Post List

  • August 24, 2010
  • 12:00 AM

The dark side of photonics

by Joerg Heber in All That Matters

Photonics is all about light. Processing of light for applications ranging from holograms and displays to optical telecommunications. Thanks to a better theoretical understanding and to advances in fabrication technology, photonic devices and gadgets have become increasingly versatile and powerful.

But photonics also has a dark side. In many light-processing devices and structures there are dark modes — oscillations of the light wave that while not forbidden cannot be directly excited by a given experimental configuration. [...]... Read more »

Papasimakis, N., Luo, Z., Shen, Z., De Angelis, F., Di Fabrizio, E., Nikolaenko, A., & Zheludev, N. (2010) Graphene in a photonic metamaterial. Optics Express, 18(8), 8353. DOI: 10.1364/OE.18.008353  

Mirin, N., Bao, K., & Nordlander, P. (2009) Fano Resonances in Plasmonic Nanoparticle Aggregates. The Journal of Physical Chemistry A, 113(16), 4028-4034. DOI: 10.1021/jp810411q  

Fan, J., Wu, C., Bao, K., Bao, J., Bardhan, R., Halas, N., Manoharan, V., Nordlander, P., Shvets, G., & Capasso, F. (2010) Self-Assembled Plasmonic Nanoparticle Clusters. Science, 328(5982), 1135-1138. DOI: 10.1126/science.1187949  

Hentschel, M., Saliba, M., Vogelgesang, R., Giessen, H., Alivisatos, A., & Liu, N. (2010) Transition from Isolated to Collective Modes in Plasmonic Oligomers. Nano Letters, 10(7), 2721-2726. DOI: 10.1021/nl101938p  

Luk'yanchuk, B., Zheludev, N., Maier, S., Halas, N., Nordlander, P., Giessen, H., & Chong, C. (2010) The Fano resonance in plasmonic nanostructures and metamaterials. Nature Materials, 9(9), 707-715. DOI: 10.1038/nmat2810  

  • August 23, 2010
  • 09:05 PM

A Web Server for Identifying the "Hot Spot" of Protein-Protein Interfaces

by Michael Long in Phased

Narcis Fernandez-Fuentes (University of Leeds, United Kingdom) and coworkers' web server will greatly accelerate the development of drugs which target protein-protein interfaces. This news feature was written on August 23, 2010.... Read more »

  • August 23, 2010
  • 08:30 PM

Rats Pee During the Night. A Surprise? Not Really

by Allison in Dormivigilia

Researchers have behaviorally confirmed an entrained rhythm of urination in the rat. Though this information is consistent with the recent shift in funding focus in circadian research (i.e. funding crutches), this is an example of a study that doesn't take advantage of advanced neuroscience techniques or at least attempts to elucidate the mechanisms. I mean, gosh, it was published in PLoS.... Read more »

Gerald M. Herrera1,2, Andrea L. Meredith3*. (2010) Diurnal Variation in Urodynamics of Rat . PLoS ONE. info:/10.1371/journal.pone.0012298

  • August 23, 2010
  • 05:06 PM

When genome size changes and hybrid vigor?

by James in James and the Giant Corn

A group of researchers at Masaryk University in the Czech Republic study how different members of the same grass species (Festuca pallens) have different total amounts of DNA per cell. have a new paper out in New Phytologist  they found that plants with the most unusual genome sizes (really big or really small) are less [...]... Read more »

  • August 23, 2010
  • 04:28 PM

Supply Chain Risk: Culture Shock

by Jan Husdal in

Is culture shock the reason why so many global and cross-culture business relationships fail? When it comes to Western buyers and Chinese suppliers this may very well be the case, and while issues related to product quality or supplier reliability may seem as the obvious cause externally, cultural differences may be the root cause internally. [ ... ]... Read more »

  • August 23, 2010
  • 04:00 PM

Why Do Orb-Weaving Spiders Decorate Their Webs?

by Michael Long in Phased

Daiqin Li (National University of Singapore) and coworkers have shown that silk decorations help orb-weaving spiders attract prey, although the jury is still out on the effect of dead plant matter decorations and their effect on predator defense. This news feature was written on August 23, 2010.... Read more »

  • August 23, 2010
  • 03:47 PM

Life History theory and eight stage evo-devo model

by sandygautam in The Mouse Trap

Image via Wikipedia I’ve touched upon life history theory earlier, in an oblique fashion, while discussing evolutionary perspectives on personality. Life History theory posits that an individual’s life efforts can be subsumed under two headings- somatic life efforts and reproductive life efforts. The latter relates to selection due to being able to successfully replicate one-self;Rating: 0.0/10 (0 votes cast)... Read more »

  • August 23, 2010
  • 03:41 PM

Learning without thinking

by Carl in The motor chauvinist

Scratching around on the internet this afternoon on my first day back from holiday, I was kind of reluctant to dive straight back into taking papers apart. After all, I have spent the majority of the last three weeks drinking beer and eating pies in the UK, and the increase in my waistline has most likely been mirrored by the decrease in my critical faculties (as happens when you spend time away from the cutting edge). However, I ran across a really cool little article that reminded me just why I enjoy all this motor control stuff. So here goes nothing!There’s been some work in recent years on the differences between implicit and explicit motor learning – that is, the kind of learning the brain does by itself, relying on cues from the environment, vs. using a well-defined strategy to perform a task. For example, learning to carry a full glass of water without spilling by just doing it and getting it wrong a lot until you implicitly work out how, or by explicitly telling yourself, “Ok, I’m going to try to keep the water as level as possible.” A fun little study on this was performed by Mazzoni and Krakauer (2006) in which they showed that giving their participants an explicit strategy in a visuomotor rotation task (reaching to a target where the reach is rotated) actually hurt their performance. Essentially they started off being able to perform the task well using the explicit strategy, which was something like ‘aim for the target to the left of the one you need to hit’. However as the task went on the implicit system doggedly learned it – and conflicted with the explicit strategy – so that the participants were making more errors at the end than at the beginning.The paper I’m looking at today follows up on this result. Implicit error-based learning is thought to be the province of the cerebellum, the primitive, walnut-shaped bit at the back of the brain. The researchers hit upon the idea that if the cerebellum is important for implicit learning, then perhaps patients with cerebellar impairments would actually find it easier to perform the task relative to healthy control participants. To test this, they told both sets of participants to use an explicit strategy in a visuomotor rotation task, just like in the previous study, and measured their ‘drift’ from the ideal reaching movement.Below you can see the results (Figure 2A in the paper):Target error across movementsOpen circles are all control participants, whereas filled circles are all patients. The black circles at the start show baseline performance – both groups performed pretty well and similarly. Red circles show the first couple of movements after the rotation was applied, and before participants were told to use the strategy. You can see that the participants are reaching completely the wrong way. The blue section shows reaching while using the strategy. Here’s the nice bit: the cerebellar patients are doing better than the controls, as their error is closer to zero, whereas the controls are steadily drifting away from the intended target. Magenta shows when the participants are asked to stop using the strategy and the final cyan markers show the ‘washout’ phase as both groups get back to baseline without an imposed rotation – though the patients manage much more quickly than the controls.So it looks very much like the cerebellar patients, because their cerebellums are impaired at implicit learning, are able to perform this task better than healthy people. What’s kind of interesting is that other research has shown that cerebellar patients aren’t very good at forming explicit strategies on their own, which is something that healthy people do without even thinking about it. The tentative conclusion of the researchers is that it’s not so much that the implicit and explicit systems are completely separate, but that the implicit system can inform the development of explicit strategies – which is impaired if the cerebellum isn’t working properly.I didn’t like everything in this paper. I was particularly frustrated with the method section, which talks about the kind of screen they used. I wasn’t sure whether the images shown to participants were on a screen in front of them or whether the screen was placed over the workspace in a virtual-reality setup; it was unclear. There was also a sentence claiming that the cerebellar patients’ performance was ‘less’ than the controls, when in fact it was better. Other than these minor niggles though, it’s a really nice paper showing a very cool effect.--Taylor JA, Klemfuss NM, & Ivry RB (2010). An Explicit Strategy Prevails When the Cerebellum Fails to Compute Movement Errors Cerebellum PMID: 20697860Images copyright © 2010 Taylor, Klemfuss & Ivry... Read more »

  • August 23, 2010
  • 03:35 PM

Information is to behaviour change as spaghetti is to a brick

by Bronwyn Thompson in Healthskills: Skills for Healthy Living

I’m a great fan of books like ‘Explain Pain’. This delightful publication by David Butler and Lorimer Moseley gives accurate information about pain, particularly chronic pain, in an accessible format for both patients and clinicians, and I’ve used it often with people I’m seeing. I’m also a fan of helping people to understand what we … Read more... Read more »

  • August 23, 2010
  • 03:14 PM

Lights! Action! Kids!

by Psychology 379 bloggers in Cognition & the Arts

Originally posted on Cognitive Daily. This is a guest post by Laura Younger, one of Greta’s top student writers for Spring 2007. Take a look at these static images from a video clip. Can you tell what the person is doing? It might be hard to make it out from these still pictures, but when [...]... Read more »

Golinkoff RM, Chung HL, Hirsh-Pasek K, Liu J, Bertenthal BI, Brand R, Maguire MJ, & Hennon E. (2002) Young children can extend motion verbs to point-light displays. Developmental psychology, 38(4), 604-14. PMID: 12090489  

  • August 23, 2010
  • 01:59 PM

Yawns help cool the brain?

by Arunn in nOnoScience (a.k.a. Unruled Notebook)

Yawning when it is extremely cold may be maladaptive, as this may send unusually cold air to the brain, which may produce a thermal shock."

Shouldn't I yawn anymore in a department meeting conducted in an air conditioned room? ... Read more »

  • August 23, 2010
  • 12:34 PM

High Excitement in Review: "Quantum information with Rydberg atoms"

by Chad Orzel in Uncertain Principles

I'm a big fan of review articles. For those not in academic science, "review article" means a long (tens of pages) paper collecting together the important results of some field of science, and presenting an overview of the whole thing. These vary somewhat in just how specific they are-- some deal with both experiment and theory, others just theoretical approaches-- and some are more readable than others, but typically, they're written in a way that somebody from outside the field can understand.

These are a great boon to lazy authors, or authors facing tight page limits ("Ref. [1] and references therein" takes up a lot less space than individual citations for the ten most important historical papers), and also to people who would like to get a technical introduction to a new field. They have a slight tendency to overemphasize the particular interests or results of the people writing the review, but that's not too big a distortion, provided the authors are chosen well.

The journal Reviews of Modern Physics is primarily review articles of this type, and a recent paper there caught my eye as something worth talking about on the blog. Hence this post.

Waitaminute-- do you seriously expect us to wade through 51 pages of a physics article? No, not really. Not unless you really want a thorough overview of the field. It's more that this is an area of work that is generating some interest these days, and this article is a convenient collection of the important results. You don't need to read the whole thing, though-- you can just skim it for the good parts if you like.

All right, then. So, what do loathsome bipedal crustaceans have to do with quantum information? That's a Zoidberg, not a Rydberg. A "Rydberg atom" is an atom in a highly excited state, very close to the ionization limit-- technically, it probably ought to be "quantum information with atoms in Rydberg states," but "Rydberg atom" is well established jargon and there's nothing to be done about it now.

The name comes from the Rydberg formula, which was the first really good description of the emission spectrum of hydrogen, which Niels Bohr eventually showed could be interpreted as describing transitions between discrete electronic states of the atom. The Rydberg formula only works well for the low-lying states of hydrogen, because interactions between the electrons in more complicated atoms (i.e., everything else) shift all the energy states. If you take one electron and excite it to a very high level, though, the states up there start to follow something like the Rydberg formula again.
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Saffman, M., Walker, T., & Mølmer, K. (2010) Quantum information with Rydberg atoms. Reviews of Modern Physics, 82(3), 2313-2363. DOI: 10.1103/RevModPhys.82.2313  

  • August 23, 2010
  • 12:02 PM

How Language Affects Thought -- plus book giveaway!

by Livia Blackburne in A Brain Scientist's Take on Writing

I recently read Dreaming in Hindi, Katherine Russell Rich’s memoir of her year in India learning Hindi. Rich intersperses quirky anecdotes of learning and culture shock with scientific insights about learning a second language. I was excited see her mention two of my favorite studies on language and thought.

Psychologists and philosophers have long debated whether language shapes the way we think. While the most drastic viewpoint – that thought can’t exist without language -- has fallen out of favor, psychologists still study more subtle effects.

The first study has to do with gender in language. Many languages assign genders to words. For example, in Spanish, the word for “key” is feminine, while the German word for” key” is masculine. Gender for the most part is arbitrary and varies from language to language, which allows for some interesting experiments.
Psychologist Lera Boroditsky and colleagues asked Spanish and German speakers to provide descriptive adjectives for different objects. Interestingly, people produced adjectives that were consistent with gender stereotypes. For example, German speakers described keys as hard, heavy, jagged, metal, and useful, while Spanish speakers described them as golden, intricate, little, lovely, and shiny. For the word “bridge,” which is feminine in German and masculine in Spanish, the opposite happened. Germans described bridges as beautiful, elegant, fragile, and peaceful, while Spanish speakers said they were big, dangerous, long, and strong.

(Methodological note: the masculinity or femininity of adjectives was determined by a separate group of English speakers, blind to the study’s purpose, who rated these adjectives on masculinity and femininity. It's kind of amusing to see which words received which rating.)

In a second experiment, Boroditsky looked at language and the conception of time. English speakers primarily speak of time in horizontal terms. For example, we talk about moving meetings forward, or pushing deadlines back. Mandarin speakers, on the other hand, use up/down metaphors as well. So a Mandarin speaker would refer to the previous week as “up week” and next week as “down week.”

Boroditsky performed an experiment to see whether priming people to think either vertically or horizontally would affect their ability to think about time. Participants first answered a question about horizontally or vertically placed objects. For example, they saw two worms in a row and had to say whether the black worm was in front. Or they’d see two vertically stacked balls and say whether the black ball was above the white ball. Then the participants answered a question about time (“ Does March come before April”, etc.).

They found that English speakers were quicker to answer questions about time after answering horizontal spatial questions, while Mandarin speakers were quicker after vertical spatial questions. This reminds me of the scaffolded mind idea, in which concrete experiences provide a way to understand abstract concepts.

What do these studies say to me as a writer? It's interesting to see how subtle aspects of language affect the way we think. It argues for thinking like poets and valuing each word were not just a dictionary meaning, but all the other layers of associations and meanings that come with it. I don’t think it’s worth obsessively wondering about subconscious associations, but it’s certainly something interesting to think about.

Dreaming in Hindi was given to me as a review copy, and I would now like to pass it onto one of you. If you would like to enter the drawing, there are two ways you can do it. Either:
1. Retweet this post and paste the link in the comments or
2) 2. If you're an RSS subscriber, there is a secret code on the bottom of this entry. Send an e-mail to liviablackburne [at] with a secret code as the SUBJECT LINE.

I will draw a winner next Monday.

Boroditsky, L. (2001). Does Language Shape Thought?: Mandarin and English Speakers' Conceptions of Time Cognitive Psychology, 43 (1), 1-22 DOI: 10.1006/cogp.2001.0748

Dreaming in Hindi Giveaway Code: Udiapur

... Read more »

  • August 23, 2010
  • 11:37 AM

Neuroscience of Murder and Aggression: Part 1

by William Yates, M.D. in Brain Posts

I have been interested in the genetics and environmental factors involved in aggression since working with Dr. Remi Cadoret at the University of Iowa in the 1990s.  We published an early study in adoptees that found an interaction between a biological background of antisocial personality and an adverse childhood environment in an additive effect in adoptee agression.  Adoptees with a biological relative with antisocial personality (usually fathers) were more aggressive when there were raised in an adverse environment during childhood and adolescence.Jim Fallon, Ph.D. neurobiologist at the University of California recently summarized some of this neuroscience issues in this area in a TED talk titled: "Exploring the Mind of a Killer".   This six and one half minute presentation is summarized in my notes here:Fallon was asked by colleague to examine brains of psychopathic killersHe was blind to identity of the killers at the time of analysisMurder risk seems to be linked to interactions between environment and geneticsThere are also epigenetic effects-biological damage to the genesMurders had damage to the orbital cortex--seen in all murders in his studyA high risk gene is the MAOA gene--sex-linked you only get effect in males from motherMAOA-monoamine oxidase A affects serotonin metabolismGene expression is increased with severe adverse traumatic environment during the period of early childhood through adolescenceIncreased violence in the environment expressed through generationsToughness seen as a protective factor preferred by some women in mates--this effect may concentrate the genetic effectDr. Fallon was surprised when he learned of his own genetic backgroundHis cousin was Lizzi Borden the female murderer and he also had a distant grandmother killed who murdered a sonSeven male murderers have been identified on his father's sidePET scanning study completed on his own family with genetic analysisLed him to suspect bad news to come in his family--he doesn't know when it will pop upI ran across an interesting piece from NPR by Dr. Michael Stone who developed a hierarchy of evilness among psychopathic individuals.  This scale ranks 22 levels of evilness.  Charles Manson ranked 15 on the scale of 22 levels (with 22 the worst) and Jeffrey Dahmer topped out at the most evil level.  I ran a Pub Med search and have not been able to find a scientific reference to this scale.  If a reader runs into the citation please comment as I would appreciate the citation.It's gratifying that some of the research conducted by Dr. Cadoret in being supported by additional studies of the genetics of violence, murder and antisocial personality. I will be posting more on this issue in the next Brain Posts where I focus on the epidemiology, genetics, imaging and medical care needs of this important public health problem. Cadoret RJ, Yates WR, Troughton E, Woodworth G, & Stewart MA (1995). Genetic-environmental interaction in the genesis of aggressivity and conduct disorders. Archives of general psychiatry, 52 (11), 916-24 PMID: 7487340Gunter TD, Vaughn MG, & Philibert RA (2010). Behavioral genetics in antisocial spectrum disorders and psychopathy: a review of the recent literature. Behavioral sciences & the law, 28 (2), 148-73 PMID: 20422643... Read more »

  • August 23, 2010
  • 11:10 AM

Long, deep and broad

by CJA Bradshaw in ConservationBytes

Thought that would get your attention ;-) “More scientists need to be trained in quantitative synthesis, visualization and other software tools.” D. Peters (2010) In fact, that is part of the title of today’s focus paper in Trends in Ecology and Evolution by D. Peters – Accessible ecology: synthesis of the long, deep,and broad. As a [...]... Read more »

  • August 23, 2010
  • 11:04 AM

In the news this month: pulsar irregularities

by Megan in Rigel

After massive stars like explode, the object left behind is thought to be either a or a black hole, depending on the final mass of the progenitor star. are neutron stars that have strong magnetic fields and behave somewhat like cosmic lighthouses, projecting beams of radio emission into space as they spin. Studying the pulses of radiation as the beams sweep past the Earth can provide valuable information on the physics of these extreme objects, allowing astronomers to probe physics under conditions which are not possible to create in a terrestrial laboratory. While pulsars are known to be extremely accurate , their pulse rates are very stable over time, there are however unexplained deviations from the expected spin rate, a phenomenon known as timing noise. Now, a team led by Andrew Lyne at the , have uncovered a mechanism which could explain this noise.Over long timescales, the rate at which a pulsar spins (known as the rate) decreases slowly in a predictable way due to the conversion of rotational energy into photons. By studying a large number of pulsars repeatedly over 40 years, the team found that the deviations from the expected spin down rate were actually quasi-periodic on timescales between one and ten years, and that several other pulsar characteristics may be linked to the same phenomenon. One particular pulsar, known as B1931+24, only displays radio pulses intermittently, and long term study showed that it also had two different spin down rates: its spin rate decreased faster when the radio signal was detectable.The team analysed the data on a large sample of pulsars and found a further seventeen which show evidence of quasi-periodic spin down rates, many of which also show variations in the shape of the pulse profile. The authors suggest that the likely explanation is that the pulsar's is switching between two distinct states. Exactly what causes the pulsar to switch between states is not yet known, but if the changes can be accurately modeled then the timing noise can be reduced, and astronomers will find it easier to compensate for errors in pulsar ;clocks; in highly sensitive experiments designed to detect .This blog post is a news story from the , aired in the edition.... Read more »

Lyne, A., Hobbs, G., Kramer, M., Stairs, I., & Stappers, B. (2010) Switched Magnetospheric Regulation of Pulsar Spin-Down. Science, 329(5990), 408-412. DOI: 10.1126/science.1186683  

  • August 23, 2010
  • 11:00 AM

To Hear A Mockingbird: The Plight of the Iguana

by Jason Goldman in The Thoughtful Animal

Predator-prey interactions are often viewed as evolutionary arms races; while predators improve their hunting behaviors and their ability to sneak up on their prey, the prey improve upon their abilities to detect and escape from their predators. The problem, of course, is that there is a trade-off between maintaining vigilance - the attention necessary to be consistently aware of others in the environment takes quite a bit of physical and mental energy - and doing all the other things that an animal must do, such as finding its own food. As a result of this trade-off, many social species, especially mammalian and avian species, have developed alarm calls. Alarm calls are specific vocalizations that signal the presence of a danger in the environment to nearby conspecifics, and sometimes contain additional information about the type of threat or predator.

As we've discussed before, subsequent to the introduction of predatory birds, howler monkeys on Barro Colorado Island near Panama rapidly developed an alarm call specific for those birds that indicated the presence of an avian predator; something like "danger from above!" That is, they did not merely adapt an already existing alarm call to the new predator, they developed an entirely new one.

In certain cases, prey species have developed the additional ability to eavesdrop on the alarm calls of other species, gaining access to an additional source of information relevant to the presence of danger in the environment. This ability could be the consequence of a learned association between the alarm calls of another species and the presence of the predator, or it could be due to certain auditory properties common to the alarm calls of both species, and innate. More research is required to tease apart these possibilities. However, until recently, it was thought that the ability to identify and react to the alarm calls of other species was only possible in species that already had vocal communication. Several years ago, however, researchers from Princeton University observed this behavior in an unlikely species - a non-vocal reptile - the Galapagos marine iguana (amblyrhynchus cristatus).

Figure 1: The Galapagos Marine Iguana.
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Vitousek MN, Adelman JS, Gregory NC, & Clair JJ. (2007) Heterospecific alarm call recognition in a non-vocal reptile. Biology letters, 3(6), 632-4. PMID: 17911047  

  • August 23, 2010
  • 10:45 AM

Do new neurons go through a critical period and then retire, never to be used again?

by Jason Snyder in Functional Neurogenesis

And here we have the latest, craziest hypothesis of granule cell function. Crazy not because the authors have lost their minds but because the story of the dentate gyrus, where adult neurogenesis occurs, is becoming more peculiar every day. The underlying premise of this paper by Alme et al. (which we will examine later) is [...]... Read more »

Alme, C., Buzzetti, R., Marrone, D., Leutgeb, J., Chawla, M., Schaner, M., Bohanick, J., Khoboko, T., Leutgeb, S., Moser, E.... (2010) Hippocampal granule cells opt for early retirement. Hippocampus. DOI: 10.1002/hipo.20810  

  • August 23, 2010
  • 10:29 AM

The Disparity of Pills

by Rob Mitchum in ScienceLife

A great deal of attention has been paid in recent years to the issue of racial and ethnic health disparities. Statistic after statistic reveals that minorities in the United States, particularly African-American and Hispanic populations, are in poorer health on average compared to American whites. Infant mortality, heart disease, diabetes, obesity, cancer and other maladies [...]... Read more »

  • August 23, 2010
  • 10:12 AM

The dog-human connection in evolution

by gregdowney in Neuroanthropology

Evolutionary theorists have long recognized that the domestication of animals represented a major change in human life, providing not just a close-at-hand food source, but also non-human muscle power and a host of other advantages. Penn State anthropologist Prof. Pat Shipman argues that animal domestication is one manifestation of a larger distinctive trait of our [...]... Read more »

Bleed, Peter. (2006) Living in the human niche. Evolutionary Anthropology: Issues, News, and Reviews, 15(1), 8-10. DOI: 10.1002/evan.20084  

Miklósi A, Kubinyi E, Topál J, Gácsi M, Virányi Z, & Csányi V. (2003) A simple reason for a big difference: wolves do not look back at humans, but dogs do. Current biology : CB, 13(9), 763-6. PMID: 12725735  

Paxton, D. (2000) A Case for a Naturalistic Perspective. Anthrozoos: A Multidisciplinary Journal of The Interactions of People , 13(1), 5-8. DOI: 10.2752/089279300786999996  

Schleidt, Wolfgang M., & Shalter, Michael D. (2003) Co-evolution of Humans and Canids: An Alternative View of Dog Domestication: Homo Homini Lupus?. Evolution and Cognition, 9(1), 57-72. info:/

Shipman, Pat. (2010) The Animal Connection and Human Evolution. Current Anthropology, 51(4), 519-538. DOI: 10.1086/653816  

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