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Tuesday, June 28, 2011

Complex interactions among epilepsy genes

A debate has been raging over the last few years over the nature of the genetic architecture of so-called “complex” disorders. These are disorders - such as schizophrenia, epilepsy, type II diabetes and many others - which are clearly heritable across the population, but which do not show simple patterns of inheritance. A new study looking at the profile of mutations in hundreds of genes in patients with epilepsy dramatically illustrates this complexity. The possible implications are far-reaching, especially for our ability to predict risk based on an individual’s genetic profile, but do these findings apply to all complex disorders?

Complex disorders are so named because, while it is clear that they are highly heritable (risk to an individual increases the more closely related they are to someone who has the disorder), their mode of inheritance is far more difficult to discern. Unlike classical Mendelian disorders (such as cystic fibrosis or Huntington’s disease), these disorders do not show simple patterns of segregation within families that would peg them as recessive or dominant, nor can they be linked to mutations in a single gene. This has led people to propose two very different explanations for how they are inherited.

One theory is that such disorders arise due to unfortunate combinations of large numbers of genetic variants that are common in the population. Individually, such variants would have little effect on the phenotype, but collectively, if they surpass some threshold of burden, they could tip the balance into a pathological state. This has been called the common disease/common variant (CD/CV) model.

The alternative model is that these “disorders” are not really single disorders at all – rather they are umbrella terms for collections of a large number of distinct genetic disorders, which happen to result in a similar set of symptoms. Within any individual or family, the disorder may indeed be caused by a particular mutation. Because many of the disorders in question are very severe, with high mortality and reduced numbers of offspring, these mutations will be rapidly selected against in the population. They will therefore remain very rare and many cases of the disorder may arise from new, or de novo, mutations. This has therefore been called the multiple rare variants (MRV) model.

Lately, a number of mixed models have been proposed by various researchers, including myself. Even classical Mendelian disorders rarely show strictly Mendelian inheritance – instead the effects of the major mutations are invariably affected by modifiers in the genetic background. (These are variants with little effect by themselves but which may have a strong effect in combination with some other mutation). If this sounds like a return to the CD/CV model, there are a couple important distinctions to keep in mind. One is the nature of the mutations involved – the mixed model would still invoke some rare mutation that has a large effect on protein function. It may not always cause the disorder by itself (i.e., not every one who carries it will be affected), but could still be called causative in the sense that if the affected individual did not carry it one would expect they would not suffer from the disorder. The other is the number of mutations or variants involved – under the CD/CV model this could number in the thousands (a polygenic architecture), while under the mixed model one could expect a handful to be meaningfully involved (an oligogenic architecture – see diagram from review in Current Opinion in Neurobiology).

The new study, from the lab of Jeff Noebels, aimed to test these models in the context of epilepsy. Epilepsy is caused by an imbalance in excitation and inhibition within brain circuits. This can arise due to a large number of different factors, including alterations in the structural organisation of the brain, which may be visible on magnetic resonance imaging. Many neurodevelopmental disorders are therefore associated with epilepsy as a symptom (usually one of many). But it can also arise due to more subtle changes, not in the gross structure of the brain or the physical wiring of different circuits, but in the way the electrical activity of individual neurons is controlled.

The electrical properties of any neuron – how excitable it is, how long it remains active, whether it fires a burst of action potentials or single ones, what frequency it fires at and many other important parameters – are determined in large part by the particular ion channel proteins it expresses. These proteins form a pore crossing the membrane of the cell, through which electrically charged ions can pass. Different channels are selective for sodium, potassium or calcium ions and can be activated by different types of stimuli – binding a particular neurotransmitter or a change in the cell’s voltage for example. Many channels are formed from multiple subunits, each of which may be encoded by a different gene. There are hundreds of these genes in several large families, so the resultant complexity is enormous.

Many familial cases of epilepsy have been found to be caused by mutations in ion channel genes. However, most epilepsy patients outside these families do not carry these particular mutations. Therefore, despite these findings and despite the demonstrated high heritability, the particular genetic cause of the vast majority of cases of epilepsy has remained unknown. Large genome-wide association studies have looked for common variants that are associated with risk of epilepsy but have turned up nothing of note. The interpretation has been that common variants do not play a major role in the etiology of idiopathic epilepsy (epilepsy without a known cause).

The rare variants model suggests that many of these cases are caused by single mutations in any of the very large number of ion channel genes. A straightforward experiment to test that would be to sequence all these candidate genes in a large number of epilepsy patients. The hope is that it would be possible to shake out the “low hanging fruit” – obviously pathogenic mutations in some proportion of cases. The difficulty lies in recognising such a mutation as pathogenic when one finds it. This generally relies on some statistical evidence – any individual mutation, or such mutations in general, should be more frequent in epilepsy patients than in unaffected controls. The experiment must therefore involve as large a sample as possible and a control comparison group as well as patients.

Klassen and colleagues sequenced 237 ion channel genes in 152 patients with idiopathic epilepsy and 139 healthy controls. What they found was surprising in several ways. They did find lots of mutations in these genes, but they found them at almost equal frequency in controls as in patients. Even the mutations predicted to have the most severe effects on protein function were not significantly enriched in patients. Indeed, mutations in genes already known to be linked to epilepsy were found in patients and controls alike (though 96% of patients had such a mutation, so did 67% of controls). Either these specific mutations are not pathogenic or their effects can be strongly modified by the genetic background.

More interesting results emerged from looking at the occurrence of multiple mutations in these genes in individuals. 78% of patients vs 30% of controls had two or more mutations in known familial epilepsy genes. A similar trend was observed when looking at specific ion channel gene families, such as GABA receptors or sodium channels.

These data would seem to fit with the idea that an increasing mutational load pushes the system over a threshold into a pathological state. The reality seems more complicated, however, and far more nuanced. Though the average load was lower, many controls had a very high load and yet were quite healthy. It seems that the specific pattern of mutations is far more important than the overall number. This fits very well with the known biology of ion channels and previous work on genetic interactions between mutations in these genes.

Though one might expect a simple relationship between number of mutations and severity of phenotype, that is unlikely to be the case for these genes. It is well known that the effects of a mutation in one ion channel gene can be suppressed by mutation in another gene – restoring the electrical balance in the cell, at least to a degree sufficient for performance under normal conditions. The system is so complex, with so many individual components, that these interactions are extremely difficult to predict. This is complicated further by the fact that there are active processes within the system that act to normalise its function. It has been very well documented, especially by Eve Marder and colleagues, that changes to one ion channel in a neuron can be compensated for by homeostatic mechanisms within the cell that aim to readjust the electrical set-points for optimal physiological function. In fact, these mechanisms do not just happen within one cell, but across the circuit.

The upshot of the study is that, though some of the mutations they discovered are indeed likely to be the pathogenic culprits, it is very difficult to discern which ones they are. It is very clear that there is at least an oligogenic architecture for so-called “channelopathies” – the phenotype is determined by several mutations in each individual. (Note that this is not evidence for a highly polygenic architecture involving hundreds or thousands of genetic variants with tiny individual effects). The important insight is that it is not the overall number or mutational load that matters but the pattern of specific mutations in any individual that is crucial. Unfortunately, given how complicated the system is, this means it is currently not possible to predict an individual’s risk, even with this wealth of data. This will likely require a lot more biological information on the interactions between these mutations from experimental approaches and computational modelling.

What are the implications for other complex disorders? Should we expect a similarly complicated picture for diseases like schizophrenia or autism? Perhaps, though I would argue against over-extrapolating these findings. For the reasons described above, mutations in ion channel genes will show especially complex genetic interactions – it is, for example, even possible for two mutations that are individually pathogenic to suppress each other’s effects in combination. This is far less likely to occur for classes of mutations affecting processes such as neurodevelopment, many of which have been implicated in psychiatric disorders. Though by no means unheard of, it is far less common for the effects of one neurodevelopmental mutation to be suppressed by another – it generally just makes things worse. So, while modifying effects of genetic background will no doubt be important for such mutations, there is some hope that the interactions will be more straightforward to elucidate (mostly enhancing, far fewer suppressing). Others may see it differently of course (and I would be pleased to hear from you if you do); similar sequencing efforts currently underway for these disorders may soon tell whether that prediction is correct.


Klassen T, Davis C, Goldman A, Burgess D, Chen T, Wheeler D, McPherson J, Bourquin T, Lewis L, Villasana D, Morgan M, Muzny D, Gibbs R, & Noebels J (2011). Exome sequencing of ion channel genes reveals complex profiles confounding personal risk assessment in epilepsy. Cell, 145 (7), 1036-48 PMID: 21703448

Kasperaviciute, D., Catarino, C., Heinzen, E., Depondt, C., Cavalleri, G., Caboclo, L., Tate, S., Jamnadas-Khoda, J., Chinthapalli, K., Clayton, L., Shianna, K., Radtke, R., Mikati, M., Gallentine, W., Husain, A., Alhusaini, S., Leppert, D., Middleton, L., Gibson, R., Johnson, M., Matthews, P., Hosford, D., Heuser, K., Amos, L., Ortega, M., Zumsteg, D., Wieser, H., Steinhoff, B., Kramer, G., Hansen, J., Dorn, T., Kantanen, A., Gjerstad, L., Peuralinna, T., Hernandez, D., Eriksson, K., Kalviainen, R., Doherty, C., Wood, N., Pandolfo, M., Duncan, J., Sander, J., Delanty, N., Goldstein, D., & Sisodiya, S. (2010). Common genetic variation and susceptibility to partial epilepsies: a genome-wide association study Brain, 133 (7), 2136-2147 DOI: 10.1093/brain/awq130

Mitchell KJ (2011). The genetics of neurodevelopmental disease. Current opinion in neurobiology, 21 (1), 197-203 PMID: 20832285

Tuesday, June 21, 2011

Synaesthesia and savantism

“We only use 10% of our brain”. I don’t know where that idea originated but it certainly took off as a popular meme – taxi drivers seem particularly taken with it. It’s rubbish of course – you use more than that just to see. But it captures an idea that we humans have untapped intellectual potential – that in each of us individually, or at least in humans in general lies the potential for genius.

Part of what has fed into that idea is the existence of so-called “savants” – people who have some isolated area of special intellectual ability far beyond most other individuals. Common examples of savant abilities include prodigious mental calculations, calendar calculations and remarkable feats of memory. These can arise due to brain injuries, or be apparently congenital. In congenital cases, savant abilities are often encountered against a background of the general intellectual, social or communicative symptoms of autism. (The portrayal by Dustin Hoffman in Rain Man is a good example, based on the late, well known savant Kim Peek).

A new hypothesis proposes that savantism arises due to a combination of autism and another condition, synaesthesia. Synaesthesia is commonly thought of as a cross-sensory phenomenon, where, for example, different sounds will induce the experience of particular colours, or tastes will induce the tactile experience of a shape. But in most cases the stimuli that induce synaesthesia are not sensory, but conceptual categories of learned objects, such as letters, numbers, days of the week, months of the year. The most common types involve coloured letters or numbers and what are called mental “number forms”.

These go beyond the typical mental number line that most of us can visualise from early textbooks. They are detailed, stable and idiosyncratic forms in space around the person, where each number occupies a specific position. They may follow complicated trajectories through space, even wrapping around the individual’s body in some cases. These forms can be related to different reference points (body, head or gaze-oriented) and can sometimes be mentally manipulated by synaesthetes to examine them more closely at specific positions.

The suggestion in relation to savantism is that such forms enable arithmetical calculations to be carried out in some kind of spatial, intuitive way that is distinct from the normal operations of formal arithmetic – but only when the brain is wired in such a way to take advantage of these special reprepsentations of numbers, as apparently can arise due to autism.

It has been proposed that the intense and narrowly focused interests typical of autism can lead to prolonged practice of these skills, which thus emerge and improve over time. While certainly likely to be involved in the development of these skills, on its own this explanation seems insufficient. It seems more likely that these special abilities arise from more fundamental differences in the way the brains of autistic people process information, with a greater degree of processing of local detail, paralleled by greater local connectivity in neural circuits and reductions in long-range integration.

Local processing may normally be actively inhibited. This idea has been referred to as the tyranny of the frontal lobes (especially of the left hemisphere), which impart top-down expectations with such authority that they override lower areas, conscripting them into service for the greater good. The potential of the local elements to process detailed information is thus superseded in order to achieve optimal global performance. The idea that local processing is actively suppressed is supported by the fact that savant abilities can sometimes emerge after frontal lobe injuries or in cases of frontotemporal dementia. Increased skills in numerical estimation can also, apparently, be induced in healthy people by using transcranial magnetic stimulation to temporarily inactivate part of the left hemisphere.

This kind of focus on local details, combined with an exceptional memory, may explain many types of savant skills, including musical and artistic ones. As many as 10% of autistics show some savant ability. These “islands of genius” (including things like perfect pitch, for example) are typically remarkable only on the background of general impairment – they would be less remarkable in the general population. Really prodigious savants are much more rare – these are people who can do things outside the range of normal abilities, such as phenomenal mathematical calculations. In these cases, the increased local processing typical of autism may not be, by itself, sufficient to explain the supranormal ability.

The idea is that such prodigious calculations may also rely on the concrete visual representations of numbers found in some types of synaesthesia. This theory was originally proposed by Simon Baron-Cohen and colleagues and arose from case studies of individual savants, including Daniel Tammett, an extraordinary man who has both Asperger’s syndrome and synaesthesia.

I had the pleasure of speaking with Daniel recently about his particular talents on the FutureProof radio programme for Dublin’s Newstalk Radio. (The podcast, from Nov 27th, 2010, can be accessed, with some perseverance, here). Daniel is unique in many ways. He has the prodigious mental talents of many savants, for arithmetic calculations and memory, but also has the insight and communicative skills to describe what is going on in his head. It is these descriptions that have fueled the idea that the mental calculations he performs rely on his synaesthetic number forms.

Daniel experiences numbers very differently from most people. He sees numbers in his mind’s eye as occupying specific positions in space. They also have characteristic colours, textures, movement, sounds and, importantly, shapes. Sequences of numbers form “landscapes in his mind”. This is vividly portrayed in the excellent BBC documentary “The Boy With the Incredible Brain” and described by Daniel in his two books, “Born on a Blue Day” and “Embracing the Wide Sky”.

His synaesthetic experiences of numbers are an intrinsic part of his arithmetical abilities. (I say arithmetical, as opposed to mathematical, because his abilities seem to be limited to prodigious mental calculations, as opposed to a talent for advanced calculus or other areas of mathematics). Daniel describes doing these calculations by some kind of mental spatial manipulation of the shapes of numbers and their positions in space. When he is performing these calculations he often seems to be tracing shapes with his fingers. He is, however, hard pressed to define this process exactly – it seems more like his brain does the calculation and he reads off the answer, apparently deducing the value based at least partly on the shape of the resultant number.

Daniel is also the European record holder for rembering the digits of the number pi - to over 20,000 decimal places. This feat also takes advantage of the way that he visualises numbers – he describes moving along a landscape of the digits of pi, which he sees in his mind’s eye and which enables him to recall each digit in sequence. The possible generality of this single case study is bolstered by reports of other savants, who similarly utilise visuospatial forms in their calculations and who report that they simply “see” the correct answer (see review by Murray).

Additional evidence to support the idea comes from studies testing whether the concrete and multimodal representations of numbers or units of time are associated with enhanced cognitive abilities in synaesthetes who are not autistic. Several recent studies suggest this is indeed the case.

Many synaesthetes say that having particular colours or spatial positions for letters and numbers helps them remember names, phone numbers, dates, etc. Ward and colleagues have tested whether these anecdotal reports would translate into better performance on memory tasks and found that they do. Synaesthetes did show better than average memory, but importantly, only for those items which were part of their synaesthetic experience. Their general memory was no better than non-synaesthete controls. Similarly, Simner and colleagues have found that synaesthetes with spatial forms for time units perform better on visuospatial tasks such as mental rotation of 3D objects.

Synaesthesia and autism are believed to occur independently and, as each only occurs in a small percentage of people, the joint occurrence is very rare. Of course, it remains possible that, even though most people with synaesthesia do not have autism and vice versa, their co-occurrence in some cases may reflect a single cause. Further research will be required to determine definitively the possible relationship between these conditions. For now, the research described above, especially the first-person accounts of Daniel Tammett and others, gives a unique insight into the rich variety of human experience, including fundamental differences in perception and cognitive style.


Murray, A. (2010). Can the existence of highly accessible concrete representations explain savant skills? Some insights from synaesthesia Medical Hypotheses, 74 (6), 1006-1012 DOI: 10.1016/j.mehy.2010.01.014

Bor, D., Billington, J., & Baron-Cohen, S. (2008). Savant Memory for Digits in a Case of Synaesthesia and Asperger Syndrome is Related to Hyperactivity in the Lateral Prefrontal Cortex Neurocase, 13 (5), 311-319 DOI: 10.1080/13554790701844945

Simner, J., Mayo, N., & Spiller, M. (2009). A foundation for savantism? Visuo-spatial synaesthetes present with cognitive benefits Cortex, 45 (10), 1246-1260 DOI: 10.1016/j.cortex.2009.07.007

Yaro, C., & Ward, J. (2007). Searching for Shereshevskii: What is superior about the memory of synaesthetes? The Quarterly Journal of Experimental Psychology, 60 (5), 681-695 DOI: 10.1080/17470210600785208

Monday, June 13, 2011

Where do morals come from?

Review of “Braintrust. What Neuroscience Tells Us about Morality”, by Patricia S. Churchland

The question of “where morals come from” has exercised philosophers, theologians and many others for millennia. It has lately, like many other questions previously addressed only through armchair rumination, become addressable empirically, through the combined approaches of modern neuroscience, genetics, psychology, anthropology and many other disciplines. From these approaches a naturalistic framework is emerging to explain the biological origins of moral behaviour. From this perspective, morality is neither objective nor transcendent – it is the pragmatic and culture-dependent expression of a set of neural systems that have evolved to allow our navigation of complex human social systems.



“Braintrust”, by Patricia S. Churchland, surveys the findings from a range of disciplines to illustrate this framework. The main thesis of the book is grounded in the approach of evolutionary psychology but goes far beyond the just-so stories of which that field is often accused by offering not just a plausible biological mechanism to explain the foundations of moral behaviour, but one with strong empirical support.

The thrust of her thesis is as follows:

Moral behaviour arose in humans as an extension of the biological systems involved in recognition and care of mates and offspring. These systems are evolutionarily ancient, encoded in our genome and hard-wired into our brains. In humans, the circuits and processes that encode the urge to care for close relatives can be co-opted and extended to induce an urge to care for others in an extended social group. These systems are coupled with the ability of humans to predict future consequences of our actions and make choices to maximise not just short-term but also long-term gain. Moral decision-making is thus informed by the biology of social attachments but is governed by the principles of decision-making more generally. These entail not so much looking for the right choice but for the optimal choice, based on satisfying a wide range of relevant constraints, and assigning different priorities to them.

This does not imply that morals are innate. It implies that the capacity for moral reasoning and the predisposition to moral behaviour are innate. Just as language has to be learned, so do the codes of moral behaviour, and, also like language, moral codes are culture-specific, but constrained by some general underlying principles. We may, as a species, come pre-wired with certain biological imperatives and systems for incorporating them into decisions in social situations, but we are also pre-wired to learn and incorporate the particular contingencies that pertain to each of us in our individual environments, including social and cultural norms.

This framework raises an important question, however – if morals are not objective or transcendent, then why does it feel like they are? This is after all, the basis for all this debate – we seem to implicitly feel things as being right or wrong, rather than just intellectually being aware that they conform to or violate social norms. The answer is that the systems of moral reasoning and conscience tap into, or more accurately emerge from ancient neural systems grounded in emotion, in particular in attaching emotional value or valence to different stimuli, including the imagined consequences of possible actions.

This is, in a way, the same as asking why does pain feel bad? Couldn’t it work simply by alerting the brain that something harmful is happening to the body, which should therefore be avoided? A rational person could then take an action to avoid the painful stimulus or situation. Well, first, that does not sound like a very robust system – what if the person ignored that information? It would be far more adaptive to encourage or enforce the avoidance of the painful stimulus by encoding it as a strong urge, forcing immediate and automatic attention to a stimulus that should not be ignored and that should be given high priority when considering the next action. Even better would be to use the emotional response to also tag the memory of that situation as something that should be avoided in the future. Natural selection would favour genetic variants that increased this type of response and select against those that decoupled painful stimuli from the emotional valence we normally associate with them (they feel bad!).

In any case, this question is approached from the wrong end, as if humans were designed out of thin air and the system could ever have been purely rational. We evolved from other animals without reason (or with varying degrees of problem-solving faculties). For these animals to survive, neural systems are adapted to encode urges and beliefs in such a way as to optimally control behaviour. Attaching varying levels of emotional valence to different types of stimuli offers a means to prioritise certain factors in making complex decisions (i.e., those factors most likely to affect the survival of the organism or the dissemination of its genes).

For humans, these important factors include our current and future place in the social network and the success of our social group. In the circumstances under which modern humans evolved, and still to a large extent today, our very survival and certainly our prosperity depend crucially on how we interact and on the social structures that have evolved from these interactions. We can’t rely on tooth and claw for survival – we rely on each other. Thus, the reason moral choices are tagged with strong emotional valence is because they evolved from systems designed for optimal control of behaviour. Or, despite this being a somewhat circular argument, the reason they feel right or wrong is because it is adaptive to have them feel right or wrong.

Churchland fleshes out this framework with a detailed look at the biological systems involved in social attachments, decision-making, executive control, mind-reading (discerning the beliefs and intentions of others), empathy, trust and other faculties. There are certain notable omissions here: the rich literature on psychopaths, who may be thought of as innately deficient in moral reasoning, receives surprisingly little attention, especially given the high heritability of this trait. As an illustration that the faculty of moral reasoning relies on in-built brain circuitry, this would seem to merit more discussion. The chapter on Genes, Brains and Behavior rightly emphasises the complexity of the genetic networks involved in establishing brain systems, especially those responsible for such a high-level faculty as moral reasoning. The conclusion that this system cannot be perturbed by single mutations is erroneous, however. Asking what does it take, genetically speaking, to build the system is a different question from what does it take to break it. Some consideration of how moral reasoning emerges over time in children would also have been interesting.

Nevertheless, the book does an excellent job of synthesising diverse findings into a readily understandable and thoroughly convincing naturalistic framework under which moral behaviour can be approached from an empirical standpoint. While the details of many of these areas remain sketchy, and our ignorance still vastly outweighs our knowledge, the overall framework seems quite robust. Indeed, it articulates what is likely a fairly standard view among neuroscientists who work in or who have considered the evidence from this field. However, one can presume that jobbing neuroscientists are not the main intended target audience and that both the details of the work in this field and its broad conclusions are neither widely known nor held.

The idea that right and wrong - or good and evil - exist in some abstract sense, independent from humans who only somehow come to perceive them, is a powerful and stubborn illusion. Indeed, for many inclined to spiritual or religious beliefs, it is one area where science has not until recently encroached on theological ground. While the Creator has been made redundant by the evidence for evolution by natural selection and the immaterial soul similarly superfluous by the evidence that human consciousness emerges from the activity of the physical brain, morality has remained apparently impervious to the scientific approach. Churchland focuses her last chapter on the idea that morals are absolute and delivered by Divinity, demonstrating firstly the contradictions in such an idea and, with the evidence for a biological basis of morality provided in the rest of the book, arguing convincingly that there is no need of that hypothesis.
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