between the digits  cells have to die to create the famous five. Now it seems that hox genes control the expression of sonic hedgehog.  In mice, knocking  them out causes a progressive increase in digits – 14 being the maximum attained so far. The researchers  interpret the extra digits in terms of Turing’s theory: the wavelength  of the reaction–diffusion patterns has been changed by the hox genes, resulting in more toes in the same space. There’s lets more to learn about this but new insights into form  such as this are coming thick and fast now.

Science, 2012, 338, pp. 1406 and 1476.

Sam Wollaston, in the Guardian, pretending not to understand Brian Cox’s Wonders of Life, actually hit on a good paraphrase:  “Life, that's it – not a thing, but a series of chemical processes that harness the flow of energy to create islands of order, like a tree, or me.” Actually, Cox was excellent in explaining the emerging thermodynamic, chemical gradient theory of the origin of life, as expounded in detail in Nick Lane’s Life Ascending. Absolutely brilliant that Cox was able to present this on primetime BBC TV.