Wednesday, 13 June 2018

Debunking DNA: A new search for the Loch Ness monster

I was recently surprised to read that a New Zealand genomics scientist, Neil Gemmell of Otago University, is about to lead an international team in the search for the Loch Ness monster. Surely, I thought, that myth has long since been put to bed and is only something exploited for the purposes of tourism? I remember some years ago that a fleet of vessels using side-sweeping sonar had covered much of the loch without discovering anything conclusive. When combined with the fact that the most famous photograph is a known fake and the lack of evidence from the plethora of tourist cameras (never mind those of dedicated Nessie watchers) that have convened on the spot, the conclusion seems obvious.

I've put together a few points that don't bode well for the search, even assuming that Nessie is a 'living fossil' (à la coelacanth) rather than a supernatural creature; the usual explanation is a cold water-adapted descendant of a long-necked plesiosaur - last known to have lived in the Cretaceous Period:
  1. Loch Ness was formed by glacial action around 10,000 years ago, so where did Nessie come from? 
  2. Glacial action implies no underwater caves for hiding in
  3. How can a single creature maintain a long-term population (the earliest mentions date back thirteen hundred years)? 
  4. What does such a large creature eat without noticeably reducing the loch's fish population?
  5. Why have no remains ever been found, such as large bones, even on sonar?
All in all, I didn't think much of the expedition's chances and therefore I initially thought that the new research would be a distinct waste of money that could be much better used elsewhere in Scotland. After all, the Shetland seabird population is rapidly decreasing thanks to over-fishing, plastic pollution and loss of plankton due to increasing ocean temperatures. It would make more sense to protect the likes of puffins (who have suffered a 98% decline over the past 20 years), along with guillemots and kittiwakes amongst others.

However, I then read that separate from the headline-grabbing monster hunt, the expedition's underlying purpose concerns environmental DNA sampling, a type of test never before used at Loch Ness. Gemmell's team have proffered a range of scientifically valid reasons for their project:
  1. To survey the loch's ecosystem, from bacteria upwards 
  2. Demonstrate the scientific process to the public (presumably versus all the pseudoscientific nonsense surrounding cryptozoology)
  3. Test for trace DNA from potential but realistic causes of 'monster' sightings, such as large sturgeon or catfish 
  4. Understand local biodiversity with a view to conservation, especially as regards the effect caused by invasive species such as the Pacific pink salmon. 
Should the expedition find any trace of reptile DNA, this would of course prove the presence of something highly unusual in the loch. Gemmell has admitted he doubts they will find traces of any monster-sized creatures, plesiosaur or otherwise, noting that the largest unknown species likely to be found are bacteria. Doesn't it seem strange though that sometimes the best way to engage the public - and gain funding - for real science is to use what at best could be described as pseudoscience?

Imagine if NASA could only get funding for Earth observation missions by including the potential to prove whether our planet was flat or not? (Incidentally, you might think a flat Earth was just the territory of a few nutbars, but a poll conducted in February this year suggests that fully two percent of Americans are convinced the Earth is a disk, not spherical).

Back to reality. Despite the great work of scientists who write popular books and hold lectures on their area of expertise, it seems that the media - particularly Hollywood - are the primary source of science knowledge to the general public. Hollywood's version of de-extinction science, particularly for ancient species such as dinosaurs, seems to be far better known than the relatively unglamorous reality. Dr Beth Shapiro's book How to clone a mammoth for example is an excellent introduction to the subject, but would find it difficult to compete along side the adventures of the Jurassic World/Park films.

The problem is that many if not most people want to believe in a world that is more exciting than their daily routine would suggest, with cryptozoology offering itself as an alternative to hard science thanks to its vast library of sightings over the centuries. Of course it's easy to scoff: one million tourists visit Loch Ness each year but consistently fail to find anything; surely in this case absence of evidence is enough to prove evidence of absence?

The Loch Ness monster is of course merely the tip of the mythological creature iceberg. The Wikipedia entry on cryptids lists over 170 species - can they all be just as suspect? The deep ocean is the best bet today for large creatures new to science. In a 2010 post I mentioned that the still largely unexplored depths could possibly contain unknown megafauna, such as a larger version of the oarfish that could prove to be the fabled sea serpent.

I've long had a fascination with large creatures, both real (dinosaurs, of course) and imaginary. When I was eight years old David Attenborough made a television series called Fabulous Animals and I had the tie-in book. In a similar fashion to the new Loch Ness research project, Attenborough used the programmes to bring natural history and evolutionary biology to a pre-teen audience via the lure of cryptozoology. For example, he discussed komodo dragons and giant squid, comparing extant megafauna to extinct species such as woolly mammoth and to mythical beasts, including the Loch Ness Monster.

A few years later, another television series that I avidly watched covered some of the same ground, namely Arthur C. Clarke's Mysterious World. No less than four episodes covered submarine cryptozoology, including the giant squid, sea serpents and of course Nessie him (or her) self. Unfortunately the quality of such programmes has plummeted since, although as the popularity of the (frankly ridiculous) seven-year running series Finding Bigfoot shows, the public have an inexhaustible appetite for this sort of stuff.

I've read that it is estimated only about ten percent of extinct species have been discovered in the fossil record, so there are no doubt some potential surprises out there (Home floresiensis, anyone?) However, the evidence - or lack thereof - seems firmly stacked against the Loch Ness monster. What is unlikely though is that the latest expedition will dampen the spirits of the cryptid believers. A recent wolf-like corpse found in Montana, USA, may turn out to be coyote-wolf hybrid, but this hasn't stopped the Bigfoot and werewolf fans from spreading X-Files style theories across the internet. I suppose it’s mostly harmless fun, and if Professor Gemmell’s team can spread some real science along the way, who am I to argue with that? Long live Nessie!

Wednesday, 30 May 2018

Photons vs print: the pitfalls of online science research for non-scientists

It's common knowledge that school teachers and university lecturers are tired of discovering that their students' research is often limited to one search phrase on Google or Bing. Ignoring the minimal amount of rewriting that often accompanies this shoddy behaviour - leading to some very same-y coursework - one of the most important questions to arise is how easy is it to confirm the veracity of online material compared to conventionally-published sources? This is especially important when it comes to science research, particularly when the subject matter involves new hypotheses and cutting-edge ideas.

One of the many problems with the public's attitude to science is that it is nearly always thought of as an expanding body of knowledge rather than as a toolkit to explore reality. Popular science books such as Bill Bryson's 2003 best-seller A Short History of Nearly Everything follow this convention, disseminating facts whilst failing to illuminate the methodologies behind them. If non-scientists don't understand how science works is it little wonder that the plethora of online sources - of immensely variable quality - can cause confusion?

The use of models and the concurrent application of two seemingly conflicting theories (such as Newton's Universal Gravitation and Einstein's General Theory of Relativity) can only be understood with a grounding in how the scientific method(s) proceed. By assuming that scientific facts are largely immutable, non-scientists can become unstuck when trying to summarise research outcomes, regardless of the difficulty in understanding the technicalities. Of course this isn't true for every theory: the Second Law of Thermodynamics is unlikely to ever need updating; but as the discovery of dark energy hints, even Einstein's work on gravity might need amending in future. Humility and caution should be the bywords of hypotheses not yet verified as working theories; dogma and unthinking belief have their own place elsewhere!

In a 1997 talk Richard Dawkins stated that the methods of science are 'testability, evidential support, precision, quantifiability, consistency, intersubjectivity, repeatability, universality, and independence of cultural milieu.' The last phrase implies that the methodologies and conclusions for any piece of research should not differ from nation to nation. Of course the real world intrudes into this model and so culture, gender, politics and even religion play their part as to what is funded and how the results are presented (or even which results are reported and which obfuscated).

For those who want to stay ahead of the crowd by disseminating the most recent breakthroughs it seems obvious that web resources are far superior to most printed publications, professional journals excepted - although the latter are rarely suitable for non-specialist consumption. The expenses associated with producing popular science books means that online sources are often the first port of call.

Therein lies the danger: in the rush to skim seemingly inexhaustible yet easy to find resources, non-professional researchers frequently fail to differentiate between articles written by scientists, those by journalists with science training, those by unspecialised writers, largely on general news sites, and those by biased individuals. It's usually quite easy to spot material from cranks, even within the quagmire of the World Wide Web (searching for proof that the Earth is flat will generate tens of millions of results) but online content written by intelligent people with an agenda can be more difficult to discern. Sometimes, the slick design of a website offers reassurance that the content is more authentic than it really is, the visual aspects implying an authority that is not justified.

So in the spirit of science (okay, so it's hardly comprehensive being just a single trial) I recently conducted a simple experiment. Having read an interesting hypothesis in a popular science book I borrowed from the library last year, I decided to see what Google's first few pages had to say on the same subject, namely that the Y chromosome has been shrinking over the past few hundred million years to such an extent that its days - or in this case, millennia - are numbered.

I had previously read about the role of artificial oestrogens and other disruptive chemicals in the loss of human male fertility, but the decline in the male chromosome itself was something new to me. I therefore did a little background research first. One of the earliest sources I could find for this contentious idea was a 2002 paper in the journal Nature, in which the Australian geneticist Professor Jennifer Graves described the steady shrinking of the Y chromosome in the primate order. Her extrapolation of the data, combined with the knowledge that several rodent groups have already lost their Y chromosome, suggested that the Home sapiens equivalent has perhaps no more than ten million years left before it disappears.

2003 saw the publication of British geneticist Bryan Sykes' controversial book Adam's Curse: A Future Without Men. His prediction based on the rate of atrophy in the human Y chromosome was that it will only last another 125,000 years. To my mind, this eighty-fold difference in timescales suggests that for these early days in its history, very little of the hypothesis could be confirmed with any degree of certainty.

Back to the experiment itself. The top results for 'Y chromosome disappearing' and similar search phrases lead to articles published between 2009 and 2018. They mostly fall into one of two categories: (1) that the Y chromosome is rapidly degenerating and that males, at least of humans and potentially all other mammal species, are possibly endangered; and (2) that although the Y chromosome has shrunk over the past few hundred million years it has been stable for the past 25 million and so is no longer deteriorating. A third, far less common category, concerns the informal polls taken of chromosomal researchers, who have been fairly evenly divided between the two opinions and thus nicknamed the "leavers" and the "remainers". Considering the wildly differing timescales mentioned above, perhaps this lack of consensus is proof of science in action; there just hasn't been firm enough evidence for either category to claim victory.

What is common to many of the results is that inflammatory terms and hyperbole are prevalent, with little in the way of caution you would hope to find with cutting-edge research. Article titles include 'Last Man on Earth?', 'The End of Men' and 'Sorry, Guys: Your Y Chromosome May Be Doomed ', with paragraph text contain provocative phrases such as 'poorly designed' and 'the demise of men'. This approach is friendly to organic search at the same time as amalgamating socio-political concerns with the science.

You might expect that the results would show a change in trend of time, first preferring one category and then the other, but this doesn't appear to be the case. Rearranged in date order, the search results across the period 2009-2017 include both opinions running concurrently. This year however has seen a change, with the leading 2018 search results so far only offering support to the rapid degeneration hypothesis. The reason for this difference is readily apparent: publication of a Danish study that bolsters support for it. This new report is available online, but is difficult for a non-specialist to digest. Therefore, most researchers such as myself would have to either rely upon second-hand summaries or, if there was enough time, wait for the next popular science book that discusses it in layman's terms.

As it is, I cannot tell from my skimming approach to the subject whether the new research is thorough enough to be completely reliable. For example, it only examined the genes of sixty-two Danish men, so I have no idea if this is a large enough sample to be considered valid beyond doubt. However, all of the 2018 online material I read accepted the report without question, which at least suggests that after a decade and a half of vacillating between two theories, there may now be an answer. Even so, by examining the content in the "remainers" category, I wonder how the new research confirms a long term trend rather than short term blip in chromosomal decline. I can't help thinking that the sort of authoritative synthesis found in the better sort of popular science books would answer these queries, such is my faith in the general superiority of print volumes!

Of course books have been known to emphasise pet theories and denigrate those of opponents, but the risk of similar issues for online content is far greater. Professor Graves' work seems to dominate the "leavers" category, via her various papers subsequent to her 2002 original, but just about every reference to them is contaminated with overly emotive language. I somehow doubt that if her research was only applicable to other types of animals, say reptiles, there would be nearly so many online stories covering it, let alone the colourful phrasing that permeates this topic. The history of the Y chromosome is as extraordinary as the chromosome itself, but treating serious scientific speculation - and some limited experimental evidence - with tabloid reductionism and show business hoopla won't help when it comes to non-specialists researching the subject.

There may be an argument here for the education system to systematically teach such basics as common sense and rigour, in the hopes of giving non-scientists a better chance of detecting baloney. This of course includes the ability to accurately filter online material during research. Personally, I tend to do a lot of cross-checking before committing to something I haven't read about on paper. If even such highly-resourced and respected websites as the BBC Science News site can make howlers (how about claiming that chimpanzees are human ancestors?) why should we take any of these resources on trust? Unfortunately, the seductive ease with which information can be found on the World Wide Web does not in any way correlate with its quality. As I found out with the shrinking Y chromosome hypothesis, there are plenty of traps for the unwary.