Post List

  • June 17, 2011
  • 10:34 PM

Seven new species of Philippine forest mice (Genus: Apomys) discovered

by nath in Imprints of Philippine Science

In early 2000, a team of Filipino and American scientists headed by L.R. Heaney conducted a comprehensive survey of Luzon mammals. Recently, they presented seven new species in the genus Apomys which were identifed from this expedition. They also proposed a new subgenus Megapomys based on the morphological and DNA data of the 10 already known species and the 7 new ones.... Read more »

Heaney, L., Balete, D., Rickart, E., Alviola, P., Duya, M., Duya, M., Veluz, M., VandeVrede, L., & Steppan, S. (2011) Chapter 1: Seven New Species and a New Subgenus of Forest Mice (Rodentia: Muridae: Apomys) from Luzon Island. Fieldiana Life and Earth Sciences, 1-60. DOI: 10.3158/2158-5520-2.1.1  

  • June 17, 2011
  • 06:47 PM

Nociception and pain in fish, a tough question part I

by David Lagman in Fish addict...

This thursday the Swedish Centre for Animal Welfare (SCAW) at the Swedish University of Agricultural Sciences published a report dealing with wether or not fish can feel pain and if they can suffer. This is getting more and more relevant as more people become aware of what they eat and do not want to cause unnecessary suffering to the animal being put on the dinner table. In a few blog post starting from this i will discuss the different articles cited in this report about fish welfare. Sadly its only available in swedish but if you know swedish heres the link: authors of the report discuss several reviews and articles some of them giving contradictory conclusions in this question. Nociceptors seem to be present in some invertebrates and most if not all vertebrates. They are important instruments in sensing and reacting to various harmful stimuli. Pain on the other hand is the "feeling" we often refer to in our daily life. The feeling of pain is processed in the neocortex in humans. Fish which lacks the layered cortex present in mammals are according to some researchers not able to have the "feeling" of pain. This would mean that they would just react to a painful stimuli and not learn to avoid it since it would be more of a reflex response rather than a response that have been processed in the higher brain centers. Is this the case for fish, do they only react by a reflex to a harmful stimuli or do they process such stimuli in the brain and perceive the feeling of pain? The authors of the report give several examples of different studies on this and one of them caught my attention. This was a study done by Dunlop & Laming in 2005 showing an activation of several brain areas including telencephalon in both goldfish and rainbow trout as response to given mechanoceptive and nociceptive stimuli. One of the criteria for determining if a animal feel pain is the presence of receptor cells that link to forebrain areas, a criteria which would be fulfilled if their results is correct. To investigate wether or not the nociceptive cells link to forebrain areas of these two species they removed the bone covering the top of the skull on the fish and inserted electrodes in the spinal cord, cerebellum, tectum and telencephalon. Then they gave both mechanoceptive and nociceptive stimuli on the sides of the fish. They recorded responses in all brain areas included to both types of stimuli. In goldfish the nociceptive stimuli yielded a larger response than the mechanoceptive stimuli in the brain while they did not differ in the rainbow trout.What their study show is that the response to nociceptive stimuli in these fish are not based solely on reflexes alone since the forebrain, not only the spinal cord, is activated upon stimulation. In telencephalon some of the structures suggested to be homologous to hippocampus and amygdala of tetrapod brains are located, which would imply a processing of these stimuli in the brain to in the future avoid these harmful experiences. Other studies have shown that fish seem to remember and do not bite a fishing hook a second time other than if it is food deprived. Then it might be the only way for the fish to find food at the moment and they have to bite the hook a second or third time. Taken together this data would suggest at least that fish are somewhat able to "feel" pain and remember it to avoid being in this situation in the future.In my next blog post I will continue to discuss fish welfare, and focus a bit of stress and how that affect fish during sport fishing. References:Dunlop R, & Laming P (2005). Mechanoreceptive and nociceptive responses in the central nervous system of goldfish (Carassius auratus) and trout (Oncorhynchus mykiss). The journal of pain : official journal of the American Pain Society, 6 (9), 561-8 PMID: 16139775... Read more »

  • June 17, 2011
  • 05:28 PM

EP Therapy: Foraging Camp for Autistics

by Cris Campbell in Genealogy of Religion

Everyone knows the experience: you happen upon a wreck and know you shouldn’t look but can’t help it. You know there is a chance of seeing something you don’t want to see and which may haunt you, but you look regardless. There should be a word for this and in the absence of one, I [...]... Read more »

Reser, Jared E. (2011) Conceptualizing the Autism Spectrum in Terms of Natural Selection and Behavioral Ecology: The Solitary Forager Hypothesis. Evolutionary Psychology, 9(2), 207-238. info:/

  • June 17, 2011
  • 05:03 PM

Where does your empathy come from?

by eHarmony Labs in eHarmony Labs Blog

Do you ever get to the point where you feel as though you and your partner have absolutely nothing in common? Read further to find out the one common thread that lies in almost all of us. ... Read more »

Ramachandran, V. S. . (2001) Synaesthesia - a window into perception, thought and language. Journal of Consciousness Studies, 3-34. info:/

  • June 17, 2011
  • 04:03 PM

Fast Calculation of van der Waals Volume as a Sum of Atomic and Bond Contributions

by egonw in Chem-bla-ics

I was recently asked about a volume descriptor in Bioclipse, which is not yet available. Jmol can calculate surfaces, so that was my first thought. However, I then ran into a paper from 2003 by Zhao, called Fast Calculation of van der Waals Volume as a Sum of Atomic and Bond Contributions and Its Application to Drug Compounds (doi:10.1021/jo034808o).

The paper presents a very simple mathematical model, which approximates the molecular volume by a sum of atomic contributions, and a three terms to correct for atom-atom overlap, via the number of bonds, and corrections based on the number or aromatic and non-aromatic rings. The paper is clearly written, and the mathematics simple.

One problem with the publication though, are the numbers in the main text. They are wrong. I started of using the coefficients of the equations presented in the paper, but very soon ran into problems when I was writing up unit tests based on the volumes for compounds given as examples. In fact, the numbers in the main text are internally inconsistent. Not good. I believe it is partly caused by rounding, but that does not correct for the differences fully.

Fortunately, the Excel sheet in the supplementary information has the exact numbers, and those are numerically consistent.

The paper has been cited 46 times now, so, a fast volume descriptor seems relevant indeed. I am not sure how fast it will propagate to Bioclipse, as I do not have time soon to update the CDK version of Bioclipse (the major part of which is to ensure the Bioclipse-JChemPaint editor does not get broken, again).

Another thought about this paper, is that it is using the evil aromaticity concept, where the authors forgot to mention when they consider a ring to be aromatic.

Zhao, Y., Abraham, M., & Zissimos, A. (2003). Fast Calculation of van der Waals Volume as a Sum of Atomic and Bond Contributions and Its Application to Drug Compounds The Journal of Organic Chemistry, 68 (19), 7368-7373 DOI: 10.1021/jo034808o... Read more »

  • June 17, 2011
  • 02:01 PM

Dogs Defeat DNA

by Elizabeth Preston in Inkfish

Planning on committing a crime anytime soon? You'd better be careful not to leave your DNA behind. If crime scene investigators can collect any hair, skin cells, blood, or other bits of you from the crime scene, they'll have a pretty convincing case against you once you're in custody. Unless, of course, you have an identical twin. If that's the case, commit all the crimes you want, because there is absolutely no way for scientists to tell the difference between your DNA and your twin's.According to a new study from the Czech Republic, though, a dog can do one better than a DNA technician. A group of trained German shepherds were able to reliably tell apart the scents of identical twins.The study used four sets of twins, two identical and two non-identical. The identical twins were 5 and 7 years old, and the others were 8 and 13. The researchers used children because they wanted to give the dogs the greatest challenge possible: telling apart two people with identical genes who live in the same environment and eat the same food. As twins get older and develop different eating habits, move into different homes, and perhaps face different health problems, their personal scents will presumably grow apart. But identical twin children are just about as similar as two humans can get.The German shepherds were police dogs trained in scent matching. This is a forensic technique used in a few European countries such as Russia, Poland, and Denmark, but not used in the United States. A dog is given a scent sample from the crime scene to sniff. Then the dog is led to a scent line-up: a row of seven identical glass jars, each holding a piece of cotton. The dog sniffs every jar, and if it finds one that matches the crime scene scent, it alerts its handler by lying down next to that jar.Ten dogs participated in the study. Each trial was like the normal scent line-ups the dogs were used to. A dog sniffed a piece of cotton, then checked for a match among seven possibilities. Every dog consistently matched the humans to their scents, regardless of whether the human was an identical twin. If a dog sniffed Twin A and Twin A was in the lineup, the dog chose that jar. But if a dog sniffed Twin A and only Twin B was in the lineup, it walked right past. They never made a mistake.(In case you're wondering how scientists bottle a person's smell, the answer is: belly skin. The kids held scent-absorbing cotton pads against their bellies for 20 minutes to create a kind of smell swatch.)In earlier studies, researchers had found that dogs have trouble smelling the difference between identical twins. The dogs in this study succeeded because they've been highly trained by the police. It's not an easy task--and that means our genes must have a lot of responsibility for our personal scents. The differences in the children's scents must have come from very small variations in their lifestyles. Maybe one twin has a greater preference for peanut butter, or one twin likes to exercise more and has a different metabolism.Not much is known about why people smell the way they do. It would be interesting to see a follow-up study using a larger group of twins at different ages. Do three-year-old twins smell different? Do some ten-year-old twins smell exactly the same? Is there any way for newborn twins to not smell identical? If we weak-nosed humans had a better understanding of the scents that come from our bodies, it might give us new tools for medical diagnoses. (Here, for example, is a story about a woman who detected her husband's hidden disease based on a change in how his breath smelled.)In this country, perhaps we should consider giving dogs a larger role in forensic investigations. As long as identical-twin criminals don't strike, DNA is still a reliable and (usually) convincing form of evidence. But it's easy for us to forget that other animals have access to a whole layer of information we can't begin to decode.Ludvík Pinc (2011). Dogs Discriminate Identical Twins PLoS ONE : 10.1371/journal.pone.0020704... Read more »

Ludvík Pinc. (2011) Dogs Discriminate Identical Twins. PLoS ONE. info:/10.1371/journal.pone.0020704

  • June 17, 2011
  • 01:43 PM

Friday Feedback Favourites

by pennydeck in Feedback Solutions for Obesity

Each Friday, I share a collection of stories, research, or other news and notes related to the role of feedback in complex systems that catch my attention during the previous week. Most of these I share on twitter when I … Continue reading →... Read more »

  • June 17, 2011
  • 11:55 AM

Smelly Hangups for Mosquitoes... and Bedbugs?

by Nature Education in Student Voices

It works against mosquitoes... can it work against bedbugs? A study in Nat...... Read more »

Turner SL, Li N, Guda T, Githure J, Cardé RT, & Ray A. (2011) Ultra-prolonged activation of CO2-sensing neurons disorients mosquitoes. Nature, 474(7349), 87-91. PMID: 21637258  

  • June 17, 2011
  • 10:57 AM

Smelly Hangups for Mosquitoes... and Bedbugs?

by Paige Brown in From The Lab Bench

A study in Nature this month reveals a promising new line of defense against disease-carrying, bloodthirsty critters, namely the mosquito. The new line of defense is based on smelly chemicals, or inhibitory odorants, that disrupt the mosquito's ability to detect and travel towards human breath. Mosquitoes, as well as other blood-feeding insects, are attracted towards the carbon dioxide that we exhale with every breathe cycle (oxygen in, carbon dioxide out).... Read more »

Turner SL, Li N, Guda T, Githure J, Cardé RT, & Ray A. (2011) Ultra-prolonged activation of CO2-sensing neurons disorients mosquitoes. Nature, 474(7349), 87-91. PMID: 21637258  

  • June 17, 2011
  • 10:56 AM

Peloroplites: That’s One Big Ankylosaur

by Brian Switek in Dinosaur Tracking

The "monstrous heavy one" was stout, armored and may have supported huge spikes on its neck and shoulders... Read more »

  • June 17, 2011
  • 10:53 AM

FGFR1 mutations in squamous cell lung cancer

by Sally Church in Pharma Strategy Blog

“Using SNP array analysis, we found that a region of chromosome segment 8p11-12 containing three genes–WHSC1L1, LETM2, and FGFR1–is amplified in 3% of lung adenocarcinomas and 21% of squamous cell lung carcinomas.” Dutt et al., (2011) This snippet from a … Continue reading →
... Read more »

Dutt A, Ramos AH, Hammerman PS, Mermel C, Cho J, Sharifnia T, Chande A, Tanaka KE, Stransky N, Greulich H.... (2011) Inhibitor-Sensitive FGFR1 Amplification in Human Non-Small Cell Lung Cancer. PloS one, 6(6). PMID: 21666749  

  • June 17, 2011
  • 09:04 AM

The Ants Came Marching: Did Periods of Arctic Warming Help Giant Ants Migrate?

by Kelly Grooms in Promega Connections

I guess you could say that I have been programmed to notice giant creepy crawly things. Starting when my son brought home a book about “Real Life Monsters”, my family has not been able to stop talking about one of the book’s featured monsters, the Goliath Bird Eater spider. While the book’s other stars, the [...]... Read more »

  • June 17, 2011
  • 09:00 AM

Summer of the pill: why do we menstruate?

by Kate Clancy in Context & Variation

The first in a series on hormonal contraception. This post explores why human women menstruate and how that may impact their contraceptive decisions.... Read more »

  • June 17, 2011
  • 08:30 AM

Discovering my promiscuous past

by Maria Delaney in Science Calling

My dad knows nothing about our ancestors so I thought some family history would be perfect for a father’s day present. After a quick scan of genealogy sites I discovered that according to folklore the Ó Dálaigh (Daly) clan were descendents of the 5th century warlord Niall of the Nine Hostages. This meant they were part of the Úi Néill (descendents of Niall), a lineage of high kings of Ireland. An excellent start to my quest but being more interested in science than trailing through the archives, I turned to genetics.... Read more »

Moore, L., McEvoy, B., Cape, E., Simms, K., & Bradley, D. (2006) A Y-Chromosome Signature of Hegemony in Gaelic Ireland. The American Journal of Human Genetics, 78(2), 334-338. DOI: 10.1086/500055  

Forstmeier W, Martin K, Bolund E, Schielzeth H, & Kempenaers B. (2011) Female extrapair mating behavior can evolve via indirect selection on males. Proceedings of the National Academy of Sciences of the United States of America, 108(26), 10608-13. PMID: 21670288  

  • June 17, 2011
  • 08:00 AM

Brain Growth in Autism

by Shaheen Lakhan in Brain Blogger

Brain overgrowth has been noted among children with autism spectrum disorder (ASD). Now, a new imaging study suggests that the accelerated brain growth appears before 2 years of life, offering new avenues for early identification and intervention of ASD. Investigators conducted a longitudinal magnetic resonance imaging (MRI) study of 59 children with ASD and 38 [...]... Read more »

Courchesne E, Carper R, & Akshoomoff N. (2003) Evidence of brain overgrowth in the first year of life in autism. JAMA : the journal of the American Medical Association, 290(3), 337-44. PMID: 12865374  

Courchesne E, Redcay E, & Kennedy DP. (2004) The autistic brain: birth through adulthood. Current opinion in neurology, 17(4), 489-96. PMID: 15247547  

Hazlett HC, Poe MD, Gerig G, Styner M, Chappell C, Smith RG, Vachet C, & Piven J. (2011) Early brain overgrowth in autism associated with an increase in cortical surface area before age 2 years. Archives of general psychiatry, 68(5), 467-76. PMID: 21536976  

  • June 17, 2011
  • 07:40 AM

Why Click Beetles Cannot Control Their Landing Orientation

by Michael Long in Phased

Physics calculations lend support to the idea that click beetles evolved their jumping mechanism for righting themselves after landing on their back, rather than as a predation escape mechanism.... Read more »

Gal Ribak, & Daniel Weihs. (2011) Jumping without Using Legs: The Jump of the Click-Beetles (Elateridae) Is Morphologically Constrained. PLoS ONE, 6(6). info:/10.1371/journal.pone.0020871

  • June 17, 2011
  • 07:02 AM

Pretrial publicity & jury deliberations

by Doug Keene in The Jury Room

There was much discussion when the Supreme Court decided Jeffrey Skilling had gotten a fair trial despite extreme pre-trial publicity. The letter published in the Orlando Sentinel from a dismissed Casey Anthony trial juror raises the issue again. I was one of the 50 potential jurors excused from service on the Casey Anthony trial today because [...]

Related posts:Educating Jurors: How NOT to start deliberations
Deliberations & the role of the presiding juror
Simple Jury Persuasion: Countering jury decision-making biases
... Read more »

Ruva, CL, & LeVasseur, MA. (2011) Behind closed doors: The effect of pretrial publicity on jury deliberations. . Psychology, Crime . info:/

  • June 17, 2011
  • 06:51 AM

Conference summaries

by Joana Guedes in BHD Research Blog

In April, a previous blog post summarised the various conferences we had attended, and how the data presented could be applied to BHD research. More recently, we have reviewed the scientific content and the patient and family sessions of the … Continue reading →... Read more »

  • June 17, 2011
  • 06:30 AM

A window on protein-carbohydrate interactions

by Becky in It Takes 30

It is a truth universally acknowledged that a single new method, especially one relevant to an area that has hitherto been resistant to study, often opens up enormous possibilities for increased understanding.  And yet, new methods often don’t get the publicity they deserve.  Possibly this is because a good new method, like a good new [...]... Read more »

Rogers CJ, Clark PM, Tully SE, Abrol R, Garcia KC, Goddard WA 3rd, & Hsieh-Wilson LC. (2011) Elucidating glycosaminoglycan-protein-protein interactions using carbohydrate microarray and computational approaches. Proceedings of the National Academy of Sciences of the United States of America, 108(24), 9747-52. PMID: 21628576  

  • June 17, 2011
  • 04:31 AM

Good news and bad for a popular willpower-enhancing strategy

by BPS Research Digest in BPS Research Digest

In rich countries, temptation is never far and many of us struggle to achieve our long-term aims of moderation, dedication and fidelity. An increasingly popular strategy for regaining control is to form so-called implementation intentions. Rather than having the vague goal to eat less or exercise more, you spell out when, where and how you will perform a given activity, and rehearse that thought regularly. For example, "when in the cafeteria at lunch I will buy orange juice rather than cola". A more specific variant is to form an 'if-then' plan, as in "if it is a Tuesday morning, then I will go for a run," and again, this is rehearsed mentally on a regular basis.

Past research has found these plans to be successful, helping people to live more healthily. There's even evidence that they are particularly beneficial to those who have had their willpower compromised by brain damage or by taxing laboratory tasks. Two new studies add to this literature, one of them cautionary, the other more hopeful.

Sue Churchill and Donna Jessop studied 323 students tasked with eating more fruit and vegetables. They found that implementation intentions helped students achieve this task over a 7-day period, but only if they scored low on a measure of "urgency", as revealed by their agreement or not with statements like "When I am upset, I often act without thinking." The researchers said this suggests implementation intentions may not be a panacea: "Ironically, people who possess poor self-regulatory skills insofar as they tend to act on impulse when distressed, who are arguably most in need of assistance in achieving their goals, may benefit least from behaviour change interventions based on implementation intention formation."

Why the contradiction with earlier research showing implementation intentions are most helpful to those with compromised willpower? Churchill and Jessop can't be sure, but they said one possibility could be because their task of eating more fruit and veg is more complex than some of the lab tasks studied previously.

That's the cautionary news. The good news comes from a study by Barbel Knauper and her colleagues who found that using mental imagery boosted the benefit of implementation intentions for students attempting to increase their fruit consumption over seven days. Rather than merely forming an if-then plan, such as "If I see orange juice at lunch, then I will buy it", they also imagined themselves performing this act, with as much sensory detail as possible. A promising result, and the researchers expressed their surprised that no-one had thought to investigate the combination of these two strategies before.

Here's a curious observation across both studies. Knauper's team failed to find the usual benefit of forming simple implementation intentions (without the addition of mental imagery) and her team said one possible explanation for this was the simplicity of their task of eating more fruit. Recall that Churchill and Jessop thought the same task (admittedly, also including vegetables) was relatively complicated compared with tasks used in earlier research. It just shows how much room there is for interpretation.

Both studies suffered from a reliance on retrospective self-report - the students told the researchers whether they'd managed to eat more fruit and veg or not over the preceding week. They also had short study durations - we need our newfound healthy habits to last longer than a week. But together the studies point to some interesting avenues for future research. Perhaps implementation intentions plus imagery will prove to be effective for people who have particularly weak willpower?

S Churchill, and D Jessop (2011). Too impulsive for implementation intentions? Evidence that impulsivity moderates the effectiveness of an implementation intention intervention. Psychology and Health DOI: 10.1080/08870441003611536

B Knauper, A McCollam, A Rosen-Brown, J Lacaille, E Kelso, and M Roseman (2011). Fruitful plans: Adding targeted mental imagery to implementation intentions increases fruit consumption. Psychology and Health DOI: 10.1080/08870441003

This post was written by Christian Jarrett for the BPS Research Digest.

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