Friday mystery object #218 answer

Last Friday I gave you this skull to identify:

mystery218

There was strong consensus on this being a mustelid – which is good, because that’s what it is. There was also good agreement on it being one of the Martens, which is where things become a bit more difficult.

After looking at a lot of different Marten skulls online without much success in finding a way of telling them apart, this diagram  proved quite helpful.

Images compiled by Mariomassone

Skulls in the sequence: M. zibellina, M. martes, M. foina

If you look at the skull in the middle of the top and centre rows, the auditory bullae (the rounded bones under the skull that house the anatomy used in hearing) have quite distinctive shapes in the three species pictured.

In addition, the the little nub of bone (called the mastoid process) that sticks out behind the ear hole (or external auditory meatus as it’s also known) is very differently developed in the three species. Looking at this character and checking back against other Marten skulls online the clues suggested that the mystery object is the skull of a Pine Marten Martes martes (Linnaeus, 1758).

So well done to everyone who commented – particularly Jake who got the ball rolling with a Martes identification from the start!

The Aquatic Ape Hypothesis

You may have noticed some coverage in the press recently about the Aquatic Ape Hypothesis (AAH), sparked by a conference on the topic due to be held in May.

If you’re not familiar with the AAH it basically suggests that human ancestors passed through a semiaquatic stage which provided the selective pressure that has led to the differences seen between humans and other primates. Some people call it the Aquatic Ape Theory, but it lacks the necessary scientific support to be considered a theory so it remains a hypothesis [see comments for discussion of the terminology].

The idea was first suggested by pathologist Max Westenhöfer in 1942 and the first line of evidence in support of the hypothesis was proposed by marine biologist Alister Hardy in 1960. Hardy noted that subcutaneous fat is unusual in terrestrial mammals and is normally associated with marine mammals – raising the very good question ‘why do humans have subcutaneous fat?’ (the answer being because we eat too much and exercise too little – just like some lab monkeys).

The baton was then picked up by writer Elaine Morgan who has championed the AAH since 1972. Here’s Elaine in action on a TED video from 2009:

Elaine Morgan is a great communicator and she’s done a remarkable job of delivering the AAH to a wide audience, but I have concerns that the packaging is more impressive than the contents, from a scientific perspective.

In the video Elaine does a cracking job of setting up the AAH in opposition to the more established Savanna Hypothesis (SavH), which suggests that humans diverged from other primates as a result of exploiting more arid environments. She then suggests that the SavH has been discounted on the basis of palaeoenvironmental data, leaving a paradigm gap that should (she suggests) be filled by the AAH.

But of course, a paradigm gap should only be filled by a robust theory and when it comes to plotting evolutionary trajectories there is not solid theoretical foundation on how to do it, beyond relying on the physical evidence provided by the fossil record.

In this case that would require fossils of human ancestors to be found in primarily aquatic deposits, something which we do not see, which is surprising, since aquatic environments are usually far better for fossil preservation than terrestrial environments. In fact, taphonomy suggests that early hominid fossils would be more common if the individuals were living and dying in water with any frequency.

Map of the fossil sites and spread of the generi Australopithecus and Paranthropus, from 4.3 M BP until 1 M BP. From PARKER (G.). Compact History of the World. London, HarperCollins Publishers, 2008, pp 12 - 13

Without having physical data in the form of fossils linking hominids to water, it becomes difficult to make a connection without falling back on evolutionary ‘just-so stories‘, that try to explain an observation by relying on a plausible narrative.

The trouble with this is that the public and media love a good narrative, but it simply isn’t scientific unless it can be falsified. I think this is the part of the process that Elaine Morgan doesn’t quite grasp – she is convinced by her own narrative and believes in the hypothesis, but for a scientist it is more appropriate to subscribe to none of the available hypotheses if they cannot provide factual evidence in support. This is where I currently stand.

I am certainly not convinced by statements like:

“Docosahexaenoic acid (DHA) is an omega-3 fatty acid that is found in large amounts in seafood,… It boosts brain growth in mammals. That is why a dolphin has a much bigger brain than a zebra, though they have roughly the same body sizes. The dolphin has a diet rich in DHA. The crucial point is that without a high DHA diet from seafood we could not have developed our big brains. We got smart from eating fish and living in water.” [Quote attributed to Dr Michael Crawford]

This statement starts by comparing two utterly different species, with a very different evolutionary history and current mode of life, then offers a single dietary explanation for the difference in brain size. This is patently nonsense.

If a seafood diet is the main driver of large brain size then the relatively very large brains of Chimpanzees and other Apes become a remarkable oddity and the relatively small brains of Blue Whales become bizarre variants. Moreover, what about people that don’t have access to seafood? Are they unable to grow large brains? No. Clearly there is more going on.

Brain size is not directly linked to a single dietary chemical, it is linked to managing interactions in and with a complex environment – keeping track of seasonal and spatial variation in fruiting or schooling of fish, coordinating group efforts and understanding prey behaviour to hunt more effectively, or problem solving to access food sources that are hard to acquire. Where a big brain provides a selective advantage, it will evolve.

I don’t want this post to turn into a refutation of the AAH, since there’s a lot to say and much has been done elsewhere. What I do want this post to do is highlight that a scientific theory needs to be testable, it needs to consider contradictory information and it needs to be aware of confirmation bias.

The AAH relies strongly on observed similarities in condition between humans and aquatic mammals, but it dismisses other similarities out of hand. For instance, Naked Mole-rats are simply dismissed by Morgan as an example of a non-aquatic mammal that has lost body hair, but they provide evidence that hair loss can occur for reasons beyond aquatic adaptations – which is worthy of note.

It is also worth considering the supporting examples in the context of phylogeny and physiology, which doesn’t seem to happen often. For instance, the Cetacea, walruses and Sirenia are examples of naked aquatic mammals cited in the AAH, but both the Sirenia and walruses retain a short coat of hairs, quite different in structure to the fine body hair of humans. Whales and Sirenia have also been adapting to an aquatic habitat for 50 million years and the ‘nakedness’ of modern examples may be more related to the evolution of large body size and the benefits to thermoregulation provided by mass – which is supported by the fact that the largest species in the Pinnipedia (like the Elephant Seal and Walrus) are much less reliant on fur than the smaller species of seal.

Unless our ancestors were massive, it seems unlikely that they would have been losing their hair in order to survive better in the water.

Of course, that’s not to say that our ancestors avoided water – far from it. Marginal environments are rich sources of food and most terrestrial animals that live near water will exploit it in some way or another. I’m sure our ancestors would have done the same, I’m just unsure about how immersive and influential that exploitation was on our evolutionary trajectory.

Japanese Macaques, Nagano, Japan. By Yblieb

So far I am unconvinced by the AAH and the more bad science and overstated arguments I see in support of it, the less convinced I become. Let’s see if any good supporting science with hard facts emerge from the conference in May.

Friday mystery object #192 answer

On Friday I gave you this unidentified specimen from the Horniman’s collections to take a look at. I had already had a go at working out what it is, but it never hurts to get a second opinion.

mystery192

It’s actually a bit of a generic looking overall shape, perhaps reminiscent of a owl or a maybe a pheasant of some sort. However, the nares (nostrils) are very small and round and set in a bill that is sharp, shortish and very solidly constructed, which is something you only really see in a few passerines, some parrots and the falcons. The skull is too big for a passerine and the bill is totally the wrong overall shape for a parrot, which leaves us with a falcon – a fairly small one at that.

From there the shape of the palate and the proportions of the cranium led me to a species identification that I’m pleased to say agreed with that proposed by Tony Irwin and Wouter van Gestel (who eloquently explained the indicative characters that I mentioned above). We all think that this is the cranium of a  Continue reading

Friday mystery object #179 answer

On Friday I gave you this really tricky mystery object to identify:

mystery179

Despite it being one of the hardest so far, Barbara Powell managed to not only work out what piece of morphology this specimen represents, but the species it came from. Remarkable skills Barbara!

These plates of bone fit together to make a ring like this:

mystery179b

You probably have a better chance of identifying the structure when it’s assembled like this and the tubular shape is characteristic of a particular order of birds. This is the sclerotic ring of an  Continue reading

Friday mystery object #173 answer

On Friday I gave you this odd-looking piece of bone to identify:

It’s something I tentatively identified a couple of weeks ago and thought you might be able to add your ideas, to make sure I wasn’t missing something. Jake was quick off the mark in suggesting it was the ear bone of a Whale, which is what I thought when I first saw it. This fitted with the large size and high density of the bone, but on closer inspection it doesn’t quite match any of the Whales.

There were a few other ideas, but none that really matched the specimen, except for a suggestion from henstridgesj that it may come from a member of the Trichechidae, which agreed with my identification of  Continue reading

Friday mystery object #166 answer

On Friday I gave you this great skull from the Grant Museum of Zoology to identify:

A big list of you (Mieke RothJakemcarnall, Anthony wilkes, 23thorns, Cam Weir, henstridgesj, Rhea, leigh and Robin) managed to work out what this specimen was from and there were some really interesting explanations about how you came to your conclusions in response to Steven D. Garber’s comment:

Now, I’d like it even more if people explained why this skull looks the way it does.

This is a really interesting thing to consider, as it underlies the process of recognition and identification. As a biologist I might start by saying that the lacrimal foramina is on the edge of the orbit (as henstridgesj pointed out) which is indicative of a marsupial and that the dentition is indicative of a carnivorous mammal that isn’t a member of the placental Carnivora as it lacks carnassials, plus the dental formula appears to be ‘primitive’ from the photo ?.1.3.4/?.1.2.4 which narrows down the possibilities to just a few marsupial carnivores, and given the scale of the skull there is just one that fits the bill.

However, if I’m honest I’d say that the overall shape and robust structure of this specimen is very similar to specimens I’ve seen before belonging to the  Continue reading

Evolving Ideas and Intelligent Design

Well, it seems that my earlier post on Darwin has ruffled some feathers in the Intelligent Design (ID) camp, so they’ve been trolling the comments section on my personal blog. This post started out as a response, but I decided to expand it to include some of the context surrounding Darwin’s work.

A comment by VMartin

…One wonders why no one noticed “natural selection” before. And there were ingenous minds in the history! One answer might be this – it was never observed because it doesn’t exist. Darwin implanted this speculation there. And “On the origin of species” reads sometimes like comedy. One should try to count how many times Darwin used words like “which seems to me extremely perplexing” etc….

One reason why some scientific theories have been slow to come to light

One reason why some scientific theories may have been slow to come to light

It’s interesting how ‘simple’ natural mechanisms and systems can take longer to be acknowledged than one might have thought. Heliocentrism is another example of something that now seems very obvious, but was historically slow to be recognised (and is still not recognised or not known about by some). It’s easy to blame organised religion for the suppression of such observational truths about the universe, since challenges to traditional belief were seen as heresy and dealt with accordingly, but there’s far more to it than that.

Let’s set the scene – Darwin’s formative years were tumultuous with regard to sociopolitical events. The Napoleonic wars drew to an end with the Battle of Waterloo when Darwin was six years old, the Peterloo Massacre occurred and the Six Acts were drawn up by the Tories to suppress radical reformers when he was ten – reflecting the ongoing social division between the establishment and the public. When Darwin was in his twenties the power of the strongly traditional British establishment finally began to wane, when the Whigs came to government allowing the 1832 Reform Act and the 1833 Slavery Abolition Act to be passed. There was also the devastating Great Famine in Ireland when Darwin was in his thirties and all of this was set against a background of the Industrial Revolution, which was providing the impetus for science to play an increasingly important role in society.

Peterloo Massacre

This meant that Darwin’s work was by no means formulated in intellectual isolation. Theories of evolution had been proposed 2,400 years previously, but they were poorly developed. Natural philosophers like Darwin’s own grandfather Erasmus and Jean-Baptiste Lamarck raised the issue of evolution at around the time of Darwin’s birth, but the mechanisms for evolution were either ignored or flawed. Evolution was an established topic of discussion and publication by the time Charles Darwin came onto the scene, with people like Robert Grant being more radical on the subject than Darwin found palatable in his early manhood. Despite this interest, the mechanism of evolution remained elusive – perhaps unsurprisingly, since the academic community addressing natural sciences was largely composed of members of the clergy and the natural theology of the time was seen as being mechanism enough.

But a literature base that was to inspire non-traditional hypotheses was also developing at the time – Vestiges of the Natural History of Creation in particular offered an alternative view that was seen as too radical by many – clearing a path for subsequent works that challenged orthodox views.  Given this context, it is perhaps unsurprising that Darwin and Alfred Russell Wallace converged on the same premise at the same time. In short, the ideas evolved to fit the intellectual and social environment. The same has been true of other discoveries and inventions where there was a requirement for the right intellectual groundwork to be laid in advance. This groundwork is required before a robust theory can take root – and Natural Selection is a component of the robust theory of Descent with modification.

Intelligent Design

The Intelligent Design agenda

The critiques I have seen of evolutionary theory  have come from people who quite clearly don’t understand it – and such critiques tend to rely on statements of incredulity rather than a strong factual base. No well-supported alternative hypotheses have been constructed or presented and a lack of understanding hardly counts as a robust refutation of a well supported theory.

An accusation by IDers is that ‘Darwinists’ (N.B. I don’t know anyone who would call themselves a Darwinists following the New Synthesis) stick with Natural Selection because they are atheist. I think I see the real agenda emerging here, particularly when you see evolution as a theory being conflated with just one of the mechanisms involved. After all, Natural Selection is not the only mechanism involved in evolutionary adaptation and speciation – there are also other factors like hybridisation, horizontal gene transfergenetic drift, perhaps some epigenetic influences and artefacts of EvoDevo processes. But these factors are still constrained by the simple fact that if they are selected against, they will not be perpetuated.

John A. Davison left this comment on a previous post:

Natural selection is a powerful force in nature. It has but one function which is to prevent change. That is why every chickadee looks like every other chickadee and sounds like every other chickadee – chickadee-dee- dee, chickadee-dee-dee. Sooner or later natural selection has always failed leading to the extinction of nearly all early forms of life. They were replaced by other more prefected forms over the millions of years that creative evolution ws in progress…

Salamander ring species (picture from Thelander, 1994)

Salamander ring species

First and foremost, the suggestion that Natural Selection prevents change is erroneous – change will occur if there is a change in the environment and/or if beneficial mutations arise in a population (tell me that mutations don’t happen – I dare you…). The obvious response to the next statement is that I can think of six different ‘chickadee’ species, with an additional three subspecies (and this is ignoring numerous other very similar members of the Paridae), all are similar, but all are different – so the statement makes no sense as it stands. Getting to the meat of what is being implied about the Creationist interpretation of species, another bird provides a good example to the contrary. The Greenish Warbler shows a distinct pattern of hybridising subspecies across their vast range, until they form reproductively isolated species at the extreme ends of their range, where they happen to overlap yet not hybridise (a classic ring species [pdf of Greenish Warbler paper]). This is a well-known example of how genetic variation can accrue and give rise to new species without any supernatural intercession.

Another comment by VMartin

…But no wonder that Darwin considered “natural selection” for such a complicated force. Even nowadays Dawkins speculates that NS operates on genes, whereas E.O.Wilson has brushed up “group selection” recently (citing of course Darwin as debeatur est .

So may we “uncredulous” ask on which level “natural selection” operates?

As to this question about the level on which Natural Selection operates, I thought the answer was pretty obvious – it operates at every level. Change the focus of Natural Selection from passing on genes to the only alternative outcome – the inability to pass on genes. It doesn’t really matter which level this occurs at or why – be it a reduction in reproductive success when not in a group, or a deleterious single point mutation – if it happens then Natural Selection can be said to have occurred. Being ‘fit’ simply means that an organism has not been selected against.

There’s a lot more to modern evolutionary thought than Darwin’s key early contribution, but Darwin is still respected because he was the first to provide a viable mechanism by which evolution is driven. This mechanism has helped make sense of an awful lot of observations that were previously unaccounted for and, moreover, evolution has been observed and documented on numerous occasions [here's a pdf summary of some good examples].

I fail to see why Intelligent Design has been taken seriously by some people – it relies on huge assumptions about supernatural interference (so it fails to be a science) and I have as yet never seen a single piece of evidence that actually supports ID claims. The only research I have seen mentioned by proponents of ID are old, cherry-picked studies that report a null result from an evolutionary study – this is not the same thing as support for ID, as anyone who can spot the logical fallacies of false dichotomy and Non sequitur (in particular the fallacy of denying a conjunct) will tell you.

Intelligent design as a scientific idea

Intelligent design as a scientific idea

I like to keep an open mind, but as soon as I see logical fallacies being wheeled out I lose interest in getting involved in the discussion. This may be a failing on my part, because I should probably challenge misinformation, but quite frankly I don’t have the time or the patience – much as I hate to stoop to an ad hominem, my feelings on this are best summed up by the paraphrase:

when you argue with the ID lot, the best outcome you can hope for is to win an argument with the ID lot

and my time is far too precious to waste arguing with people who ignore the arguments of others and construct Straw man arguments based on cherry-picked and deliberately misrepresented information. I have no problem with other people believing in a god, but please don’t try to bring any god into science (and heaven-forbid the classroom) – since it is neither necessary nor appropriate.

Friday mystery object #65 answer

On Friday I gave you this bit of geology to identify:

I used this because I had it to hand on Thursday afternoon after doing a behind the scenes tour of the Horniman’s store for some of the attendees of TAM London. I also used it so I would have the chance to tell the story behind this innocuous looking, if pretty, bit of stone.

Before I get started on the story I must congratulate Steven D. Garber, PhD on spotting that one of the main components of this is serpentine (the other being calcite) and I have to hand a big dose of kudos to Dave Godfrey who got the answer spot-on when he suggested that this was a sample of  Continue reading

UK homeopathy awareness week

June 14th – 21st 2010 [and 2012] is the UK homeopathy awareness week, so I thought it might be a good idea to try and raise awareness of homeopathy.

Cinchona

Homeopathy is based on the principle of similia similibus curantu (likes are cured by likes). The hypothesis is that symptoms of illness are caused by a derangement of the ‘vital force‘ assumed to be present in a living organism and substances which elicit the same derangement (i.e. symptoms) will rid the body of the illness. This was originally identified in the context of homeopathy by Hahnemann with reference to cinchona bark (source of quinine) and malaria. The previous proposed mechanism of effectiveness of quinine against malaria was its bitterness, but Hahnemann sensibly identified that other bitter substances did not offer the same protection. Instead, after taking cinchona and experiencing a reaction similar to the reaction he associated with malaria, he hypothesised that it was this similarity in symptoms that made cinchona bark effective.

Modern homeopaths still use a similar method to identify their treatments. When in a healthy state they try a preparation and keep a detailed diary of any effects that they feel the treatment has on them. This is called ‘proving’ although what it is supposed to prove is hard to determine since there are no rigorous controls in place and the results are not statistically tested to see if they are anything other than random. Consider the perceived effects of taking peregrine falcon blood for example:

Short statement on peregrine falcons:

The Peregrine Falcon is widely renowned for its incredible speed. Estimates vary, but commonly cited top velocities are in the range of 290-320 km/h (180-200 mph), achieved only during the characteristic swoop (hunting dive)…the Peregrine Falcon is the fastest creature on earth.

Observation during proving:

‘Drove back from the party (had some wine but not so much) quite fast but well, changing speed as necessary. It seemed faster to the others in the car than to me.’

I heartily recommend reading the entire page about the proving of peregrine falcon blood – it is an education into how homeopaths derive their information about the treatments they prescribe (and it is ludicrous to the point of hilarity). Is this really a rigorous approach to testing healthcare products or is this more about symbolism, appeal to the mystical and delusion?

Evidence based medicine occasionally does use elements of  similia similbus curantu such as with inoculation and vaccination – where a small or denatured dose of a disease causing agent is introduced with the intent of stimulating an autoimmune response that will prevent the full blown disease from becoming established should the person come into contact with a large active dose of the pathogen.

Foxglove

Also, many physiologically active compounds have medicinal uses because they act on particular organs and metabolic pathways via a biochemical route that can have apparent similarities to the illness being treated. For example, digoxin is a cardiac glycoside found in foxgloves that decreases heart rate and increases force of heart contraction – fatal in large doses, but useful for treating atrial fibrillation in small doses – so at a very gross level this could be considered ‘like treating (rather than curing) like’. It is also vaguely plausible that a substance which elicits a physiological response which mimics symptoms of an illness that arise as part of the body’s  immune response (such as raising temperature) may have the effect of fighting an infection (although I have not seen any evidence for this).

Hahnemann’s experience with cinchona happened in 1790 when the medical community of the time was still dominated by the miasma theory and humourism of the Middle Ages. Vitalism was a standard of the medical profession at the time, with good health being dependent on balancing the four vital humours. The idea of a biochemical autoimmune system did not take shape until a century later, but when it did it revolutionised the medical field, bringing about treatments with previously unprecedented success (eradication of smallpox anyone?). Hahnemann had no idea about the mechanism by which the body actually heals itself, he also had no idea that malaria was not caused by a miasma, but by a microscopic parasitic protist of the genus Plasmodium.

Plasmodium falciparum – the protozoan that causes malaria

In short Hahnemann was trying to fit his limited observations into a theoretical framework consistent with the body of assumed knowledge available at the time. The same way that scientists have always worked. However, over time the body of knowledge has changed – vitalism has been rejected as evidence has been amassed which demonstrates that all of the functions historically proposed for vital energy are demonstrably biochemical in nature. Disease is now well recognised as being caused by bacteria, viruses, proteins and biochemical abnormalities rather than by derangement of ‘vital energy’. The idea of a vitalistic treatment for a biochemical problem seems rather at odds with the facts, particularly since there is no evidence to suggest that vital energy even exists. Sticking with malaria, we now know that the antimalarial component of cinchona is quinine, which is no longer effective as an antimalarial due to the resistance evolved by Plasmodium – how such immunity might have evolved in response to vital energy is hard to fathom.

Homeopathy also subscribes to the principle that the smaller the dose, the more effective it is at influencing the vital energy – to the point where homeopathic remedies are diluted until they no longer contain even one molecule of their active ingredient. Indeed it would take a ball of water the size of the solar system to contain one molecule of active ingredient in the more ‘potent’ homeopathic remedies – making them even less tangible than the Emperor’s new clothes. Of course this idea of smaller doses having a bigger effect flies in the face of everything that is demonstrated in evidence based medicine, where dose dependent effects increase with increasing dose size, through a therapeutic window until a plateau is reached or there is an overdose.  The Ten23 campaign was all about this misplaced faith in super-dilution.

If homeopaths were able to demonstrate that vital energy exists then homeopathy might have a theoretical leg to stand on, as would chiropractic and a suite of Ayruvedic medicines, but without any evidence for vital energy they remain theoretically unfounded. Interestingly, mainstream medicine was once based on the concept of vital energy, which has only been discarded due to improvements in experimental methods. Vital energy is one of those strange forces in nature that becomes harder to see the harder you look for it – probably because it only exists as a cultural concept that has no relevance in the physical world. This erosion of evidence for vital energy not only leaves homeopathic theory unfounded, but necessarily rejected.

Headstone for 9 month-old girl who died because her parents chose homeopathy over conventional treatments

Theory aside, if there was strong evidence for efficacy of homeopathic remedies then there would be very good reason to question the laws of physics and our current understanding of biology and medicine. However, there is no persuasive evidence for homeopathy’s efficacy. As such it seems bizarre that people still hold on to this outdated and superseded faith-based system of medicine; but then again there are still Flat EarthersFaith healers and people who drink their own pee, so I suppose it’s no great surprise. There are dangers however – if people choose to use homeopathy in place of medicines that have evidence of efficacy, they run the risk of harm or even death – and I think that’s something everyone should be aware of.

Back from extinction

Imagine if you could bring a species back from extinction - what would you choose and why would you choose it? There are so many factors to take into consideration it all becomes a bit bewildering – do you choose something on the basis of how well it would reintegrate with existing ecosystems, how useful it might be, how much novel information we could learn from it, how plausible it would be to actually carry out the resurrection process, or simply how awesome it would be to see something that hasn’t walked the Earth for millions of years?

I recently asked four palaeontologists what species they would choose to resurrect and their responses were presented at a Café Scientifique balloon debate at the Horniman Museum, as part of the International Year of Biodiversity activities in conjunction with the Royal Society (who are celebrating their 350th anniversary!). The result was a very enjoyable evening for all involved and an insight into some of the considerations that should be taken into account when contemplating resurrecting extinct species.

Continue reading