Post List

  • March 22, 2010
  • 02:00 PM

Making a PML map

by Maria Hodges in Wood for the trees

I’ve been to a few conferences recently and I’ve witnessed a divide opening up between the scientists that use high-throughput methods and everybody else. A recent paper on the ‘PML interactome' is a nice example of how assembling the data in one place gives a very good overview of the situation and provides some functional clues too.... Read more »

  • March 22, 2010
  • 12:32 PM

A weight lifted?

by Daniel Simons in The Invisible Gorilla

People are generally bad at estimating the slopes of hills, often overestimating their steepness many times over. The overestimates are even greater when subjects are asked to wear a heavy backpack. The effect of the backpack was thought to be due to an influence of physiology on conscious perception, but a new study by Durgin and colleagues suggests it might result from subjects guessing the purpose of the experiment.... Read more »

Proffitt, D. R. P., Bhalla, M., Gossweiler, R., & Midgett, J. (1995) Perceiving geographical slant. Psychonomic Bulletin , 409-428. info:/

Bhalla M, & Proffitt DR. (1999) Visual-motor recalibration in geographical slant perception. Journal of experimental psychology. Human perception and performance, 25(4), 1076-96. PMID: 10464946  

Durgin, F., Baird, J., Greenburg, M., Russell, R., Shaughnessy, K., & Waymouth, S. (2009) Who is being deceived? The experimental demands of wearing a backpack. Psychonomic Bulletin , 16(5), 964-969. DOI: 10.3758/PBR.16.5.964  

  • March 22, 2010
  • 12:00 PM

Dispatches from Antarctica – Farewell Weddell Sea

by Kevin Zelnio in Deep Sea News

David Honig is a graduate student in marine science at Duke University in the lab of Dr. Cindy Van Dover. He is participating in LARISSA, a 2 month multinational expedition to study the causes and consequences of the ice shelf collapse. He will be posting regular updates on the expedition exclusively for [...]... Read more »

Domack, E., Ishman, S., Leventer, A., Sylva, S., Willmott, V., & Huber, B. (2005) A Chemotrophic Ecosystem Found Beneath Antarctic Ice Shelf. Eos, Transactions American Geophysical Union, 86(29), 269-276. DOI: 10.1029/2005EO290001  

H. Niemann1, D. Fischer, D. Graffe, K. Knittel1, A. Montie, O. Heilmayer, K. Nöthen, T. Pape, S. Kasten, G. Bohrmann.... (2009) Biogeochemistry of a low-activity cold seep in the Larsen B area, western Weddell Sea, Antarctica. Biogeosciences Discussions, 2383-2395. info:other/

  • March 22, 2010
  • 11:15 AM

Reconstructing full-glacial Europe

by Jeremy in Voltage Gate

When Charles Lyell first used the term Pleistocene in 1839 to replace the "long and awkward" use of Newer Pliocene (preceded by, of course, the Older Pliocene), it was done in the interest of streamlining the terminology, but the split of Newer and Older Pliocene was based on the fossil evidence of the time. Lyell designated the split of the Pliocene by recognizing a higher percentage of extant snails and other mollusks found in strata from this Newer Pliocene or, now, Pleistocene period. About ........ Read more »

  • March 22, 2010
  • 11:00 AM

New tool aims to help coral reefs survive climate change

by Rob Goldstein in Conservation Maven

Scientists have developed a practical method for assessing the resilience of coral reefs to climate change and for prioritizing local actions to help reefs survive. Jeff Maynard and fellow scientists tested the method in Keppel Bay of the southern Great Barrier Reef Marine Park and found that it can be a useful tool for conservation planning...... Read more »

  • March 22, 2010
  • 10:49 AM

How do I Describe Thee? Let Me Count the Ways

by Isobel Maciver in Promega Connections

Did you know that the microorganisms living in and on the human body (most on the skin, in the gut, and in the mouth) outnumber all our human cells by a factor of ten? But read on before you grab the hand sanitizer and schedule a colonic, these “germs” may be an integral [...]... Read more »

Fierer, N., Lauber, C., Zhou, N., McDonald, D., Costello, E., & Knight, R. (2010) Forensic identification using skin bacterial communities. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1000162107  

  • March 22, 2010
  • 10:39 AM

Aphids have mutualistic viruses!

by Cheshire in Cheshire

Aphids can be a pain in the ass to gardeners and farmers. Although they look pretty harmless, they’re to plants what mosquitoes are to people and more. They transmit some pretty serious diseases which cause millions of dollars in damage per year. They’re also famous for their fecundity-they’re parthenogenic and their daughters are actually born [...]... Read more »

  • March 22, 2010
  • 10:30 AM

Monday Pets: Is My Dog Playing or Fighting With That Other Dog?

by Jason Goldman in The Thoughtful Animal

Happy Monday. Mondays are usually pretty rough, but now they’re about to become a little bit better for you, dear reader. And that is because I’m now several months into this blogging thing, and since I seem to enjoy it, and some of you seem to enjoy it, I’m going to make an attempt at [...]... Read more »

  • March 22, 2010
  • 10:29 AM

Counselling, Conflict, Men and Abortion

by Ultimo167 in Strong Silent Types

Coyle et al. (2009) discuss how the lack of appropriate preabortion counselling, and conflict over the decision-making process, can lead to distinct psychological symptoms in women, and in men.

... Read more »

  • March 22, 2010
  • 09:30 AM

Aquatic Invasive Species and the Effectiveness of Education and Outreach

by JL in Analyze Everything

Apparently my friends from Notre Dame are continuing to publish at a feverish rate, because I keep stumbling onto their papers.  The latest is by Rothlisberger, Chadderton, McNulty and Lodge, and is all about aquatic invasive species (full cite is below), and I think this paper really throws into question the value of education and outreach.

There are a lot of big questions out there regarding ... Read more »

Rothlisberger, J.D., Chadderton, W.L., McNulty, J., & Lodge, D.M. (2010) Aquatic invasive species transport via trailered boats: What is being moved, who is moving it, and what can be done. American Fisheries Society, 35(3), 121-132. info:/

  • March 22, 2010
  • 09:06 AM

Dominant transposases, becoming famous for your lab mistakes and more, in my Picks of the Week from RB.

by Alejandro Montenegro-Montero in MolBio Research Highlights

Another week has gone by and some very interesting molbio blog posts have been aggregated to Every week [see my opening post on the matter], I'll select some blog posts I consider particularly interesting in the field of molecular biology [see here to get a sense of the criteria that will be used], briefly describe them and list them here for you to check out.Note that I'm ... Read more »

Christodoulou, F., Raible, F., Tomer, R., Simakov, O., Trachana, K., Klaus, S., Snyman, H., Hannon, G., Bork, P., & Arendt, D. (2010) Ancient animal microRNAs and the evolution of tissue identity. Nature, 463(7284), 1084-1088. DOI: 10.1038/nature08744  

  • March 22, 2010
  • 08:58 AM

Branch Lengths and Species

by Bob O'Hara in Deep Thoughts and Silliness

Some creationists have become terribly excited by a recent paper and accompanying New Scientist article It'll come as no surprised that they have failed to understand the paper, and I'm confident that explaining the paper in a post won't...... Read more »

  • March 22, 2010
  • 08:30 AM

Responding to Anti-vaccine Misinformation: Understanding the Issues

by Scott in Science-Based Pharmacy

Pharmacists pride themselves as being the most accessible health professionals. In community pharmacy settings, pharmacists speak with hundred of patients per day, and are available (free, and without an appointment) for quick consultations. Building good relationships is a rewarding part of being a pharmacist, and the level of trust that can develop supports open dialogue [...]... Read more »

  • March 22, 2010
  • 08:00 AM

Beware, predator, I have ink!

by Zen Faulkes in NeuroDojo

If you were a predator trying to design the perfect food source, you’d probably want something that was slow moving, reasonably large, and had no annoying hard bits that you couldn’t really eat. In other words, it would probably looks something like a nudibranch mollusk. Nudibranchs are also known as sea slugs or sea hares, and at first glance, they look like snack packs for predators.

Of course, nudibranchs don’t take this lightly. Rather than physical defenses, they put up chemical ones........ Read more »

  • March 22, 2010
  • 07:52 AM

Adaptation and Anthropoid origins

by zinjanthropus in A Primate of Modern Aspect

Blythe Williams, Richard Kay, and Christopher Kirk have published a new article in the PNAS which does a very nice job in synthesizing some new fossils and new genetic data with current hypotheses for the origins of anthropoids, the group which includes old world monkeys (catarrhines), new world monkeys (platyrrhines) and apes (hominoids).
One of the [...]... Read more »

Williams, B., Kay, R., & Kirk, E. (2010) New perspectives on anthropoid origins. Proceedings of the National Academy of Sciences, 107(11), 4797-4804. DOI: 10.1073/pnas.0908320107  

  • March 22, 2010
  • 06:00 AM

News reports on cancer don’t give the full story

by Helen Jaques in In Sickness and In Health

Cancer stories seem to make the news on a daily basis.  For example, just today in the UK there are stories about a gene that could predispose non-smokers to lung cancer, how infertile men are at raised risk of prostate cancer, and how testing for the HPV virus during cervical screening doesn’t help pick up [...]... Read more »

  • March 22, 2010
  • 04:13 AM

The sight of their own blood is important to some people who self-harm

by BPS Research Digest in BPS Research Digest

The sight of their own blood plays a key role in the comfort that some non-suicidal people find in deliberately cutting themselves. That's according to a new study by Catherine Glenn and David Klonsky that suggests it is those self-harmers who have more serious psychological problems who are more likely to say the sight of blood is important.There are plenty of anecdotal reports hinting at the importance of the sight and taste of blood to self-harmers, as well as references in popular music. 'Ye........ Read more »

  • March 22, 2010
  • 03:01 AM

A Bayesian Brain is a Freudian Brain

by The Neurocritic in The Neurocritic

Anna O.'s Default Mode. Anna O. is the famous patient whose case was included in Studies on Hysteria by Josef Breuer and Sigmund Freud. Midsagittal brain image (PALS cortical surface atlas, Van Essen 2005) shows resting state functional connectivity in three cortical networks: (i) dorsal attention system (DAS, blue); (ii) the salience system (light green); and (iii) the default mode network (orange). [Taken from Fig. 2 of Carhart-Harris & Friston 2010. Justin Vincent and Randy Buckner are ........ Read more »

  • March 21, 2010
  • 10:29 PM

What the @$#! is wrong with carbon budgets?

by Dr. M in Deep Sea News

[Note the following post makes gratuitous use of keyboard symbols to denote adult language]
In the coolest titled paper ever “Assessing the apparent imbalance between geochemical and biochemical indicators of meso- and bathypelagic biological activity: What the @$! is wrong with present calculations of carbon budgets?” with the world’s coolest handling editor, Burd et al tackle one of the [...]... Read more »

  • March 21, 2010
  • 05:12 PM

Cancer and the media

by Martin Fenner in Gobbledygook @ Nature Network

Last Tuesday the Archives of Internal Medicine released a study that anayzed the news reporting about cancer in 8 large-readership newspapers and 5 national magazines in the United States. The authors identified 2228 cancer-focused articles published between 2005-2007 and...... Read more »

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