The Twelve (Scientific) Days Of Christmas

As Christmas approaches and we get over-saturated in seasonal pop songs and the occasional carol, I thought it would be appropriate to look at a science-themed variation to this venerable lyric. So without further ado, here are the twelve days of Christmas, STEM-style.

12 Phanerozoic periods

Although there is evidence that life on Earth evolved pretty much as soon as the conditions were in any way suitable, microbes had the planet to themselves for well over three billion years. Larger, complex organisms may have gained a kick-start thanks to a period of global glaciation - the controversial Snowball Earth hypothesis. Although we often hear of exoplanets being found in the Goldilocks zone, it may also take an awful lot of luck to produce a life-bearing environment. The twelve geological periods of the Phanerozoic (literally, well-displayed life) cover the past 542 million years or so and include practically every species most of us have ever heard of. Hard to believe that anyone who knows this could ever consider our species to be the purpose of creation!

11 essential elements in humans

We often hear the phrase 'carbon-based life forms', but we humans actually contain over three times the amount of oxygen than we do of carbon. In order of abundance by mass, the eleven vital elements are oxygen, carbon, hydrogen, nitrogen, calcium, phosphorus, potassium, sulfur, sodium, chlorine and magnesium. Iron, which you might think to be present in larger quantities, is just a trace mineral; adults have a mere 3 or 4 grams. By comparison, we have about 25 grams of magnesium. In fact, iron and the other trace elements amount to less than one percent of our total body mass. Somehow, 'oxygen-based bipeds' just doesn't have the same ring to it.

10 fingers and toes

The evolution of life via natural selection and genetic mutation consists of innumerable, one-off events. This is science as history, although comparative studies of fossils, DNA and anatomy are required instead of written texts and archaeology. It used to be thought that ten digits was canonical, tracing back to the earliest terrestrial vertebrates that evolved from lobe-finned fish. Then careful analysis of the earliest stegocephalians of the late Devonian period such as Acanthostega showed that their limbs terminated in six, seven or even eight digits. The evolution of five-digit limbs seems to have occurred only once, in the subsequent Carboniferous period, yet of course we take it - and the use of base ten counting - as the most obvious of things. Just imagine what you could play on a piano if you had sixteen fingers!

9 climate regions

From the poles to the equator, Earth can be broadly divided into the following climate areas: polar and tundra; boreal forest; temperate forest; Mediterranean; desert; dry grassland; tropical grassland; tropical rainforest. Mountains are the odd region out, appearing in areas at any latitude that contains the geophysical conditions suitable for their formation. Natural selection leads to the evolution of species suited to the local variations in daylight hours, weather and temperature but the labels can be deceptive; the Antarctic for example contains a vast polar desert. We are only just beginning to understand the complex feedback systems between each region and its biota at a time when species are becoming extinct almost faster than they can be catalogued. We upset the relative equilibrium at our peril.

8 major planets in our solar system

When I was a child, all astronomy books described nine known planets, along with dozens of moons and numerous asteroids. Today we know of almost four thousand planets in other solar systems, some of a similar size to Earth (and even some of these in the Goldilocks zone). However, since 1996 our solar system has been reduced to eight planets, with Pluto amended to the status of a dwarf planet. Technically, this is because it fails one of the three criteria of major planets, in that it sometimes crosses Neptune’s orbit rather than sweeping it clear of other bodies. However, as there is at least one Kuiper belt object, Eris, almost as large as Pluto, it makes sense to stick to a definition that won’t see the number of planets continually rise with each generation of space telescope. This downgrading appears to have upset a lot of people, so it’s probably a good to mention that science is as much a series of methodologies as it is a body of knowledge, with the latter being open to change when required - it’s certainly not set-in-stone dogma! So as astronomer Neil DeGrasse Tyson and author of the best-selling The Pluto Files: The Rise and Fall of America's Favorite Planet put it: "Just get over it!"

7 colours of the rainbow

This is one of those everyday things that most of us never think about. Frankly, I don't know anyone who has been able to distinguish indigo from violet in a rainbow and yet we owe this colour breakdown not to an artist but to one of the greatest physicists ever, Sir Isaac Newton. As well as fulfilling most of the criteria of the modern day scientist, Newton was also an alchemist, numerologist, eschatologist (one of his predictions is that the world will end in 2060) and all-round occultist. Following the mystical beliefs of the Pythagoreans, Newton linked the colours of the spectrum to the notes in Western music scale, hence indistinguishable indigo making number seven. This is a good example of how even the best of scientists are only human.

6 mass extinction events

Episode two of the remake of Carl Sagan's Cosmos television series featuring Neil DeGrasse Tyson was called 'Some of the Things That Molecules Do'. It explored the five mass extinction events that have taken place over the past 450 million years. Tyson also discusses what has come to be known as the Holocene extinction, the current, sixth period of mass dying. Although the loss of megafauna species around the world has been blamed on the arrival of Homo sapiens over the past 50,000 years, the rapid acceleration of species loss over the last ten millennia is shocking in the extreme. It is estimated that the current extinction rate is anywhere from a thousand to ten thousand times to the background rate, resulting in the loss of up to two hundred plant or animals species every day. Considering that two-thirds of our pharmaceuticals are derived or based on biological sources, we really are shooting ourselves in the foot. And that's without considering the advanced materials that we could develop from nature.

5 fundamental forces

Also known as interactions, in order from strongest to weakest these are: the strong nuclear force; electro-magnetism; the weak nuclear force; and gravity. One of the most surprising finds in late Twentieth Century cosmology was that as the universe expands, it is being pushed apart at an ever-greater speed. The culprit has been named dark energy, but that's where our knowledge ends of this possible fifth force. Although it appears to account for about 68% of the total energy of the known universe, the label 'dark' refers to the complete lack of understanding as to how it is generated. Perhaps the most radical suggestion is that Einstein's General Theory of Relativity is incorrect and that an overhaul of the mechanism behind gravity would remove the need for dark energy at all. One thing is for certain: we still have a lot to learn about the wide-scale fabric of the universe.

4 DNA bases

Despite being one of the best-selling popular science books ever, Bill Bryson's A Short History of Nearly Everything manages to include a few howlers, including listing thiamine (AKA vitamin B1) as one of the four bases, instead of thymine. In addition to an understanding how the bases (adenine, cytosine, guanine and thymine) are connected via the double helix backbone, the 1953 discovery of DNA's structure also uncovered the replication mechanism, in turn leading to the development of the powerful genetic editing tools in use today. Also, the discovery itself shows how creativity can be used in science: Watson and Crick's model-building technique proved to be a faster way of generating results than the more methodical x-ray crystallography of Rosalind Franklin and Maurice Wilkins - although it should be noted that one of Franklin's images gave her rivals a clue as to the correct structure. The discovery also shows that collaboration is often a vital component of scientific research, as opposed to the legend of the lonely genius.

3 branches of science

When most people think of science, they tend to focus on the stereotypical white-coated boffin, beavering away in a laboratory filled with complex equipment. However, there are numerous branches or disciplines, covering the purely theoretical, the application of scientific theory, and everything in between. Broadly speaking, science can be divided into the formal sciences, natural sciences and social sciences, each covering a variety of categories themselves. Formal sciences include mathematics and logic and has aspects of absolutism about it (2+2=4). The natural or 'hard' sciences are what we learn in school science classes and broadly divide into physics, chemistry and biology. These use observation and experiment to develop working theories, but maths is often a fundamental component of the disciplines. Social or 'soft' sciences speak for themselves, with sub-disciplines such as anthropology sometimes crossing over into humanities such as archaeology. So when someone tells you that all science is impossibly difficult, you know they obviously haven't considered just what constitutes science!

2 types of fundamental particles

Named after Enrico Fermi and Satyendra Nath Bose respectively, fermions and bosons are the fundamental building blocks of the universe. The former, for example quarks and electrons, are the particles of mass and obey the Pauli Exclusion Principle, meaning no two fermions can exist in the same place in the same state. The latter are the carriers of force, with photons being the best known example. One problem with these particles and their properties such as angular momentum or spin is that most analogies are only vaguely appropriate. After all, we aren't used to an object that has to rotate 720 degrees in order to get back to its original state! In addition, there are many aspects of underlying reality that are far from being understood. String theory was once mooted as the great hope for unifying all the fermions and bosons, but has yet to achieve absolute success, while the 2012 discovery of the Higgs boson is only one potential advance in the search for a Grand Unifying Theory of creation.

1 planet Earth

There is a decorative plate on my dining room wall that says "Other planets cannot be as beautiful as this one." Despite the various Earth-sized exoplanets that have been found in the Goldilocks zone of their solar system, we have little chance in the near future of finding out if they are inhabited as opposed to just inhabitable. Although the seasonal methane on Mars hints at microbial life there, any human colonisation will be a physically and psychologically demanding ordeal. The idea that we can use Mars as a lifeboat to safeguard our species - never mind our biosphere - is little more than a pipedream. Yet we continue to exploit our home world with little consideration for the detrimental effects we are having on it. As the environmental movement says: there is no Planet B. Apart from the banning of plastic bags in some supermarkets, little else appears to have been done since my 2010 post on reduce, reuse and recycle. So why not make a New Year’s resolution to help future generations? Wouldn’t that be the best present for your children and your planetary home?

New neurons: astrocytes, gene therapy and the public fear of brain modification

Ever since the first cyberpunk novels of the early 1980s - and the massive increase of public awareness in the genre thanks to Hollywood - the idea of artificially-enhanced humans has been a topic of intense discussion. Either via direct augmentation of the brain or the development of a brain-computer interface (BCI), the notion of Homo superior has been associated with a dystopian near-future that owes much to Aldous Huxley's Brave New World. After reading about current research into repairing damaged areas of the brain and spinal cord, I thought it would be good to examine this darkly-tinged area.

Back in 2009 I posted about how science fiction has to some extent been confused with science fact, which coupled with the fairly appalling quality of much mainstream media coverage of science stories, has led to public fear where none is necessary and a lack of concern where there should be heaps. When it comes to anything suggestive of enhancing the mind, many people immediately fall back on pessimistic fictional examples, from Frankenstein to Star Trek's the Borg. This use of anti-scientific material in the consideration of real-world STEM is not an optimal response, to say the least.

Rather than working to augment normal humans, real research projects on the brain are usually funded on the basis that they will generate improved medical techniques for individuals with brain or spinal cord injuries. However, a combination of the fictional tropes mentioned above and the plethora of internet-disseminated conspiracy theories, usually concerning alleged secret military projects, have caused the public to concentrate on entirely the wrong aspects.

The most recent material I have read concerning cutting-edge work on the brain covers three teams' use of astrocytes to repair damaged areas. This is an alternative to converting induced pluripotent stem cells (iPSCs) to nerve cells, which has shown promise for many other types of cell. Astrocytes are amazing things, able to connect with several million synapses. Apparently Einstein's brain had far more of them than usual in the region connected with mathematical thinking. The big question would be whether this accumulation was due to nature or nurture, the latter being the high level of exercise Einstein demanded of this region of his brain.

Astrocyte research for brain and spinal cord repair has been ongoing since the 1990s, in order to discover if they can be reprogrammed as functional replacements for lost neurons without any side effects. To this end, mice have been deliberately brain-damaged and then attempts made to repair that damage via converted astrocytes. The intention is to study if stroke victims could be cured via this method, although there are hopes that eventually it may also be a solution for Parkinson's disease, Alzheimer's and even ALS (motor neurone disease). The conversion from astrocyte to neuron is courtesy of a virus that introduces the relevant DNA, although none of the research has as yet proven that the converted cells are fully functional neurons.

Therefore, it would seem we are some decades away from claiming that genetic manipulation can cure brain-impairing diseases. But geneticists must share some of the blame for giving the public the wrong impression. The hyperbole surrounding the Human Genome Project gave both public and medical workers a false sense of optimism regarding the outcome of the genome mapping. In the late 1990s, a pioneer gene therapist predicted that by 2020 virtually every disease would include gene therapy as part of the treatment. We are only just over a year short of this date, but most research is still in first phase trial - and only concern diseases that don't have a conventional cure. It turned out that the mapping was just the simplest stage of a multi-part programme to understand the complexities of which genes code for which disorders.

Meanwhile, gene expression in the form of epigenetics has inspired a large and extremely lucrative wave of pseudo-scientific quackery that belongs in the same genre as homeopathy, crystal healing and all the other New Age flim-flam that uses real scientific terminology to part the gullible from their cash. The poor standard of science education outside of schools (and in many regions, probably within them too) has led to the belief that changing your lifestyle can fix genetic defects or affect cures of serious brain-based illnesses.

Alas, although gene expression can be affected by environmental influences, we are ultimately at the mercy of what we inherited from our parents. Until the astrocyte research has been verified, or a stem cell solution found, the terrible truth is that the victims of strokes and other brain-based maladies must rely upon established medical treatments.

This isn't to say that we may in some cases be able to reduce or postpone the risk with a better lifestyle; diet and exercise (of both the body and brain) are clearly important, but they won't work miracles. We need to wait for the outcome of the current research into astrocytes and iPSCs to find out if the human brain can be repaired after devastating attacks from within or without. Somehow I doubt that Homo superior is waiting round the corner, ready to take over the world from us unenhanced humans…

Setting low standards: bovine TB, badger culls and political pressure on science

If there's a single type of news story that's almost guaranteed to generate widespread sympathy across the British Isles it is one concerning the mistreatment of animals. Over the past five years, badger culls aimed at preventing the spread of bovine tuberculosis have generated much public debate, with opinions varying from those who think badgers are completely innocent victims to some who want to see the species eradicated anywhere domestic cattle are kept. Since the number of farmed cattle in the British Isles is close to ten million, this presumably means the no-badger zone is rather on the large size!

When debates concerning agriculture start to get overheated it usually reduces to a battleground between farmers and so-called townies, with mudslinging and emotive slogans taking precedence over the facts. In this particular case the badgers have an unusual ally in the form of rock musician and amateur astronomer Brian May, who has received much of the criticism usually reserved for tree huggers, animal rights' campaigners and environmentalist types in general.

As I've mentioned before, a species often receives support based more on its cuteness factor than anything else (I consider the irascible and curmudgeonly Mr Badger in Wind in the Willows as a fairly accurate representation of the true critter) so the farming community has seen fit to complain that ignorant, urban-based activists are unaware of the challenges Mother Nature throws at the agricultural sector.

Such stereotyping and reductionism does nothing to alleviate the issue, which other nations face in similar circumstances. New Zealand, for example, has a rapidly escalating battle over the use of 1080 to poison introduced predators. Even though many environmental organisations such as Forest and Bird proclaim it the most effective method the debate is far from settled, with the anti-1080 movement using emotive pleas in their campaign that at times combines hysteria and aggression in equal measure.

The UK's Department for Environment, Food and Rural Affairs (Defra) has funded an independent scientific review from Oxford University as to the efficacy of the cull, resulting in popular press reports that the evidence does not support it. Indeed, the high ratio of dead badgers in return for a 'modest' reduction in the disease has been given as a key reason to stop the culls. This might appear to be a nod towards animal welfare, until you read that other issues include their cost and complexity and a desire for the Government to gain in the opinion polls. A key scientific argument against the effectiveness of the culls come from rural vets, who support data suggesting even at maximum success, the reduction in new cases of cattle TB would only be 12-16% - in exchange for a culling of over 70% of local badger populations.

So what does this example say about humanity's attitude towards the environment and the use of science to reinforce that attitude? In terms of numbers of individuals, humans and our domesticated species (both livestock and household pets) vastly outnumber the inhabitants of the wilderness. The once diverse ecosystem has been vastly reduced, predominantly in the temperate regions suitable for intensive farming. But in return for this largely irreversible loss we have gained all-year round access to an incredible variety of inexpensive foodstuffs; clearly, our gastronomic gains take precedence over the wider ecosystem.

In the case of wild badgers as disease vectors, it isn't just the livelihood of individual farmers that are at stake. The European Union's threat to impose trade sanctions on the UK, such as a ban on the export of live cattle, must be considered as a potential loss at the national level. Little wonder then that the British Government implemented the cull after what has been termed 'a randomised trial period' or more impressively, 'over fifteen years of intensive research.' Even so, was the result of all this enough to justify the finality of the chosen method - or was the scientific data manipulated in the name of political expediency?

One telling example of how the culling might have been ordered due to political pressure rather than any scientific smarts was the use of evidence from other nations that are successfully controlling bovine TB. Australia and New Zealand have been held up as examples of how control of the disease vectors can vastly reduce or indeed remove the problem altogether. Except of course that those two nations don't have any badgers; it is the possum, a semi-arboreal marsupial, that is responsible for the spread of tuberculosis there. It seems to me that two creatures from such vastly different lineages should never have been seen as workable comparisons; the natural world just doesn't fall into the neat categories we would like it to. As a matter of fact, the UK Government has partly blamed the lack of success on the badgers themselves for failing to follow predicted behaviour. In 2013 the then Environment Secretary Owen Paterson stated that the animals had cheated by 'moving the goal posts'!

The Oxford University research reports that far more cases of bovine TB result from transmission between cattle rather than directly from badgers, explaining that farmers are not following Defra guidelines to minimise the spread. Even Defra itself states that there has been not nearly enough implementation of badger-proof feed storage and fencing, while its chief scientific adviser, Ian Boyd, has been quoted as admitting that badgers may only be responsible for as little as 6% of bovine TB! This incidentally comes from the man who in 2013 wanted complete control over what scientific results were reported to Government ministers, presumably so as to maintain a clear-cut, pro-STEM political lobby. Hmm, methinks I smell something fishy...

What can we conclude from these shenanigans? If scientific research doesn't provide reliable support for a method, shouldn't the mistake be admitted and a new approach implemented? Science is the sole invention of humanity with built-in error correction but when it gets embroiled in politics, unabashed use of political tools such as spin can prove fatal. In this particular case, the fatalities in the short term were the badgers. In the long run, an unbalanced ecosystem would have resulted. And we all know which species likes to think of itself as the pinnacle of creation. There's enough denial of scientific results as it is, without distortion for the sake of political convenience. Let's hope Defra has the courage to own up and try other tactics against the wily badger.

Swapping gasoline with gas: are hydrogen fuel cells the future of land transport?

When I was a child, I recall being impressed by the sophistication of hydrogen fuel cells, a power source used in spacecraft that generated water as a by-product. What I didn't realise at the time was that the basis for fuel cell technology had been invented back in the 1830s. Now that automobile manufacturers are promoting fuel cell vehicles for consumers, is it time for the technology to expand from niche usage to mass market?

Road vehicles of all sorts have had more than their fair share of ups and downs, not least due to the conservatism of that unholy alliance between the internal combustion engine and fossil fuels sectors.  Although there were hydrogen-powered test vehicles in 1970s, it wasn't until 1991 that the development phase was completed. There are currently three car manufacturers with fuel cell models intended for personal customers: the Honda Clarity, Hyundai Nexo and Toyota Mirai. The latter two are intended to enter to take off (not literally) across South Korea and Australia respectively over the new few years, apparently selling at a loss on the assumption of beating rivals Nissan and BMW into the market. Brand loyalty being what it is, and all.

So what do fuel cell vehicles have that makes them a credible alternative to gas guzzlers and electric cars? Their primary benefit in this time-poor age is that they take only minutes to refuel – and with a range considerably greater than that of electric vehicles. Even so, this is hardly likely to be a convincing argument for petrol heads.

To anyone with even a vague knowledge of interwar air travel, hydrogen brings to mind the Hindenburg and R101 disasters. The gas is far from safe in large quantities, hence the rapid end of airship development; even with helium as a substitute, today's airships are smaller, specialist vehicles, their lack of speed making them an unlikely substitute for passenger jets. Although fuel cells themselves provide a safe power source, large quantities of hydrogen needs to be transported to the refuelling stations. A neat solution is to transport it in the form of ammonia (admittedly hardly a pleasant substance itself) and then convert it to hydrogen at the point of use.

What is less easily resolved is the cost of manufacturing the gas and the resulting high price for the customer. Most of the world's hydrogen is produced from natural gas; it can be made from renewable sources, but only at much greater expense. Wind-to-hydrogen methods are being tested, but in general there is a distinct lack of environmental friendliness to the gas production process that counteracts the emission-friendly usage in the vehicles themselves. To date, analysis is inconclusive as to whether en masse replacement of fossil fuel vehicles with fuel cell equivalents would reduce greenhouse gas emissions. Indeed, some reports claim they use three times the amount of electricity per vehicle than the equivalent battery-powered car!

In addition to the price of hydrogen, fuel cells use rare elements such as platinum, contributing to the production costs. But most importantly of all, how will the vehicle manufacturers resolve the chicken-and-egg issue of providing adequate infrastructure when there is only a small customer base? Without enough refuelling stations and repair depots, most regions are unlikely to attract new customers, but how can a corporation afford to put these facilities in place before there is a demand for them? Most private vehicle owners would require an immediate advantage to migrate to the new technology, regardless of any environmental benefit. Unlike the early days of the internal combustion engine, fuel cell vehicles do not offer the paradigm shift that the automobile had over the horse-drawn carriage.

So with continuous improvements in battery technology, is there in fact any need for the fuel cell vehicles? Aren't electric cars the best alternative to the internal combustion engine? If so, wouldn't it make more sense to concentrate on battery development and not waste effort on a far from optimal alternative that might turn out to be a dead end? Perhaps this is a case of corporate bet hedging. After all, the telecommunications industry was taken completely unawares by the personal consumer demand for mobile phones - a device that was aimed squarely at business users - so this may be a Plan B if something happens with the growth of electric vehicles. At least vehicle manufacturers aren't anti-innovation this time, unlike their voracious gobbling up of advanced steam car development in the early 1970s.

If not for private road vehicles, could there be a future for fuel cell technology in public transport? China and some European nations such as Germany have been trialling hydrogen-powered buses and tram cars, whilst Boeing is one of the aircraft manufacturers investigating the use of fuel cells in small aircraft and unmanned aerial vehicles. That isn't to say the future of commercial air travel excludes the turbofan engine; fuel cells will probably only ever be used for auxiliary power units.

I wouldn't want to disparage innovation but can't help thinking that in this instance, the self-regulating capitalist model is failing to cope with the paradigm shifts required to face the challenges of climate change. Would it be better for governments to incentivise the front-runner replacements for environmentally poor technologies, in this particular case favouring electric-powered vehicles? Solutions are needed now and I'm just not sure that there is the time to solve all the issues surrounding hydrogen fuel cells and the necessary infrastructure. Perhaps this technology should be saved for a rainy day sometime in the future, once our current crises are over and dealt with?