Tag Archives: science in the media

Change is coming whether they like it or not

[This post is dedicated to the 100s of  MPs who  chose not to attend a debate in parliament on climate change in a week when the UK experienced its hottest ever winter’s day.]

 

Blizzards, strong winds, drifting snow, bitter cold – that was the story in early March last year when the “Beast from the East” collided with storm Emma bringing extreme weather and disruption to life across large parts of the UK.  Towards the end of June, by contrast, the sun began to shine and daytime temperatures climbed into the thirties and stayed that way across much of the country until August (the picture at the top of this post shows the effect of the long hot summer on the UK countryside).  Elsewhere across the globe, reports came in of flooding, wildfires, severe tropical storms and unusually high and low temperatures.  Many of these weather extremes can be attributed to climate change and there is considerable concern that the planet is heading for climate catastrophe.  David Attenborough expressed this fear at a climate change conference in Poland:  “If we don’t take action, the collapse of our civilisations and the extinction of much of the natural world is on the horizon.”

 

Heavy snow falling in early March while a great tit continues to feed

 

In the UK, it was the long, hot summer, the joint hottest on record, that made people think most about a changing climate.  The weather here is, of course, notoriously fickle and some will remember that in 1976, we experienced a similar long, hot, dry summer, so how can we disentangle normal weather variation from climate change?  One way of looking at this was shown by Simon Lee, a PhD student at the University of Reading, who shared graphs on Twitter of the global temperature anomalies in June 1976 and in June 2018 (see pictures below).  These show that in 1976 the UK was one of a few unusually hot spots in an otherwise cooler than average world whereas in 2018 much of the world, including the UK, was hotter than the average.   The 2018 picture shows climate change in action: the planet is warmer making heatwaves more likely.

 

The pictures show temperatures across the world in June 1976 (upper panel) and in June 2018 (lower panel) compared to the average across the period 1951-1980. Red and yellow mean higher, blue means lower. Kindly supplied by Simon Lee who generated the images from NASA/GISS data.

Careful measurements of the average surface temperature of the planet show that it is currently about 1oC hotter than in pre-industrial times.  This may not seem very much but it is enough to disturb the complex systems that create our weather.  As a result, heatwaves may be more frequent in summer and, in winter, polar air may be directed southwards bringing abnormal, freezing temperatures.  Also, a warmer atmosphere holds more moisture so that rain and snow may be more severe.  Climate breakdown might be an apt description of these changes.

This global heating is a result of human activity.  The emission of greenhouse gases, particularly carbon dioxide produced by burning fossil fuels such as coal, gas, oil and petrol, traps heat in the atmosphere so the temperature of the world increases.  We have known this for some time and we have also known that the solution is to reduce carbon emissions. Atmospheric levels of carbon dioxide have, however, continued to climb because no government has had the will to introduce the extreme lifestyle changes required to curb emissions.  Some governments, including our own, have even encouraged the continuing extraction of fossil fuels.

It is, therefore, significant that in October 2018, the Intergovernmental Panel on Climate Change (IPCC) issued a report containing a dire warning: we must make urgent and unprecedented changes to the way we live if we are to limit heating to 1.5oC above pre-industrial levels.  To achieve this target, we must reduce net global carbon emissions by 45% by 2030 and to zero by 2050 – fossil fuel use must be drastically reduced by the middle of the 21st century but we must start the reduction now.  Should we fail to achieve this 1.5oC target, the risks of drought, flooding, extreme heat, poverty and displacement of people leading to wars will increase significantly.  The world will no longer be the place we know and love and parts of it will become uninhabitable for humans and the rest of nature.

How do we achieve this reduction in carbon emissions? Voluntary measures such as suggesting people fly or drive less will not work.  The only way this reduction can be achieved is through coordinated government action based on recommendations made in the IPCC report.  These include the planting of more forests and the chemical capture of carbon dioxide to reduce atmospheric levels of carbon dioxide.  There must also be a drastic shift in energy production and in transport away from fossil fuels and this can be driven in part by investment and subsidies directed towards clean technologies.  A carbon tax can also help drive this shift but the tax will need to be high enough to force change, for example by taxing energy companies who burn fossil fuels so that they invest in cleaner technologies.  In the short term, costs to consumers may rise, so politicians would need to keep the public on side, for example, through tax incentives.  If we grasp the opportunity, the scale of change may have the unexpected bonus of allowing us to design more sustainable and equitable societies.

The IPCC report set out very clearly the changes required to avoid damaging global climate change so there was great anticipation when the UN Climate Change Conference convened in Katowice in Poland just before Christmas.  Astonishingly, given the gravity of the situation, the 200 countries represented there failed to agree new ambitious targets for greater reductions in carbon emissions. Four countries (USA, Saudi Arabia, Russia and Kuwait) would not even sign a document welcoming the IPCC report; these countries are of course all oil producers.

It was at this conference that David Attenborough issued his warning about the collapse of civilisations but there was another hugely impressive intervention.  This came from 15-year old activist Greta Thunberg from Sweden.  She had already achieved some notoriety through her weekly climate strikes where she missed one day of school to protest about climate change.  Her actions have stimulated many thousands of young people around the world to do likewise.  Thunberg also spoke in London at the launch of the new grass-roots movement, Extinction Rebellion, which intends to use peaceful protest to force governments to protect the climate.  These new trends offer some hope for the future since it is the young of today that will bear the climate of tomorrow.

Greta Thunberg, 2018 (cropped)
Greta Thunberg

Here is part of Greta Thunberg’s speech given at the Katowice conference:

“For 25 years countless people have come to the UN climate conferences begging our world leaders to stop emissions and clearly that has not worked as emissions are continuing to rise. So, I will not beg the world leaders to care for our future, I will instead let them know change is coming whether they like it or not.”

“Since our leaders are behaving like children, we will have to take the responsibility they should have taken long ago. We have to understand what the older generation has dealt to us, what mess they have created that we have to clean up and live with. We have to make our voices heard.”

I am grateful to Simon Lee for generously supplying the temperature anomaly graphs.

This article was published in the March 2019 edition of the Marshwood Vale Magazine.

A country walk, a clean beach and the fallacy of perpetual growth

The Christmas weather in south Devon was stormy and very wet so when we woke on December 27th to bright sunshine and clear, pale blue skies we had to get out for a walk.   We chose one combining countryside and sea, one we often walk after heavy rain as it mostly follows minor roads or paved paths.

We started at Townstal, a suburb on the edge of Dartmouth.  Townstal is noted for its leisure centre and two supermarkets but it does provide easy parking and quick access to open countryside.  Our route headed gradually southwards towards the sea along narrow roads edged by high grassy banks.   Volleys of gulls and crows rose from adjacent fields and the low sunshine created strongly contrasting areas of light and dark on the deep valleys and rolling countryside, emphasising even the slightest undulation.

Some steep ups and downs took us to Venn Cross where we turned to descend along the Blackpool Valley with its spirited stream, growing ever fuller as it gathered water from springs or from the sodden fields.  This part of the walk is tree lined and the minor road is cut into the hillside well above the stream.  Several former water mills are dotted along the valley; they are now rather grand private houses but one has installed a turbine to harness the power of the water once again.

Old Mill in the Blackpool Valley
Blackpool Mill, one of the old mills found along the Blackpool Valley. This hidden valley has changed very little over the years. Have a look at the painting below of a nearby farm to see how the area looked nearly a century ago.

 

Apple Blossom, Riversbridge Farm, Blackpool by Lucien Pissarro, 1921, from Royal Albert Memorial Museum Exeter

 

At this time of year, the trees are dark latticeworks of bare branches but pale brown immature catkins were showing well on some of the trees, readying themselves for the spring.  Patches of winter heliotrope spread along verges enclosing the ground with their fleshy, green, heart-shaped leaves.  Purple and white lollipop flowers struck through the leaves, broadcasting their characteristic almond odour.

Catkins and running water in the Blackpool Valley
Catkins above running water in the Blackpool Valley

 

Winter Heliotrope in the Blackpool Valley
Winter heliotrope in the Blackpool Valley

 

Eventually, we reached Blackpool Sands, a popular shingle beach and café, surrounded by pine trees and sheltered by steeply rising hills.    The low winter sun created strongly contrasting colours: the yellowish- brown shingle, the fringe of frothy white waves, the sea a rich dark blue tinged with turquoise highlights, and there were clear views across the bay to Start Point with its lighthouse.   Near the café, a hardy group of swimmers were struggling on their wet suits in readiness for a dip.  They passed me as they ventured in to the sea accompanied by audible yelps and shrieks.

View across Start Bay from Blackpool Sands to Start Point
View across Start Bay from Blackpool Sands to Start Point

 

Swimmers at Blackpool Sands
Swimmers at Blackpool Sands …… with friend.

 

I was keen to have a look at the shingle beach for two reasons.  There had been a very successful beach clean four days previously organised by Amanda Keetley of Less Plastic.  We hadn’t been able to be there owing to family commitments but there had also been storms since then and I wondered how much more plastic had washed up.  I didn’t find any, the beach was still clean which should have been good news.

To be honest, however, I was feeling disheartened about efforts to reduce the load of plastic in our seas after reading two articles in the Guardian over the Christmas period.  It seems that the US, along with financial support from Saudi Arabia, is planning a huge increase in plastic production, the driver being cheap shale gas.  If we are to reduce the amount of plastic in our seas we need to reduce the amount in circulation and this new plan runs directly counter to this.

Here are links to the two articles:

$180 billion investment in plastic factories feeds global packaging binge

World’s largest plastics plant rings alarm bells on Texas coast

I am not sure how this can be stopped but I am convinced that the drive for perpetual economic growth, espoused thoughtlessly by so many of our politicians, is ultimately very damaging for our planet.

The opium fields of England

A surprising picture appeared in the Guardian newspaper towards the end of June. It showed fields, near Blandford, Dorset in South West England, painted lilac with the flowers of the opium poppy. This controversial crop, associated in many people’s minds with war-torn countries like Afghanistan, is now being grown commercially in England to produce the medically-important pain killer morphine. But just how did opium poppies come to be grown across swathes of rural England?

Opium and the opium poppy

Illustration Papaver somniferum0.jpg
Papaver somniferum as described in a 19th century German book (from Wikipedia, click on the picture for more details)

 

The opium poppy, or Papaver somniferum as it is more correctly called, is an imposing plant with fleshy grey-green leaves, showy pastel coloured flowers and impressive pepper pot seed heads. Standing up to a metre tall, the opium poppy brings architectural interest to the garden but it has a darker side. Within the seed head is a milky liquid containing a mixture of narcotic chemicals including morphine and codeine. If the unripe seed head is pierced, this latex seeps out and, left to dry, this is opium, prized for its extraordinary psychoactive powers.

Slaapbol R0017601.JPG
The unripe seed capsule of an opium poppy pierced to release the opium (from Wikipedia)

 

Humans have used opium for many thousands of years and the earliest written reference to the drug comes from the Middle East around 4000BC. The ancient Egyptian, Greek and Roman civilisations were also well acquainted with the properties of the drug using it enthusiastically. Although growth of Papaver somniferum is typically associated with warmer climates, the opium poppy has a history of cultivation in the UK. In the 18th and 19th centuries, many houses in the East Anglian Fens grew a stand of white opium poppies so that the dried seed capsules could be used to brew a tea containing small amounts of morphine. This infusion helped counter the aches and pains suffered by people living harsh lives in what was then, a remote, unhealthy part of the country. Use was not confined to the Fens as  the Dorset-writerThomas Hardy, in The Trumpet Major, refers to poppy heads and pain relief.

By the 19th century, imported opium was freely available in the UK and was used extensively at all levels of society. Opium was supplied in many forms including laudanum, a tincture of opium in wine, popularised by the Dorset-born physician Thomas Sydenham. The drug was taken to relieve pain, to induce sleep and to treat cough and diarrhoea. Its euphoriant properties were also prized and recreational use occurred with some problems of dependence. Encouraged by the drug’s popularity, attempts were made in the late 18th and early 19th centuries to grow opium poppies commercially in the UK but these were abandoned in favour of imported Turkish opium.

From opium to morphine

Morphine was isolated from opium in the 19th century and the powerful pain killing and euphoriant properties of the pure drug were quickly recognised. These come at a price as, compared to opium, morphine has potentially dangerous side effects and is highly addictive. By the 20th century, all non-medical use was banned but, to the present day, morphine is widely prescribed to relieve moderate and severe pain especially after major surgery. Diamorphine (heroin) is also used for pain relief in the UK but we hear more about its illicit use, the problems of addiction and the associated criminal activity. All morphine used clinically is still obtained from the opium poppy, extracted either from crude opium or from the dried seed heads.

The 21st century opium fields of England

Poppy heads by Jane V Adams
Opium poppies growing near Bere Regis in Dorset, UK showing the seed heads (by Jane V Adams)

 

By the end of the 20th century, the morphine used for medical purposes in the UK was extracted from opium poppies grown in Tasmania and Spain. It was tacitly assumed that the climate in the UK was unsuitable for their commercial cultivation. In 1999, however, John Manners, a seed merchant from Oxfordshire questioned this doctrine. He had seen striking pictures of purple opium poppies growing commercially in Poland, and decided to have a go at growing the plants in the UK. He set up some small trial plots and grew the poppies successfully in the southern part of the country. But did they produce morphine when grown in the UK? With the help of the Scottish pharmaceutical company, Macfarlan Smith (now a division of Johnson-Matthey), he showed that indeed they did. A full field trial the following year in Oxfordshire was also a success and, by 2002, 100 hectares of opium poppies were being grown commercially in the UK, each hectare yielding about 15 kg of morphine. More farmers were persuaded to grow the crop and nowadays, early summer sees about 2500 hectares of farmland blooming with the unselfconscious lilac flowers, mostly in the counties of Dorset, Hampshire, Lincolnshire and Oxfordshire.

Poppy Fields - geograph.org.uk - 1361923.jpg
Opium poppies growing in Lincolnshire, UK (from Wikipedia)

 

Although they were initially uneasy about growing opium poppies, farmers now find it to be a lucrative break crop to prepare the land for growing cereals or oil seed rape the following season. Farmers contracted to Macfarlan Smith must prepare the seed bed and sow poppy seed supplied by the company which also advises on agronomy and pest control while the opium poppies are growing. The UK climate seems to suit the poppies well and after flowering they are left to dry before the seed capsule and about 5 cm of stem are harvested. The harvest is taken to a central processing facility where the poppy seeds in the capsule are separated leaving “poppy straw”. Poppy seeds contain little or no morphine and are sold for various culinary uses such as bread making. Poppy straw is processed in Macfarlan Smith’s Edinburgh factory where the morphine is isolated by solvent extraction and purification. About half of the UK requirement of medical morphine (~60 tons/year) is now made from poppies grown in the UK, including those grown in Dorset. So when you come across these beautiful lilac-painted fields next summer, think morphine, think pain relief, and think poppy extracts ending up in medicine cabinets in hospitals and pharmacies.

I should like to thank Marilyn Peddle (www.marilynjanephotography.co.uk) for generously providing the featured image which is of opium poppies growing in North Dorset
and Jane Adams (https://urbanextension.wordpress.com/) for generously providing the photograph of opium poppies growing near Dorchester.

This is a slightly  modified version of an article that appeared in the September edition of the Marshwood Vale Magazine.

We need to act now to protect the world from damaging climate change

It is clear: to restrict global warming to 2 degrees Centigrade we need to leave most of the remaining fossil fuel reserves in the ground. We must stop using oil, coal and gas and, instead, we must use renewable, zero-carbon energy sources.

And yet, politicians sit on their hands and do very little to encourage both reduced use of fossil fuels and increased use of renewables.

The Guardian Newspaper has decided to increase their coverage of these issues, giving them a much higher priority and starting with a series of articles on its front page. With the Guardian’s global on-line reach this is a step change in both thinking and action on this topic.

The articles are an excellent resource for understanding the current situation and begin with a statement from their chief editor, Alan Rusbridger: Climate change: why the Guardian is putting threat to Earth front and centre

This is followed by:

Two extracts from Naomi Klein’s book “This changes everything”

“Climate fight won’t wait for Paris, vive la resistance” by climate activist Bill McKibben

“Keep it in the ground” by George Monbiot

I urge you to read some or all of these articles.

 

Here is a link to an article by another blogger that also covers the Guardian’s climate change series.

The image at the head of this article is of a tornado and comes from Wikipedia.

Bumblebees and honeybees share diseases and the outcome is not a good one.

lyme regis february 2014
Bumblebee on Rosemary on Lyme Regis sea front (February 22nd 2014) (photo by Hazel Strange)

I recently read Dave Goulson’s excellent book “A Sting in the Tale” and learnt a lot about bumblebees. Although I was aware of the global trade in honeybees, I hadn’t realised that there was an equivalent trade in bumblebees. Some crops such as tomatoes and peppers require buzz-pollination, the rapid vibration of the flower. Bumblebees do this very well and are now used extensively by commercial growers of tomatoes and other crops. To supply the demand for these useful insects there are at least thirty factories producing bumblebees for shipping all over the world. The numbers are staggering with European factories producing up to a million nests per year. This is big business with huge financial rewards but keeping so many insects together in one place risks the rapid spread of disease unless stringent hygiene precautions are observed. To complicate matters, commercially-reared bumblebees are fed pollen from honeybees so that they are potentially exposed to all the diseases that affect honeybees.

But what about wild bumblebees? What happens when a wild bumblebee forages at a flower that has already been visited by a honeybee? Are the bumblebees exposed to honeybee diseases and what might the consequences be?

scan0001

 

Last week’s Nature magazine carried an article addressing this issue. The team who carried out the work were from Royal Holloway London, Queen’s University Belfast and Exeter University. They showed that some honeybee diseases are indeed a problem for wild bumblebees and could be causing a decline in these wild pollinators. They studied two diseases: the fungal parasite Nosema which weakens honeybee colonies, and Deformed Wing Virus (DWV) which causes abnormalities in the wings and abdomen of infected honeybees as well as severely curtailing their lifespan.

The starting point for the work was to test whether these honeybee diseases could actually infect bumblebees. The researchers inoculated bumblebees (B.terrestris) with DWV or Nosema, and found that bumblebees were indeed susceptible to infection by both diseases. In the case of DWV, infection led to reduced survival of B.terrestris workers. For Nosema, although it could infect bumblebees, this did not reduce their lifespan.

Having established that the two honeybee diseases could infect bumblebees, the researchers examined the incidence of the two diseases. They performed a large scale study on the prevalence of DWV and Nosema in honeybees and bumblebees across 26 sites in Great Britain and the Isle of Man. DWV was found in 36% of honeybees tested and in 11% of bumblebees tested. For many of the infected bumblebees, the virus was active showing that the bumblebees were not simply acting as carriers. Nosema was less prevalent being found in 9% of honeybees and 7% of bumblebees. When the geographical distribution was analysed, there was some evidence for clustering, indicating disease hotspots. Hotspots for DWV were found in the south west and east of Great Britain and for Nosema in the south east. By analysing the distribution of the two diseases they were also able to show that the prevalence of DWV in honeybees influenced the prevalence of DWV in bumblebees, implying local transmission between the two insects. Local transmission was confirmed by analysing the form (nucleotide sequence) of the virus present in the two types of bee collected from the same site.

Honeybees have a high prevalence of DWV, a consequence of infestation of colonies by Varroa mites. The most obvious conclusion from this new work is that honeybee DWV is spreading to wild bumblebees. This probably occurs when the two types of bee forage in the same environment. Because DWV infection of bumblebees reduces their lifespan, the spread of this pathogen could be contributing to the decline in bumblebee numbers.

Both honeybees and bumblebees are important pollinators and need to be maintained. Their loss would have immense financial implications. This research shows that disease control in honeybee populations, for example through the efforts of beekeepers, has important implications for the health of other pollinators as well.

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.

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.

A “Perfect Storm” for the bees

This piece is from the July edition of the Marshwood Vale Magazine.  The Magazine is published in Bridport so the piece has a Dorset focus.

For more about bees see my earlier post.

Hardy’s “Under the Greenwood Tree” contains an amusing but surprising description of honey-taking in 19th century rural Dorset.  Honey-taking in those days could be a risky business so Geoffrey Day and his family start by killing all the bees in the hives using a sulphur candle.  They can then take the honey without being stung.  From the viewpoint of the 21st century, this may seem rather harsh but life was harsh then; wildlife was seen to be at the disposal of humans.   Although beekeepers no longer kill their bees to collect honey I don’t believe our attitude to nature has really changed and we still take for granted that wildlife will always be there irrespective of what we do.   That assumption is now looking increasingly shaky.  Bees, in particular, are in trouble and it may be because of our actions.

Let’s first look at the scale of the problem in the UK.  The number of honeybees in managed populations declined by half between 1985 and 2005 and wild honeybees are virtually extinct.  Two species of bumblebee have become extinct and although some are doing well, several species are found at much lower levels.  The number of solitary bees has also decreased.   It would be foolish to ignore this decline as so many plants depend on bees for pollination.  Bees pollinate up to three quarters of our most vital crops and favourite foods and it has been estimated that without bees it would cost UK farmers £1.8 billion each year to pollinate crops.   Bees are also essential pollinators for our gardens, parks and countryside.  Without bees, not only would food be much more expensive but our countryside would look entirely different.

 

Several factors contribute to the decline in the bee population with habitat loss, climate change, pathogens and insecticides at the top of the list.  Changes in farming practices over the past half century have lead to losses of habitat for wild bees.  Since the 1930’s there has been a 97% loss of hay meadows in favour of silage production for livestock fodder over winter.  Hay meadows contained a rich mixture of grasses and flowers, providing an excellent source of bumblebee forage that does not now exist.  Warming of the climate may bring problems for bees.  New species of bee may be migrating north and these may compete with native species.  Warming could also affect the timing of plant flowering and bee emergence after the winter so that wild bees may emerge before or after ample forage is available.

Managed honey bees are now affected by several pathogens that can cause substantial colony losses.  Many consider the Varroa mite to be the worst offender.  This parasitic mite lives on bees, weakening or killing the colony and also bringing viral infections.   Bees also suffer from Nosema, a fungal pathogen that causes dysentery.  Dealing with these diseases adds to the expense and difficulty of beekeeping and may discourage people from becoming beekeepers. There is an additional concern that these diseases of managed bees may spread to wild bees.

Many people are concerned about the effect of insecticides on bee health.  In particular a group of insecticides called neonicotinoids are coming under scrutiny.  These are very widely used on a range of crops such as rapeseed to kill insect pests by poisoning their nervous system.  Unlike other insecticides, the neonicotinoids are used systemically as well as being used as seed dressings.  Either way, the insecticide is present throughout the plant which is then poisonous to the insect.    There has been concern that the poison might be picked up by bees as they collect pollen or nectar and this could contribute to the decline in wild and managed bee numbers.  The makers of the insecticides claim that the products are not harmful to bees if used correctly although not everyone agrees with that conclusion.  In France, Germany and Italy these insecticides have been banned as seed dressings because of effects on bees.  

The issue of neonicotinoid insecticides and bees has been rumbling along for some years but the controversy was reignited recently by new studies performed under field conditions.  Previous studies on the effects of neonicotinoids were done under artificial laboratory conditions, but the new work showed that these insecticides can very adversely affect bees under field conditions.  The findings were featured in the mainstream media and occasioned a flurry of letters to the Guardian including one from Bill Summers of Sturminster Newton.  Bill has been a beekeeper for 40 years and I spoke to him about the problems facing bees.  In his view, bees are suffering so many threats it is like a “Perfect Storm”.  For the managed bees, his solution is to think carefully about their health and to try to maximise it.  He has even developed a new hive, the ZEST hive, designed to make life easier for the bees.

The efforts of individual beekeepers are crucial for protecting managed bees but we also need government to take account of the problems facing both wild and managed bees when framing policy.  Friends of the Earth have recently begun a campaign to protect bees – “The Bee Cause” which includes simple actions like growing wild flowers to encourage bees.  They have also released a report entitled “The decline of England’s bees”.  The report summarises the problems and makes clear recommendations about policy.

I do hope government listen.  Bees need protection for the future.  We need to recognise that nature is not disposable or to be taken for granted.  Our future depends on learning to live side by side with wild life.

Climate change rhetoric versus climate change action

Leo blog : The Heartland Institute conference billboard in Chicago

Last week a billboard appeared over an Expressway in Illinois showing a picture of Ted Kaczynski, the Unabomber who was convicted in 1996 of a 17 year mail bombing campaign that killed three people and injured many more.  The caption read “I still believe in global warming.  Do you?”  The next day it had been removed.  The billboard was the work of the US climate-sceptic think-tank, the Heartland Institute.  There has been general condemnation of the billboard campaign and although Heartland may have received some publicity from the event, it seems likely that such a shoddy idea will have discredited the organisation in many people’s minds.   It also suggests a level of desperation on the part of the climate-sceptics.

The rhetoric has been heating up on the pro-climate change side as well.  Jim Hansen, who some describe as “the grandfather of climate change”, recently delivered the Edinburgh Medal Lecture at the Edinburgh International Science Festival.   According to Hansen, by not dealing effectively with the known issues surrounding climate change we are storing up expensive and destructive consequences for society in the future and this is an “injustice of one generation to others”.   He went on to argue that averting the worst consequences of human-induced climate change is a great moral issue on a par with slavery. 

These are strong words from both sides of the argument but perhaps this is no bad thing as it exposes the issues more clearly.  So, how do we find our way through this minefield of argument and counter-argument on climate change?   In trying to understand the background to the topic, I tend to be guided by the scientists who have been in the field for a long time and know the subject well.  Hansen is obviously one of those scientists and he and others have a paper coming out in Proceedings of the National Academy of Sciences USA where they lay out the issues and suggest solutions.  The paper is entitled “Scientific case for avoiding climate change to protect young people and nature” and can be read here.  There is a good discussion of how carbon dioxide emissions from burning of fossil fuels drive climate change and how far we need to cut emissions to stabilise the climate.  The take-home message is simple;  we need to cut carbon dioxide emissions to avoid damaging climate change in the future and the best way to do this is via a carbon tax coupled with extensive reforestation plans. 

There is also a very strong moral overtone to the paper and I want to quote a section relating to lack of action on climate change: “It is a matter of morality – a matter of intergenerational justice.  As with the earlier great moral issue of slavery, an injustice done by one race of humans to another, so the injustice of one generation to all those to come must stir the public’s conscience to the point of action”.

Perhaps you might feel that Hansen is too close to one side of the argument?  Where do you then look for guidance?  One possibility is the Royal Society, the premier scientific body in the UK, who should know what they are talking about.  In 2010 the Royal Society produced a report: “Climate change: a summary of the science”.  The report concluded that there was indeed warming of the planet and that human activity (burning of fossil fuels and changes in land use) was the major cause of the warming over the past 50 years.  Continuing increases in atmospheric carbon dioxide caused by continuing use of fossil fuels would lead to further warming of the planet.  The report is very cautious in its conclusions but it agrees with Hansen’s ideas.  If you want a more detailed discussion of the levels of carbon dioxide desirable for climate stability and the need to reduce emissions, have a look at 350.org and Skeptical Science.

It doesn’t feel to me like there is much argument.  Climate change driven by carbon dioxide emissions from burning of fossil fuels is happening and needs to be stopped for the future of the planet.  We know this now and yet we are not doing enough to prevent climate change.  It doesn’t really matter whether you dress it up as a moral issue or not but if we don’t get on and do something soon, history and our grandchildren will judge us very badly.

The Higgs Boson and faster-than-light neutrinos – what should we believe and can statistics help us?

I’ve been pondering this topic ever since I read Philip Ball’s column in the Guardian on Christmas Eve.  The recent announcement of tentative evidence for the Higgs Boson and the report of neutrinos travelling faster than the speed of light have created both interest and confusion.   In his article, Philip Ball proposed some guidelines on how we should respond to these new “discoveries”.   In his view, statistical measures associated with the experiments should be ignored but rather we should be lead by the prevailing beliefs of scientists in the field.  Taking this approach, we could conclude that the Higgs boson might have been found but that neutrinos might not travel faster than light.

I had always thought that scientists should follow the statistics and that following opinion might run the risk of being tainted by bias so I wanted to write something about this apparent paradox.   I am also not really sure why we need to second guess the outcome of these experiments.  It might be better to wait until more data are available and, in the case of the neutrinos, to wait until the experiments have been repeated by other groups.  But scientists are intrinsically gossipy and will always want to speculate on the science done by others so here we go.

If you delve a little, you find that Philip Ball’s piece was triggered by an article by Italian particle Physicist Giulio D’Agostini.  Now this is a difficult read but it makes some good points.  D’Agostini is concerned about the misuse of statistics by journalists, by lay people and by scientists.    It’s easier to see his argument with an example.  He uses data from a study at Fermilab in the US that were interpreted by some as evidence of a “new physics”.  Scientists at Fermilab had seen an unexpected “bump” in their data and wanted to evaluate whether this was a real difference (implying a “new physics”) or just part of the variation seen in any experiment (no “new physics”).  Here they used a p-value which is a statistical measure of the probability that the results they had observed would be seen even if there were no “new physics”.  

The Fermilab scientists came up with a p-value of 0.00076 for the experiment and this tells us that with no “new physics” the probability of seeing the “bump” would be 0.076% or about 0.1%.  Putting this in a different way, the results seen by the Fermilab scientists could have occurred with standard physics although the probability is quite low.   What worries D’Agostini is that this probability value is then misused.  The misuse is to turn the p-value into a predictor of the hypothesis, in this case “new physics”, and he quotes several media reports that made this error. These reports suggested that because the p-value was very low there was a very high chance that the hypothesis was correct.  As D’Agostini points out, the p-value tells us about the experimental data (i.e. what is the probability of observing the data in the absence of new ideas) but not about what the experiment means i.e. the hypothesis.   

If the statistics can’t help then how do we understand this experiment?  Here D’Agostini suggests we look at what is already known and ask what other scientists in the field believe.  Do they believe the hypothesis that a “new physics” is required to explain the results or do they not?  Here we have to look at the way science works.   Scientists perform experiments to test hypotheses and gradually, as the data emerge, networks of beliefs about science arise.  These networks of beliefs can be called theories.  These theories will be believed by many scientists in the community although there may be dissenters.  If a prevailing theory, based on extensive prior information, is challenged by new data indicating an alternative idea then we will require substantial further experimental work to make us change our beliefs.  As D’Agostini points out, this is why many people did not believe the Fermilab results.  The faster-than-light neutrinos also fit this category, being a completely new observation that challenges existing ideas.  If new data can be interpreted within existing theories then they are more likely to be believed.  This seems to be the case for the data obtained on the Higgs Boson at the Large Hadron Collider. 

This scheme, proposed by D’Agostini and endorsed by Ball does not, however, completely fit the way progress is made in other branches of science.  In the life sciences, for example, p-values are a mandatory aspect of reporting the results of experiments and they are used extensively to assess outcomes of experiments.  In examining the possible effect of a perturbation on a system, typically the experiment is set up with two groups, control and treated.  The data are analysed and mean values calculated for the two groups.  The two means may differ and the p-value is then the probability that the mean for the treated group (different from the control group mean) will be seen even if there is no real effect of the treatment.  A low p-value implies a low probability and, as we have seen above, this should not be taken to infer the magnitude of the probability that the treatment has had an effect.  Nevertheless, we need to be able to make progress and typically life scientists take a p-value of 0.05 (5%) as a cut off.  p-values greater than 0.05 are taken as evidence that the treatment had no effect and p-values less than 0.05 are taken as evidence that the treatment had an effect.  This is a bit different from what D’Agostini recommends but it seems to have allowed advances in the life sciences and the generation of theories of how systems function.

You may have now spotted another paradox.  The p value reported for the Fermilab experiments was 0.00076 and this is much smaller than the 0.05 figure typically used in life sciences as an indicator that data are not just a result of random fluctuation. So why were the particle physicists not more accepting of the result?  Apparently particle physicists use more stringent cut offs in their work with p-values of 4×10-7 being required for a “discovery”.   In the end, however, these figures don’t matter greatly as it is the relation between the new findings and prior knowledge that matters.  When a new finding is made, even if the experiment is supported by a strong p-value, if it goes against prior data then most scientists in the field will shrug their shoulders and wait for replication before getting too excited.

Let’s conclude by considering a potential problem in the scientific belief system.  Science proceeds by experiments that test hypotheses and gradually networks of beliefs (theories) arise.  As more data are found that are consistent with the theory, belief in the theory strengthens.  If data are found that disagree, then the theory should, in principle, be weakened.  Sometimes this weakening of belief does not work as it should because of the way people treat theories.   Within the life sciences there are large research groups and smaller research groups often working in the same field.  The larger groups often produce large numbers of papers and attain a preeminent status in the field.  Sometimes theories produced by these groups assume dominance and are awkward to dislodge.  It can even become difficult to publish data that disagree with the prevailing theory and there may be a reluctance to interpret data in terms of other frameworks.  Sometimes data that disagree with the dominant theory don’t get published at all.

Strong theories can also have insidious effects on the way experiments are performed and interpreted.  Sometimes when analysing data there can be a tendency for a researcher to reject data points that “don’t fit” and it is essential to avoid such bias.  It is for this reason that, where drugs are tested on humans, the randomised controlled trial is the only acceptable method.  This includes randomisation of subjects between, for example, control (placebo) and treatment groups.  Ideally, there should also be “blinding” where neither subject nor observer knows which group a subject is in and there should be enough subjects enrolled on the trial to eliminate chance effects.  This design provides a way to reduce bias to a minimum so that a fair appraisal of the effects of a drug can be obtained. 

The success of the randomised controlled trial system also depends on full disclosure of data.  So, for example if a pharmaceutical company performs ten trials on the effects of a new drug in different parts of the country, all of those trial data should be made public.  An editorial and associated papers in the British Medical Journal this week show that full disclosure of trial data is not occurring.  The results of many trials are not disclosed leading to deficits in knowledge.  This is a form of bias and in some cases leads to misleading conclusions (positive and negative) about the effects of a drug.