On Tuesday, January 28th, The Independent reported that: “The amount of money the Department for the Environment, Food and Rural Affairs has allocated to maintain England’s rivers fell from £108m in 2010-11 to about £92m in 2012-13, the year in which Mr Paterson took office. The cuts have accelerated under Mr Paterson. The allocation fell to about £70m this year and is scheduled to tumble again, to £60m next year, bringing the total drop in funding under the Coalition to 45 per cent.”

The government’s (at least the Tory part of it) believes that public spending is bad and that the country needs more and more private enterprise. But you  can’t deal with a country drowning under repeated flooding by means of the UK government’s nostrum: “more competition and privatisation”. It is obvious to all that being flooded for weeks, or even months, on end is akin to a war-time situation. What did we do in the last War? – We socialised most of the economy.  It must be deeply troubling to the government that a situation has arisen – and is going to get far worse –- in which collective, public action is the only possible way out of an unprecedented crisis. How mean of the climate to ruin their little boomlet! I imagine they must want us to try feel good in our heads  even as our knees are in water.

When I first heard about stem cells I wondered why such a fundamental part of life’s machinery had only been discovered decades after the DNA structure and genetic code had been worked out. DNA is a nanostructure and its teasing out was always going to difficult but cells are about half a  million times bigger than DNA and have been observed closely for more than 150 years – where had the stem cells  been hiding?

Some things in science are too obvious to be noticed and we tend to look in the wrong places. In the first stem cell work they were harvested controversially from embryos but then came a great breakthrough. Stem cells could be reprogrammed by form specialized adult cells such as skin cells by genetic transcription factors – at first it was thought that 4 were necessary, then it proved that each of these could be substituted by various other transcription factors or even by some quite simple chemical molecules.

Now it seems we shouldn’t have been surprised that reprogramming was not the mammoth feat of genetic interactions that had been envisaged. Simple physical stress can flip an adult, specialised cell such as a blood cell, nerve or muscle cell back into a stem cell that can develop in different ways depending on where in the cellular environment it is placed. This is rather as if you could bring a ruined building back to its pristine condition by giving it a good shake.

All kinds of shocks can do the trick but the most effective is an acid medium. Given that our stomachs are full of acid it is odd that our bodies are normally resistant to unwanted reprogramming into stem cells. But that is by the by; the stem cell bandwagon gathers pace.

The research is reported in the current Nature:

Nature, 505, 596 (30 January 2014) doi:10.1038/505596a

Philip Ball, Shapes (OUP)

Shapes, part of a trilogy spun out of Philip Ball’s The Self-made Tapestry (1999) takes the quest for form in life to a new level, beyond even that of Evo Devo. Because genes alone, even clever pattern-making ones like hox genes, are not solely responsible for the forms of living things. If that sounds like heresy, it shouldn’t.

Philip Ball’s hero is the great Victorian polymath D’Arcy Wentworth Thompson, who analysed natural forms in terms of the physical forces acting on them. For a good part of the 20th century, this was heresy to most biologists, who believed that either/or/both genes and natural selection could account for form.

There are obvious problems with this bland, black- box approach, as Ball brilliantly points out. How come some of the most primitive creatures, such as the Venus flower basket sponge, have the most intricate geometrical forms on earth? How do genes instruct a bird’s feathers to grown in a single piece of keratin extruded from cells like pasta from a pasta machine? There aren’t enough genes in the human body to tell all the blood vessels and nerves where to go.  Why are so many natural structures hexagons: the many hexagonal forms of carbon molecules; the micro spherical structures of the marine radiolarians; the large hexagonal patterns left by evaporating salt solutions; the huge hexagonal blocks of the Giant’s Causeway; the hexagonal cells of the bees’ honeycombs?

The answer is of course, that genetic processes act in collaboration with physical forces to create shapes. We know so much more now about nano processes, of course, but even 100 years ago, Thompson was able to demonstrate that foams must be the templates for the radiolarians, minerals being deposited in the interstices of bubbles that always meet at 120 degrees.

Philip Ball brings D’Arcy Thompson up to date. As a synthesis of what is known of pattern and shape formation in nature is not merely a popular science account of current knowledge, it is an original contribution in its own right.  

Guy Deutscher, the Unfolding of Language (Arrow)

The biggest mystery is not how the universe began and why; or how evolution started; our how modern humans evolved. It is how words like “in”, “of”, “up”, “from”, “perhaps “, “however”, “nevertheless”, “albeit”,and so on came into the world.

In The Unfolding of Language, Guy Deutscher has shown how metaphor is the key to all our language. We learned to name abstract concepts by appropriating physical things. Expressiveness in language demands that we carry on coining metaphors.

“At the cabinet meeting, ground-breaking plans were put forward to curb the power of the unions”.

This is now dead, stale language. But cabinet, ground-breaking, curb? Cabinet and ground-breaking obviously derive from the physical but what is a curb? Curb is part of a horse’s bridle but the word is almost only used now in the abstract sense.

Kitchen images have produced countless metaphors:  troubles brew, anger boils over, discontent ferments. It goes further. All abstract words had to have a concrete thing or action behind them. So “decide”  means to cut off;  “sarcastic” means flesh-tearing  (compare sarcophagus); “redundant “means overflowing – unda = wave.

So if all our abstract and functional words derive originally form physical parts of the body, the physical environment , food and its preparation, where do verbs come from? Verbs were originally nouns, a process still going on at some pace. We head the ball, hand it to them, leaf through a book, iron a shirt.

But prepositions? Prepositions come mostly from parts of the body or verbs: so the “front” in “in front of”  was originally the forehead, as in Shakespeare’s “grim visage war has smoothed his wrinkled front”. In some languages “For” can be seen to be derived from “give”: giving something means that it is “for” someone.  “With” has developed from the concept of “follow”. The process can be seen at work in a Groucho Marx joke:

 “Outside of a dog, a book is a man’s best friend.

Inside of a dog, it’s too dark to read”

So the principle of exclusion was first expressed by the concept of physical exclusion – outside and inside were originally just parts of the body, as in topside of beef. The joke relies on the old literal meaning of outside colliding with the newer meaning of abstract exclusion.

The other great revelation of Deutscher’s book is that although languages always seem to be decaying, they never actually lose their expressiveness and accuracy.  It is now known that the process of erosion is also the process of creation. In this language, resembles geology. Deutscher gives as an example the history of the French for today:

Hoc die         Latin

Hodie

Hui                 early French

Au jour d’huii

Aujourd’hui      modern French

Au jour d’aujourd’ hui     a  developing idiom

As a word decays, it is rescued from oblivion by adding to it. Although logical, this example is tautological, but the need is felt for something stronger than “hui”, which sounds so close to “oui”. So, in effect, in the latest manifestation people are saying "the day that is the day that is today". Whether Au jour d’aujourd ‘hui will catch on we don’t know but you will never think of language the same way again after reading Deutscher.

The history of nano has been dotted with bursts of excitement around particular substances. In 1972 titanium dioxide was discovered to be a semi-conductor, water-splitter, and much else. Today it finds many uses, including self-cleaning glass and various bactericidal applications. In 1985 buckminsterfullerene, the C6o nano football, created a new branch of chemistry. In 1993 it was the carbon nanotube, which has only in the last year got as far as being the basis of a nanotube computer. The greatest of all, of course, is graphene, whose 10th anniversary falls this year. In the last few months perovskite has been the name on everyone’s lips, thanks to its especial promise in solar cells.

But, increasingly, it looks as if it is a magic combination of some of these nanomaterials that will finally make the big breakthroughs. Graphene seems to figure in many of these combinations, as in the “Big Mac” transistor, paired with boron nitride or molybdenum disulphide.

In terms of applications, solar cells are prime. A Spanish/Oxford team has recently reported very promising results from a combination of three of the iconic materials: a graphene/titanium dioxide/perovskite solar cell, with an efficiency of 15.6%. To put that in perspective, the record for silicon solar cells is 44.4%. But to enter the lists at 15.6% is impressive. What will the next magic combination be?

Nano Lett., Article ASAP

DOI: 10.1021/nl403997a

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

Why Nations Fail introduces a blindingly simple and highly fertile economic theory: that societies can be divided into those that are inclusive and those that are extractive. The authors apply this idea mostly to developing nations, explaining why some countries become rich and others remain in poverty despite possessing resources that might lead to wealth.

In inclusive societies there is no totalitarian power base; no one group has a stranglehold on wealth and innovation; there is the rule of law that protects commercial enterprise and innovation against expropriation and restrictive practices.

In extractive societies, a monopolistic group stifles commercial and technical development and retains all of the country’s wealth for a few cronies. There is no recourse to law because it only operates in favour of the ruling group. There are many case examples. Before the Civil War the American South was desperately backward because the economy was run to suit the slave-owning ruling class. There was no industry, hardly any railway lines. This was a recipe for stagnation. Acemoglu and Robinson cite the case of Sierra Leone, in which a railway originally built by the British was torn up by the ruler (who had originally been democratically elected)  because it would threaten the trading monopoly of his friends.

But the sting in the tail of Acemoglu’s  thesis, as I pointed out in my review, is the Britain is the textbook model of inclusive society. Or used to be. The current economic model of “maximizing shareholder value”, private equity, hedge funds, huge tax avoidance schemes, very low investment in research and development, escalating inequality (exclusiveness), are all prime extractive traits. Britain is throwing away centuries of inclusive enterprise and making the transition to an extractive economy. This is catastrophic because once such as system is in place – see Zimbabwe or Russia or Egypt or countless more  – it is hard to ever escape it. How is it that the virtues of inclusiveness are being forgotten and that it has required an American and a Turkish-Armenian-American  economist  to point it out?  No argument in the world deserves to be better heard and understood than this.

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.

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

Once a Cinderella, earth sciences are now the most exciting and vital studies on the planet. Waking the Giant is a major contribution. In the first part, it details the salient aspects of the earth’s climatic history to establish the current state of global warming. But the crucial aspect of the book is the thesis that climate change and volcanic activity are linked.

At first surprising and unlikely, this idea becomes blindingly obvious when you understand the movement of the earth’s crust under the weight of almost 2 miles of ice and then its partial removal.  Some facts about this are well known. When the polar ice sheet contracted at the end of the last Ice Age, Scandinavia began a rise of perhaps 1000 ft. This process is still going on, one consequence of which is that Britain is being flipped about its axis, Scotland rising and southeast England sinking at the rate of about 1 mm per year.

The quest to understand the links between the air, the oceans, and the rocks has produced some remarkable correlations. GPS techniques have shown that the movement of water and ice around the world through the seasons causes the earth to bulge slightly on an annual cycle. In the Northern Hemisphere winter it contracts by 3 mm whilst the Southern Hemisphere expands and vice versa in the summer.

McGuire looks at many possible triggers for the incidence of volcanic eruptions and earthquakes. The most important one is that rebound after ice has melted. Volcanoes and faultlines are in a precarious state of equilibrium. A shift caused by rebound after ice is just the kind of mechanism to tip them into activity. The geological record shows that there was an increase in volcanic activity during the most intensive period of deglaciation from 12,000 to 5000 years ago.

Waking the Giant describes some of the major episodes and their consequences for human life, the most terrifying in recent history being the 1783 and 1815 eruptions of the Grímsvötn volcano in Iceland and the Tambora volcano on Java, respectively which blighted harvests in Europe for several years after. But these pale into insignificance compared to the giant Sumatran Toba volcano of 74,000 years ago. It was so large its signature in terms of ash deposited  in the geological  record is unmissable. It is thought to have come close to wiping out the human race. Even worse was the geologic catastrophe of 252 million years ago that destroyed 95% of living species – the greatest extinction on record.  This is now thought to have been caused by a massive eruption of magma plates in Siberia: the Siberian Traps.

The geological processes that caused the Siberian Traps and the Toba eruption are still active. In particular, the possibility that global warming will release the vast store of frozen methane hydrates could produce mayhem on a major scale.

We have been lulled into complacency by the fact that human civilisation developed against the only possible backdrop – an extended period of benign climate. It’s the only world we have known. But it’s not the only world we are going to get.

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.