Lazy linking

Even though the weather is really nice outside, I have been spending a little time reading stuff on the internet, and thought I'd share some of it.

Bjorn Lomborg Bibliography

Bjorn Lomborg, the "Skeptical Environmentalist " will go into high media rotation later this month with a sequel to his Copenhagen Consensus 2004 conference.

Hopefully this post will provide a resource for those curious about accuracy of his work, and the legitimacy of his conclusions.

Personally, I detest Lomborg. Not because of his message, which is simplistic and often quite wrong, but because of his blatant misuse of science, and dishonesty about other peoples' research and his own agenda. Always great to have an easy resource to link to.

Why We Sleep: The Temporal Organization of Recovery by Emmanuel Mignot (PLoS Biology)

Creation, Power and Violence - Blake Stacey writes about the real cases where people have been prosecuted over their beliefs regarding evolution. And it's not as Expelled tried to portrait it.

Antivaccinationist activism versus measles in the U.S.: Are the chickens coming home to roost? - Orac explains why antivaccinationists are dangerous.

The Case Against Intelligent Design - an interview with Kenneth Miller (via Ed)

Feminist speakers 'bridge' cultural boundaries

A panel of prominent feminist scholars spoke on issues of prejudice and struggle during “25 years after ‘This Bridge Called My Back,’” a special event put on by the Wismer Center for Gender and Diversity Studies in the Pigott Auditorium last Thursday.

“This Bridge Called My Back,” a book by Cherríe Moraga and Gloria Anzaldúa, was the centerpiece of the day’s event. First published in 1981, the book is a compilation of essays by feminist women of color who challenged traditional views of feminism and social change. In the book, authors present their unique struggles as women from different cultural backgrounds and upbringings, and make the inclusion of different viewpoints their central issue.

Given recent dust-ups in the feminist blogsphere, it sounds like this book is as relevant as ever.

A few inter-connected livejournal posts about men, feminism, privilege and a lot of other issues:
Don't Be That Guy, Thoughts on Men and Rape, My Tits. Mine., My turn in the can 'o worms..., and A Straight Geek Male's Guide to Interaction with Females. Also connected to these issues is this LA Times op-ed Men who explain things. (initial link via Sara).

Each and every one of these posts contains some good advice to how men should and shouldn't behave around women, but I find it really sad that it's necessary for people to write these things.

Development of the human species' mathematical ability

PLoS biology has an incredible interesting article up on the study of the Evolutionary and Developmental Foundations of Mathematics by Michael J. Beran.

Understanding the evolutionary precursors of human mathematical ability is a highly active area of research in psychology and biology with a rich and interesting history. At one time, numerical abilities, like language, tool use, and culture, were thought to be uniquely human. However, at the turn of the 20th century, scientists showed more interest in the numerical abilities of animals. The earliest research was focused on whether animals could count in any way that approximated the counting skills of humans [1,2], though many early studies lacked the necessary scientific controls to truly prove numerical abilities in animals. In addition, both the public and many in the scientific community too readily accepted cases of “genius” animals, including those that performed amazing mathematical feats. One such animal still lends its name to the phenomenon of inadvertent cuing of animals by humans: Clever Hans. Hans was a horse that seemed to calculate solutions to all types of numerical problems. In reality, the horse was highly attuned to the subtle and inadvertent bodily movements that people would make when Hans had reached the correct answer (by tapping his hoof) and should have stopped responding [3]. One consequence of this embarrassing realization was a backlash for the better part of the 20th century against the idea that animals could grasp numerical concepts. The second, more positive consequence, however, was that future researchers would include appropriate controls to account for such cues.

Beran goes on to explain how the current research shows that animals operate on approximations, rather than concrete numbers, much the same way that humans do when prevented from counting while comparing two sets of items. What's more interesting, in my opinion, is how much our symbolic representation of numbers actually mean for our math ability. Not only on the grand scale, but also on smaller problems.

Human mathematical abilities, of course, are highly dependent on symbolic representations of number. A recent paper by Diester and Nieder published in PLoS Biology shows that brain areas critical to processing symbolic and analogue numerosities in humans also support numerical processing in monkeys [38]. After monkeys learned to associate Arabic numerals with specific numbers of items, the researchers recorded from single neurons in the PFC and IPS when monkeys judged whether two successive analog arrays were the same in number or whether an analog array matched a numeral in a pairing. PFC neurons were selectively responsive to given numerical values, presented in either analog or symbolic formats. In other words, the PFC in monkeys seems to be involved in the association between symbols and numerical concepts, and it builds upon the capacities of the IPS to encode approximate numerical information early in quantity processing. By four years of age, the IPS in human children is already responsive to changes in the numerosity of visual arrays [39], but the parietal cortex shows a more protracted developmental trajectory for the representation of symbolic numbers. Specifically, children who have not yet become proficient with numerals show elevated PFC activity in response to numerals, whereas parietal areas seemingly take over as proficiency with symbols emerges [40,41]. In adult humans, representation of numerical information across many formats (numerals, analog stimuli, number words) relies substantially on parietal areas [42].

So while our brains are hardwired to math, we can only utilize it fully when using symbolic representations.

I've heard about omnipresent but omnidirectional?

PLoS Biology brings us the news about a discovery of an omnidirectional fish. The black ghost knifefish (Apteronotus albifrons) uses a weak electric field to actively monitor its surrounding. This sort of monitoring is different from the ones that we usually see in that it's active, rather than passive (which we humans engage in).

PLoS Biology has been nice enough to write an synopsis about this discovery. That makes it a lot easier for us non-biologists to understand the meaning of the original article (excellent as that might be). The articles own authors' summary isn't too bad though

Most animals, including humans, have sensory and motor capabilities that are biased in the forward direction. The black ghost knifefish, a nocturnal, weakly electric fish from the Amazon, is an interesting exception to this general rule. We demonstrate that these fish have sensing and motor capabilities that are omnidirectional. By combining video analysis of prey capture trajectories with computational modeling of the fish's electrosensory capabilities, we were able to quantify and compare the 3-D volumes for sensation and movement. We found that the volume in which prey are detected is similar in size to the volume needed by the fish to stop. We suggest that this coupling may arise from constraints that the animal faces when using self-generated energy to probe its environment. This is similar to the way in which the angular coverage and range of an automobile's headlights are designed to match certain motion characteristics of the vehicle, such as its typical cruising speed, turning angle, and stopping distance. We suggest that the degree of overlap between sensory and movement volumes can provide insight into the types of control strategies that are best suited for guiding behavior.

So, we're dealing with a fish that can sense in all directions, and then move in any direction where it might locate prey. That sounds like a pretty good advantage to have while hunting (or escaping for that matter). So, why doesn't all, or at least a large number, of animals have this ability? Well, first of all, they would have to been maritime, as they need water for the electric field. Second of all, such things comes at a cost. As the summary clearly states.

Although it's certainly useful to be able to sense in all directions, active sensing comes at a cost; energetically, it's very expensive to generate a good-sized electric field, since the signal falls off rapidly with distance.

Obviously, this leads to a shorter detection range - according to the findings, the black ghost knifefish had a averagee estimated prey detection distance of about 3.5 cm from the fish's body. Hardly a substitute for good eyes in areas with sparse food resources.

Physical and mathematical modelling gives new knowledge about the feeding habits of pterosaurs

ScienceDaily has an interesting piece about how new research shows that our theories about some pterosaurs' feeding habits have to be re-evaluated.

Feeding Habits Of Flying Reptiles Uncovered

Using new physical and mathematical modelling, Dr Stuart Humphries from the University of Sheffield, along with scientists from the Universities of Portsmouth and Reading, has shown that suggestions that extinct pterosaurs gathered their food by 'skimming' the surface of the ocean with their beaks are inaccurate.

Previous studies have suggested that some pterosaurs may have fed like modern-day 'skimmers', a rare group of shorebirds, belonging to the Rynchops group. These sea-birds fly along the surface of lakes and estuaries scooping up small fish and crustaceans with their submerged lower jaw. Inferred structural similarities between pterosaur and Rynchops jaws had previously been used to suggest that some pterosaur were anatomically suited for skimming.

However, new evidence provided by the researchers suggests that the fossilised jaws of suggested pterosaur skimmers mean that these creatures may have found it impossible to feed in this way.

According to the research, the thicker jaws of pterosaurs would make it difficult for them to deflect water the way the extraordinarily slim bills of Rynchops do. By combining experiments using life-size models of pterosaur and skimmer jaws with hydrodynamic and aerodynamic modelling, the researchers demonstrated that skimming requires more energy than the giant reptilian fliers were likely able to supply.

In other words, what we assumed about the feeding habits of these prehistoric creatures is almost certainly wrong, and other ideas have to be tested. Due to the simple fact that these creatures cannot be observed while feeding, we can never be entirely certain about how they feed, but we can at least remove some possibilities, and make a case for the most likely way.

The findings are also interesting because they show that we can't assume anything from just the shape and form and form of the fossils. Something the article also states.

Discovering the ecological traits of these reptiles though is far more complicated. One way scientists currently gain an insight into ecological traits of extinct animals is by comparing fossilized morphological (shape and form) features to those of living animals.

However, as this new research shows, these records do not provide direct evidence of behaviour and ecology. Dr Humphries, from the Department of Animal and Plant Sciences, said: "Our results illustrate the pitfalls involved in using morphological data to study the ecology of extinct animals, including dinosaurs and pterodactyles."

This shows the importance of re-evaluating and testing our ideas frequently. In this case, it probably makes little difference that our assumptions were wrong, but in other cases, those assumptions could be the basis of other assumptions, which would have to be re-evaluated, or maybe even discarded, as an result of the first assumptions being wrong.

Annoyingly, the ScienceDaily article didn't state where the study was published, but I managed to locate it at PLoS Biology
Did Pterosaurs Feed by Skimming? Physical Modelling and Anatomical Evaluation of an Unusual Feeding Method

Author Summary

Just because a component of an extinct animal resembles that of a living one does not necessarily imply that both were used for the same task. The lifestyles of pterosaurs, long-extinct flying reptiles that soared ancient skies above the dinosaurs, have long been the subject of debate among palaeontologists. Similarities between the skulls of living birds (black skimmers) that feed by skimming the water surface with their lower bill to catch small fish, and those of some pterosaurs have been used to argue that these ancient reptiles also fed in this way. We have addressed this question by measuring the drag experienced by model bird bills and pterosaur jaws and estimating how the energetic cost of feeding in this way would affect their ability to fly. Interestingly, we found that the costs of flight while feeding are considerably higher for black skimmers than previously thought, and that feeding in this way would be excessively costly for the majority of pterosaurs. We also examined pterosaur skulls for specialised skimming adaptations like those seen in modern skimmers, but found that pterosaurs have few suitable adaptations for this lifestyle. Our results counter the idea that some pterosaurs commonly used skimming as a foraging method and illustrate the pitfalls involved in extrapolating from living to extinct forms using only their morphology.

Generalized reciprocity between rats demonstrated

PLoS Biology has an article about some experiments with cooperation between rats that showed that rats that had been helped by others before were more willing to help others, regardless of who those others were. In other words, they seemed to behave according to the old principle "what comes around, goes around".

Generalized Reciprocity in Rats by Claudia Rutte, Michael Taborsky

The evolution of cooperation among nonrelatives has been explained by direct, indirect, and strong reciprocity. Animals should base the decision to help others on expected future help, which they may judge from past behavior of their partner. Although many examples of cooperative behavior exist in nature where reciprocity may be involved, experimental evidence for strategies predicted by direct reciprocity models remains controversial; and indirect and strong reciprocity have been found only in humans so far. Here we show experimentally that cooperative behavior of female rats is influenced by prior receipt of help, irrespective of the identity of the partner. Rats that were trained in an instrumental cooperative task (pulling a stick in order to produce food for a partner) pulled more often for an unknown partner after they were helped than if they had not received help before. This alternative mechanism, called generalized reciprocity, requires no specific knowledge about the partner and may promote the evolution of cooperation among unfamiliar nonrelatives.

The authors sums up the finding pretty well, and I see no real need to elaborate on the findings

Author Summary

The evolution of cooperation is based on four general mechanisms: mutualism, where an action benefits all partners directly; kin selection, where related individuals are supported; “green beard” altruism that is based on a genetic correlation between altruism genes and respective markers; and reciprocal altruism, where helpful acts are contingent upon the likelihood of getting help in return. The latter mechanism is intriguing because it is prone to exploitation. In theory, reciprocal altruism may evolve by direct, indirect, “strong,” and generalized reciprocity. Apart from direct reciprocity, where individuals base their behavior towards a partner on that partner's previous behavior towards themselves, and which works under only highly restrictive conditions, no other mechanism for reciprocity has been demonstrated among conspecifics in nonhuman animals. Here, we tested the propensity of wild-type Norway rats to help unknown conspecifics in response to help received from other unknown partners in an instrumental cooperative task. Anonymous receipt of help increased their propensity to help by more than 20%, revealing that nonhuman animals may indeed show generalized reciprocity. This mechanism causes altruistic behavior by previous social experience irrespective of partner identity. Generalized reciprocity is hence much simpler and therefore more likely to be important in nature than other reciprocity mechanisms.

Of course, it's not possible to say if this behavior is abnormal, until similar tests have been carried out on other species. It does, however, tell us that it is possible that such behavior happens in nature, which is something that has only been speculated about before.

Need I say what this would mean regarding the percepted uniqueness of human altruism? If generalized reciprocity is the norm, then altruism would make evolutionary sense on a species level, and should be quite comment in nature (and it has been observed before among several species, so that supports this idea).

Could the laws of thermodynamics explain life?

We all know how Creationists and neo-Creationists misuses the 2nd law of thermodynamics to explain why life couldn't have been here without an intelligent designer/God.

Well, according to a feature article by John Whitfield in PLoS Biology, some physicists thinks that life can be explained by the laws of thermodynamics.

At first glance, life and the laws of thermodynamics seem to be at loggerheads. Most glaringly, the second law states that over time, any system will tend to the maximum level of entropy, meaning the minimum level of order and useful energy. Open a bottle of perfume in a closed room, and eventually the pool of scent will become a smelly cloud. Organisms do their damnedest to avoid the smelly cloud of equilibrium, otherwise known as death, and a common argument of anti-evolutionists is that the universe's tendency toward disorder means that natural selection cannot make living things more complex. The usual counter to this argument is that organisms maintain internal order and build complexity by exporting entropy—importing energy in one form, and radiating it out in another, higher-entropy form. One of the first physicists to ponder these questions, Erwin Schrödinger, described food as negative entropy: “The essential thing in metabolism is that the organism succeeds in freeing itself from all the entropy it cannot help producing while alive.”

I hadn't heard the counter-argument being phrased like that before, but it's certainly more precise than the usual counter-argument (the 2nd law only applies to closed systems).

But recently, some physicists have gone beyond this and argued that living things belong to a whole class of complex and orderly systems that exist not despite the second law of thermodynamics, but because of it. They argue that our view of evolution, and of life itself, should likewise be based in thermodynamics and what these physical laws say about flows of energy and matter. Darwinian selection, these researchers point out, isn't the only thing that can create order. Throughout the universe, the interaction of energy and matter brings regular structures—be they stars, crystals, eddies in fluids, or weather systems in atmospheres—into being. Living things are the most complex and orderly systems known; could they be part of the same phenomenon? And could the process that brings them about—natural selection, driven by competition between organisms—be ultimately explicable in thermodynamic terms?

Eric Smith, a theoretical physicist at the Santa Fe Institute in New Mexico, certainly thinks so. “Darwinian competition and selection are not unique processes,” he says. “They're a complicated version of more fundamental chemical competitive exclusion.” In a paper published last year [2], Smith and his colleagues argued that natural selection is a highly sophisticated version of a physical process called self-organization, the still poorly understood means by which energy plus matter can equal order.

Such orderly, self-organized systems are like engines designed to level out energy gradients—while they persist, they produce more entropy, more quickly, than a disordered mishmash of molecules. Weather systems, for example, transport heat from the tropics toward the poles far more quickly than a homogeneous, static atmosphere would. Life does the same thing, Smith points out. Indeed, he believes that this might have been the reason for its origin—that, under the conditions on early Earth, life was the best way to release the build-up of geothermal energy and an inevitable consequence of that energy [3]. Once biochemistry had got going, subsequent chemical and Darwinian selection would each favor the systems best at dissipating Earth's pent-up energy, whether geothermal or, following the invention of photosynthesis, solar.

It has long been suggested that self-organized systems do not just level out energy gradients more quickly than disordered ones do, they do it as quickly as possible. Models that assume maximum entropy production (MEP) make good predictions about the climates of Earth [4] and Saturn's moon Titan [5] and about the growth of crystals in solutions [6]. But until recently, MEP was just an assumption—there was no mechanism or theory to explain why such systems should tend to this state. Classical thermodynamics is no help— it explains entropy only in closed systems, with no energy going in or coming out. It says nothing about how much entropy open, nonequilibrium systems, such as organisms, ought to produce.

The article by Smith et al can be found in Journal of evolutionary biology, for those with access to that sort of things.

Smith is not alone in believing this, the PLoS Biology feature also includes interviews with several other physicists, who explains why they think there is a connection between the laws of thermodynamics, and the existence of life.

Quite an interesting read, even if some of the details certainly went over my head.

Brains....

PLoS Biology has two essays about recent brain research, which I thought might be of interest to people.

The Genetics of Brain Wiring: From Molecule to Mind

What makes some people neurotic or schizophrenic or right-handed or fearless? Are these behavioural differences caused by literal differences in how individuals' brains are wired? If so, what causes those differences? This age-old question of nature versus nurture can be recast in more realistic terms based on our modern understanding of genetics, development, and neuroscience. The challenge in this area is to understand how genotype is mapped to phenotype, not just in terms of the average effects of single genes across populations but also in terms of their combined effects in shaping the phenotypes of individuals.

There is compelling evidence that many psychiatric disorders have their origins in disturbed neurodevelopment, resulting in altered connectivity [1,2]. Similarly, many behavioural or cognitive traits are both heritable, at least moderately [3], and correlated with functional connectivity differences in various circuits [2]. The study of the genetics of behavioural or psychiatric traits may thus be directly informed by an understanding of the genetic architecture of the developmental processes underlying brain wiring. This essay presents a systems-level overview of these processes, highlighting several important properties that can have large effects on how genotype is mapped to phenotype: epistasis (meaning non-additive gene–gene interactions in this context), compensation, and stochastic developmental variation.

I don't like the "nature vs. nurture", since it seems more likely that it's "nature and nurture" in most cases. Yet obviously mental disorders are more nature than nurture in most cases. So, to understand mental disorders, it's important to understand how the brain works, and how it gets developed. The synopsis explains what work has been done in that field, and what results have been found.

To be honest, it's not the easiest PLoS Biology essay I've come across.

The other essay is dealing with a similar subject.

Law, Responsibility, and the Brain

Archaeological discoveries of traumatic injuries in primitive hominid skulls strongly hint that our species has a long history of violence [1]. Despite repeated attempts throughout history, including efforts to eliminate violence through the imposition of criminal sanctions, we have yet to dispel our violent nature. Consequently, criminal violence remains a common feature of most societies. As policy-makers seek deeper understandings of criminally violent and anti-social behaviour, many contemporary neuroscientists assume that the essential ingredients of the human condition, including free will, empathy, and morality, are the calculable consequences of an immense assembly of neurons firing. Intuitively, this view opposes Cartesian dualism (i.e., the brain and mind are separate, but interacting, entities) and assumes that violence and antisocial behaviour emanate from a mechanistically determined brain

From this standpoint, the exciting discoveries of neuroscience resonate far beyond mere philosophical banter and may have important implications for the way government institutions, including education and legal systems, operate. For example, to the extent that legal systems attempt both to move behaviour in socially desirable directions and also to adjudicate transgressions fairly, the legal system's effectiveness can be improved by deepening our understandings about why people behave as they do and both how and why people respond to various changes in legal incentives. Specifically, neuroscience may have important implications for both how we understand the multiple influences on violent behaviour and how the legal system may better engage with violent criminals.

The essay is basicly about how our deepening understanding of how the brain works might effect our legal processes, though science cannot stand alone in our process to understand how criminals act and think.

They have some concluding remarks

The goals of science and of law are different. However, important legal questions such as moral blameworthiness, culpability, responsibility, and the likelihood of recidivism depend to some degree on improved understandings of human behaviour. Therefore, biological advances in understanding human brain architecture and function may overlap in important ways with legal inquiries. New studies of the criminal brain are likely to shape moral views on responsibility and free will, with possible impacts on how legal systems punish and treat criminals [60].

A growing body of research gives us good reason to believe that some kinds of brain dysfunction can affect the probability of different kinds of criminal behaviours. However, despite our growing knowledge of the brain abnormalities associated with anti-social and psychopathic behaviour, there are as yet no concrete biological markers—genetic or physiological—that can predict such behaviours. Violent and anti-social behaviours undoubtedly arise from a symphony of factors. Optimal understanding will require cooperation among many disciplines such as economics, sociology, psychology, evolutionary biology, cellular physiology, and neuroscience

I think it cannot be emphasised enough that we cannot predict criminal behaviours through science - and it is always debatable if we should try to do so, from a standpoint of free will (a concept that the article also addresses) and presumption of innocence.

Evolution and medicine

PLoS Biology has an editorial about the role of evolution in medicine and medical school. It does a good job of explaining the different viewpoints on the issue, without going into stupid country (e.g. Egnor).

Does Medicine without Evolution Make Sense?

It is curious that Charles Darwin, perhaps medicine's most famous dropout, provided the impetus for a subject that figures so rarely in medical education. Indeed, even the iconic textbook example of evolution—antibiotic resistance—is rarely described as “evolution” in relevant papers published in medical journals [1]. Despite potentially valid reasons for this oversight (e.g., that authors of papers in medical journals would regard the term as too general), it propagates into the popular press when those papers are reported on, feeding the wider perception of evolution's irrelevance in general, and to medicine in particular [1]. Yet an understanding of how natural selection shapes vulnerability to disease can provide fundamental insights into medicine and health and is no less relevant than an understanding of physiology or biochemistry.

As can been seen from the lead paragraph, the editorial comes down on the side of teaching evolution to medical students (perhaps not surprising, given the venue).

My take on the issue, as neither a doctor/medical professional nor a evolutionary biologist, is that in a time with resistant TB on the march and the finding of other troublesome resistant diseases, we cannot ignore the need for doctors, and other medical professionals, to understand the basics of evolution, and how treating diseases might have an influence on how the diseases evolve.
On top of that, knowledge of evolution might create new vectors for fighting old diseases, which obviously would be benificial to all.

So, in other words, I am quite in agreement with the editorial about the need for medical students to learn at least basic evolutionary biology.

The perils of symbiosis

An interest area of mine are parasites. Not normal parasites, that just feeds of other creatures, but the type of parasites that actually can influence their hosts. Carl Zimmer has written an entire book about it, and has also written some good stuff about them on his blog.

A natural extension of that interest would be symbiosis, where two (or more) creatures are somewhat inter-dependent. I haven't really gotten into this subject though, even though the whole concept is rather facinating. Much of that might have to do with the fact that symbiosis is rarely as dramatic as parasites, since both types of creatures depend upon each other for mutual survival. Or so I thought.

One aspect I hadn't thought of, was the fact that since these creatures are inter-dependent, mutations in indviduals from one of the species, can have drastic effects on individuals from the other species. That's what a new paper in PLoS Biology shows us.

PLoS Biology has been kind enough to make a synopsis of the study for us non-biologists, and the findings sounds facinating.

Imagine having bacteria dictate how well you fare under extreme conditions. For the aphid Acyrthosiphon pisum, that’s the price it pays for getting the nutrients it needs. This little insect, which survives by sucking juices out of the stems of grain crops and other vegetation, depends on a bacterial sidekick, Buchnera aphidicola, for amino acids it can’t get from plants. The aphid in turn provides the bacterium with energy and carbon as well as shelter inside specialized cells.

Such interdependent relationships are not unusual in the natural world. What is unusual, report Helen Dunbar, Nancy Moran, and colleagues in a new study, is that a single point mutation in Buchnera’s genome can have consequences for its aphid partner that are sometimes detrimental, and sometimes beneficial.

Basicly, the finding is that a certain mutation in Buchnera aphidicola can have a large effect on the host Acyrthosiphon pisum ability to withstand heat. On the other hand, in cooler areas, the same mutation can be benificial.

Normally I would link to the study as well, and not only the synopsis, but PLoS Biology is really slow for me today, so I can't access the article.