Category Archives: science writing

Let’s hear it for Thomas Newcomen!

I feel a bit sorry for Thomas Newcomen.  In 1712 he designed the first workable steam-powered pump.  This revolutionised mining and got the Industrial Revolution going.  2012 is the tercentenary of this great event and so far the mainstream media have been almost silent about him.  To try to raise awareness, I have written an article about the Newcomen anniversary on another blogging network.  Here is the link: http://occamstypewriter.org/irregulars/2012/11/20/lets-hear-it-for-thomas-newcomen/

Older fathers and new genetics

[This piece appeared in the October edition of Marshwood Vale Magazine]

Pablo Picasso and children, Claude and Paloma. Their mother was Francoise Gilot.

Couples contemplating childbirth have conventionally focussed on the age of the mother as a risk factor for disorders such as Down’s syndrome.  There has been a growing feeling, however, that the age of the father, previously disregarded, could influence the occurrence of autism and schizophrenia.  A recent study sheds light on the mechanism of this effect as well as showcasing the power of the new genetics. 

The new genetics – the Genome revealed

About ten years ago, the sequence of the Human Genome was reported.  Let’s look at what this means.  Most cells in the body contain a set of instructions that allows new cells to be built.  These instructions, found in the chromosomes, are written in the form of strings of molecules of DNA (DeoxyRibonucleic Acid).  The DNA molecules are organised in to chunks called genes and each gene contains the instructions for making one protein building block.  The Human Genome is made up of about 21,000 of these genes as well as very large stretches of DNA encoding molecules that regulate expression of the genes.  Ten years ago, the sequence of all the DNA molecules (~ 3 billion) in the Genome was determined.  This was a heroic technical and intellectual effort. The Human Genome sequence was called the “blueprint for life” and was expected to lead to huge advances in human health.

The new genetics – the reality

Expansive predictions were made about the effect of the Genome sequence on clinical medicine.  Predictive genetic tests for common diseases such as cancer and heart disease would be available within ten years and new therapies would follow.  None of this has proven to be true.  It had been expected that the genetic basis of these diseases would reside in a handful of changes in the DNA sequence, or mutations as they are called, allowing predictive genetic tests to be developed.  The reality is that many mutations have been identified, each conferring only a small risk for the disease.  Many of the mutations are also in the regulatory part of the DNA, which is not well understood, although it is under intense study.   

The new genetics – whole genome sequencing

Map of Iceland

It became clear that to exploit the power of the new genetics fully, it would be necessary to sequence complete genomes from many people.  Until recently this was impossible for financial and technical reasons.  Now this is going ahead and one of the leaders in this field has been a company deCODE, based in Iceland where it is taking advantage of some of the unique features of this small country.  Iceland has a small population (about 275,000) who are genetically rather similar. This means that mutations in the Genome will stand out from the background variation more clearly than in populations with greater genetic diversity.  Iceland holds genealogical information dating back more than 1000 years allowing inheritance to be tracked between families.  It also holds comprehensive medical records on all its citizens allowing diseases to be followed in the population.  deCODE has so far sequenced the genomes of more than 2000 people and is comparing the sequences from healthy people and those suffering from certain conditions to try to identify disease-causing mutations and has already made important discoveries in stroke, schizophrenia, osteoarthritis and diabetes.

The age of the father at conception

The company has recently compared the genomes of 78 family “trios” of father/mother/child.  The genome of a child contains contributions from both the father and mother and this study examined how maternal and paternal DNA had been changed when it was incorporated in the child’s genome.  The surprising result was that the maternal DNA in the child’s genome contained about 14 new mutations independently of the age of the mother at conception.  The paternal contribution to the child’s DNA, however, contained more mutations and the number increased with increasing age of the father; 20-year old and 40-year old fathers transmitted 25 and 65 mutations respectively.  A woman receives her complement of eggs at birth so it is not surprising that there are few new mutations in maternal DNA.  Sperm, however, result from continuous division of precursor cells; this repeated division, together with environmental insults, results in mistakes (mutations) when the DNA is copied.  In older fathers the sperm precursors will have undergone more divisions with increased risk of mutations compared to younger fathers.

The implications

We now know that the age of the father at conception is the major determinant of new mutations in his child’s DNA.  This surprising finding raises many issues.  First, does the increased number of mutations have any consequence for human health?  The answer here is possibly.  It has been shown in the Icelandic population that as the father’s age at conception increases so does the risk of schizophrenia or autistic spectrum disorder (ASD).  Older fathers transmit more new mutations to their children.   Most of these mutations are harmless, but some may confer increased risk of schizophrenia or ASD.  The risks are still very low but given that age of fathers at conception in the UK has increased from 31.5 in 1998 to 32.4 a decade later, these findings on paternal age are worthy of  discussion more widely in society.  The age of the mother is still an important factor in the occurrence of abnormalities like Down’s syndrome where extra chromosomes are present rather than new mutations.  

Some commentators have wondered if men will now be mindful of ticking biological clocks in the same way women are.  Would young men be sprinting to the sperm bank to preserve their precious non-mutated treasures?  It had always been thought that men were immune to reproductive ageing.  This may now be a myth and we might look differently on the next craggy-faced rock star fathering children in his sixties.

2012: the year of the disappearing apples – and bees

Cider apples on a tree in Devon

Behold the apples’ rounded worlds:

juice-green of July rain,

the black polestar of flowers, the rind

mapped with its crimson stain.

 

The russet, crab and cottage red

burn to the sun’s hot brass

then drop like sweat from every branch

and bubble in the grass.

 

They lie as wanton as they fall,

and where they fall and break,

the stallion clamps his crunching jaws

the starling stabs his beak.

 

In each plump gourd the cidery bite

of boys’ teeth tears the skin;

the waltzing wasp consumes his share,

the bent worm enters in.

 

I, with as easy hunger, take

entire my season’s dole;

welcome the ripe, the sweet, the sour,

the hollow and the whole.

 

This poem, Apples, by Laurie Lee is a gentle celebration of the place of these fruit in a mid-twentieth century country life.   The apples mature in the “sun’s hot brass” and fall from the tree as if to herald the arrival of autumn.  Now in 2012 it is autumn.  It should be the “season of mists and mellow fruitfulness” but this year one of those seasonal signs, the apple, has been badly hit.  According to English Apples and Pears, the apple harvest is down by 25% overall compared to last year.  Some varieties such as Cox’s have been hit much harder.  It gets worse.  Even those apples that make it to our shops will be blemished, having taken a battering in the wet and windy weather.  Taste, we are assured, will not be affected but you can be sure that prices will be higher. 

Cider apples ready for pressing (2010 season)

Cider apples have been particularly badly affected and much less cider will be made this year.  One Somerset cider producer, Julian Temperley, reports a 50% overall reduction in cider apples this season, although one of his varieties, the Kingston Black, has loved the weather and cropped heavily.   

So, what has caused this apple disaster?  April, May, June this year was the wettest three month period in the UK since modern rainfall records began in 1910.  This meant that the bees were unable to fly.  Because the bees sheltered in their hives and nests, the flowers on the apple trees were not fully pollinated.  Some fruitlets did develop but a proportion of these then suffered wind damage.  It is also possible that the trees were “exhausted” by cropping so well in 2011.  Hopefully, this year’s poor harvest will be followed by a much better apple harvest in 2013. 

A honeybee foraging on a Hardy Geranium

I do also wonder how the bees are going to be affected by the poor summer.  Because they couldn’t fly in the poor weather, they couldn’t forage for pollen and nectar and many beekeepers had to feed their bees artificially.  Bees may enter the winter in a depleted state and there could be higher than usual losses of bees this winter. 

This is a grim story but it has a silver lining.  It shows very clearly how critical the bees are for agriculture in this country.  Bees act as as pollinators for so many of our crops.  Without adequate pollination the apple crop has been badly hit.  We need to make sure our bees are protected.  Friends of the Earth continue to pursue their Bee Cause campaign but it is very reassuring to see that the House of Commons Environmental Audit Committee has recently decided to examine the emotive issue of whether insecticides are harming bee health.   These are hopeful signs that the welfare of the bees is being taken seriously.

[Thanks to “A Woman of the Soil” for alerting me to the poem by Laurie Lee]

Cider apples (2010 season)

How to make Usain Bolt?

Usain Bolt

I have always wondered why I was such a poor runner.  Now Jonjoe McFadden, writing in the Guardian, has supplied the answer; it’s all down to my faulty gene switches.  It’s too late for me now but according to McFadden, in the future anyone wishing to rival Usain Bolt and run a sub-10 second 100 metres will just take a gene switch drug.   McFadden also tells us that diseases like diabetes, heart disease, cancer and Alzheimer’s disease are all caused by faulty gene switches.  In diabetes, he says, a liver cell may be “genetically tripped to stop absorbing blood sugar”.  Silly me, I had always thought insulin had something to do with diabetes.

McFadden’s musings were occasioned by the recent publication of the results of the ENCODE consortium.  About 10 years ago the DNA sequence of the human genome was reported.  Surprisingly, the part of the genome containing the information for building new proteins, the genes, constituted less than 2% of the sequence.  The other 98% was, at the time, of unknown function and some rather unwisely dubbed it “junk” DNA.  ENCODE set out to study this large part of the human genome that does not code for proteins.  ENCODE’s data rewrite our knowledge and show that much of this misunderstood DNA is functional.  Functional here is a rather broad term and includes several possible mechanisms that can be loosely described as regulating how the genomic DNA is expressed.  This regulation is important for determining why certain proteins are expressed only in certain cell types thus establishing the unique identity of liver cells, heart cells etc.  The regulation may go wrong, and this dysregulation may be at the core of some common diseases.

No one can doubt the importance of ENCODE’s work in rewriting our view of the human genome but it is very important to be clear about the implications.  McFadden uses the term “gene switch” to describe all the regulatory activities outlined above.  This idea in fact derives from the Press Release that accompanied the data.  I find the term gene switch to be misleading as it suggests a mechanistic understanding we do not have.  ENCODE showed, in a variety of ways and in different cell types, that there were potential regulatory functions associated with the non genomic DNA but they did not show how all of these worked.  It will require huge amounts of research to understand the regulatory mechanisms and using a term like gene switch trivialises the present findings and the task ahead. 

McFadden then goes on to build a huge edifice around the idea of gene switches.   Gene switch drugs will in time be developed to counter defects in the regulatory mechanisms that lead to diseases but these drugs will be also be used , he suggests, to manipulate “physiology, mood, intelligence, libido, anxiety, and appetite”, also  to create new Usain Bolts and to stave off the symptoms of old age.  He also states that “many scientists believe ….  that the differences between us and our closest relatives  …. are mostly due to differences in gene switching”.  The corollary of this, he says, is that a chimp might be enabled to talk by treatment with a gene-switch drug.    This wealth of speculation is entertaining but is pure science fiction as it can be neither proven nor disproven at present. 

When the Human Genome was reported, it was accompanied by claims that the information would revolutionise clinical medicine.  The Human Genome has sparked a biological revolution but it has so far had little effect on clinical medicine leading to some disappointment.  The results of the ENCODE project are important and require serious discussion.   Making exaggerated claims about the outcomes means that the real impact of the results may not be appreciated.   Those who read these predictions may end up disillusioned and disappointed when, inevitably, the predictions are not realised. This is bad for science.

Nowhereisland – nowhere to be seen?

Nowhereisland at Torquay

If you were in Weymouth at the start of the Olympic sailing you may have been surprised to see a mysterious new island appear off the Dorset coast.  This was Nowhereisland, part of a public arts project realised by the Devon-based artist Alex Hartley. The island and its Embassy are to travel round the South West over the next few weeks.  I went to see it at Exmouth but, although the Embassy was there, ironically the island was nowhere to be seen.  Apparently, the weather got the better of it; it couldn’t travel and this ephemeral new nation had to be protected by the motherland in Portland harbour.  Since then, it has sailed on to Torquay, Plymouth and Cornwall  and it has been “occupied” by members of the Devon and Cornwall wild swimmers who staged a coup d’état, unfurled a banner and populated the island with a plastic duck and rabbit.

The Nowhereisland project began when Hartley visited the High Arctic in 2004 under the auspices of Cape Farewell, a group who instigate cultural responses to climate change.  On that visit he discovered a previously-uncharted island that had been revealed by a glacier melting in response to global warming.  Hartley originally called the island Nymark (Norwegian for “new ground”) but it was given the official name of Nyskjæret.  Based on his experience he produced a large wall display, “Nymark (undiscovered island)”, containing framed rock samples, letters, maps, photos and other documentation on his discovery.  This was exhibited as part of the exhibition, Cape Farewell – Art and Climate Change, at the National Conservation Centre in Liverpool in 2006 and as part of the cross cultural arts/science project, Exploratory Laboratory, at the Bridport Arts Centre in 2010.

The project (now called Nowhereisland) acquired a much greater significance when Hartley was chosen as the artist for the South West in the “Artists Taking the Lead” section of the 2012 Cultural Olympiad.  The first phase of Nowhereisland involved an expedition to the Arctic with a group of sixteen “thinkers” – artists, writers, students and academics.  The group collected six tonnes of material from Nyskjæret and brought it back to the UK where it was fashioned into a floating replica of the island.  Nowhereisland was declared a new nation on September 20th 2011 after which it was possible to become a “citizen”.

The second phase of the project involves not only the current tour of the replica island, Nowhereisland, around South West seaside towns but also the Embassy which accompanies the island.  This is a converted horse box containing a display of artefacts and memorabilia associated directly or indirectly with the project.   Three “ambassadors” are present to discuss and explain Nowhereisland.   There has also been a programme of workshops in schools and local communities to disseminate and debate the issues behind the project.

The Embassy at Exmouth

So, what are the aims of Nowhereisland?  On Hartley’s web site these are stated clearly as:  “to expand people’s view of what art is; to explore sense of place; to address the most significant global issue of our time:  namely how can we respond to the urgent issue of climate change together”.   On the project web site, the aims are more focussed on exploring the idea of a nation state.

The debate about the issues behind the project began on the expedition when the sixteen “thinkers” were asked to contribute to discussions about the implications of forming a new nation.  In particular they were asked to consider how they would begin if they started a new nation from first principles given the current failure of nation states to address important global issues.  They also experienced the effects of global warming first hand.  The debate continues on the project web site where propositions for the Constitution can be posted.

Nowhereisland has attracted criticism, achieving the unusual feat of uniting the Guardian, the Daily Mail and the Taxpayer’s Alliance in common condemnation.  Some objected to the cost (£500,000) but actually this is quite low compared to the overall cost of the Olympics.   I am, however, uneasy about some aspects of Nowhereisland.  For a project concerned about the environment, was it necessary to ferry the “thinkers” to the Arctic, was it necessary to take material from the virgin island?  I feel disappointment that climate change is not at the core of the project; this is a lost opportunity to debate this crucial issue.

Having seen the project develop, however, I have warmed to it.  This is partly due to discussions with my family and discussions with the ambassadors and partly because of the public reaction.  Communities have embraced the visiting island, many people have visited the embassy and there are now about 19,000 “citizens”.  The Embassy is interesting and the ambassadors maintain enthusiasm even when the rain beats down. I have particularly enjoyed the quirky responses to the island, the occupation by the wild swimmers.

The project has brought art to the South West and has probably engaged more people than any conventional gallery-based exhibition would. As a public arts engagement project it must be seen as successful and this is summed up well by Pauline Barker, one of the wild swimmers:  “It’s designed to be an arts project to get art closer to the people, and we are the people so we decided to get as close as we possibly could”.

For more on Nowhereisland see this article.

The greatest single advance in technology?

The picturesque town of Dartmouth in Devon is well known for its annual regatta and for the Royal Naval College where naval officers in the UK are trained.  Members of the British Royal Family have spent time there and Princess (now Queen) Elizabeth had one of her first meetings with her husband to be, Philip, when he was undergoing training there.

Dartmouth

A few weeks ago, Dartmouth was honouring Thomas Newcomen, who has had, in some people’s eyes, a bigger impact on the world.  It was Newcomen who devised the first workable steam pump and 300 years ago established its first working prototype at a mine near Dudley Castle in Tipton, Staffordshire.  His pump enabled mining at greater depths by pumping away dangerous levels of water and made coal cheaper and more available.  His invention kick-started the Industrial Revolution in Britain and it has been said that “In the whole history of technology it would be difficult to find a greater single advance than this, nor one with a greater significance for all humanity”.  For a description of the Newcomen engine or atmospheric engine, as it sometimes known, see this site and scroll down to the second article .

New signs have been erected in Dartmouth celebrating Newcomen, there was a programme of lectures, a garden party and a beer (Newcomen Atmospheric Ale) has been brewed in his honour.  Newcomen was also honoured nationally by the issue of a postage stamp bearing his name.

One of the big local events was a new play written by the local author Linda Churchill and performed by the local “am dram” group, the Dartmouth players.  It was entitled “From Floods Defend”.

The play allowed the Dartmouth community to come together to celebrate Newcomen.  The play is essentially a chronology of his life and made little attempt to imagine the psychology behind the man.  So, we heard about his birth in the town and his very religious family and upbringing.  His religion, Baptism, played a huge part in his life and surfaced regularly during the play.  He is shown training as a lay preacher under the puritan, John Flavel who had been brought to Dartmouth by a group that included Newcomen’s father.  Flavel is shown during the play having to flee Dartmouth presumably as a result of the passing of the Act of Uniformity in 1662 which effectively removed non-conformists from the established church.  The play suggests that Newcomen’s religion gave him a stoicism in response to life’s events and it is known that his religion also provided him with important business contacts.  These included his long term collaborator, the plumber John Calley and his London business contact, Edward Wallin in whose house he probably died in 1729.

Newcomen trained as an ironmonger and made tools for sale in mines.  The play shows him on a sales visit to a coal mine in Worcestershire where he is confronted by a woman whose husband was killed in a mining accident.  This makes him recognise, for the first time, the problems of flooding and he and Calley resolve to try to solve the problem.  Newcomen and Calley are shown spending long nights of experimentation, finally being rewarded with a chance discovery that gives them the prize of a working pump.  The two men, although not scientifically trained, are skilled craftsmen and this may have helped them achieve their aim.

Newcomen and Calley are then shown in despair when they discover that a patent already exists on a steam-driven  pump in the name of Thomas Savery, another Devon inventor who had developed a primitive water pump in 1698.  In the play, a meeting between Savery and the two Dartmouth men seems to resolve this amicably.   I find this very unlikely.  It is true that Newcomen’s  pump depended on some of Savery’s ideas but Newcomen was also influenced by the work of the Frenchman Denis Papin, another person who had tried to harness the power of steam.  Despite this, Newcomen’s  pump was different and it worked.   The problem was that Savery’s patent was broad so that Newcomen had to settle for working under the Savery patent.  I would guess this held him back and reduced his income and I find it hard to believe this was amicable.  Even the 1712 prototype bears the names of Newcomen and Savery and this must have been difficult for the inventor.

An early Newcomen Engine

Newcomen’s discovery was a critical step in the Industrial Revolution in this and other countries and I did not feel the play brought out the broader implications of his work.  Many people believe that the steam engine was invented by James Watt; indeed I overheard someone discussing this in the audience.  In fact, James Watt modified the Newcomen design to improve its efficiency.   Watt made huge progress in the development of steam power and many Watt engines were built but Newcomen was the inventor.  The next big step forward was to use high pressure steam.  This required improved engineering and was achieved by the Cornishman, Richard Trevithick.   His engines were small and light enough to be used to make steam locomotives. The age of steam railways beckoned but it wouldn’t have happened without Newcomen’s  great invention.

Biofuels from algae?

Oil will run out sooner or later so we need to consider alternative non-petroleum based fuels for our cars and lorries.  We also need to reduce existing consumption of petroleum-based fuels so that carbon emissions are diminished and potentially damaging effects of climate change are attenuated.     There are many ways to approach these problems but one attractive way is to make biofuels from algae; in principle these are carbon-neutral fuels.  This idea has attracted quite a bit of interest but the usual bottleneck is making enough algae.  There are many players in the field including Craig Venter and ExxonMobil.  One man in South West England, James Morris, however, has some ideas about increasing production of algae that may get round the bottleneck.  He has a prototype apparatus up and running and I visited him at Plymouth Marine Labs.  You can read the full story from Devon Life Magazine here.

Spring is here…..and it’s lovemaking time for the toads!

The weather is treating us to its usual roller-coaster ride here in the UK.  Over seven days temperatures have dropped by half and summer-like weather has been replaced by chill.   Despite this, Spring is definitely here and Nature is going through its annual ritual to ensure survival for another year. 

In our garden, the birds are performing their elaborate courtship dances and scrabbling to gather all they can for nest building.   On the trees, fat buds growing bigger by the day and gaudy blossom provide the fitting backdrop for these fertility rites.

I have watched newts courting at this time of year with their elaborate ballet but I have never seen the mating ceremony of toads.  If you want to experience this, I recommend you read the beautiful description in the Country Diary section of the Guardian a few days ago.  There is a particularly striking image of mere toad’s flatus, fanned by Kestrel’s wings being transformed in to the pure sunlit gold of lark song.