February 11, 2015

3:53 PM | New in G3: Malaria, scoliosis, and a Mexican tetra map
  The new issue of G3 features Asian malarial mosquito control, familial idiopathic scoliosis, and a high-res genetic map for the Mexican tetra. Check out the Table of Contents below! Investigations Maternal Germline-Specific Genes in the Asian Malaria Mosquito Anopheles … Read MoreThe post New in G3: Malaria, scoliosis, and a Mexican tetra map appeared first on Genes to Genomes.
1:00 PM | Thinking Skinny Thoughts Won’t Help
Biology concepts – undulipodia, primary cilia, chemosensing, obesity, depression, hydrocephalus, lithiumWinston Churchill once said that men occasionally stumble on the truth, but most people pick themselves up and carry on as if nothing had happened. Gregor Mendel was Augustinian monk who really joined the order because they would allow him to study and learn for the rest of his life. Sounds like the gig I would enjoy. Since he was a monk, do you think he got angry that his discoveries […]

Tong, C., Han, Y., Shah, J., Obernier, K., Guinto, C. & Alvarez-Buylla, A. (2014). Primary cilia are required in a unique subpopulation of neural progenitors, Proceedings of the National Academy of Sciences, 111 (34) 12438-12443. DOI: 10.1073/pnas.1321425111

Han, Y., Kang, G., Byun, K., Ko, H., Kim, J., Shin, M., Kim, H., Gil, S., Yu, J., Lee, B. & Kim, M. (2014). Leptin-promoted cilia assembly is critical for normal energy balance, Journal of Clinical Investigation, 124 (5) 2193-2197. DOI: 10.1172/JCI69395

Davenport JR, Watts AJ, Roper VC, Croyle MJ, van Groen T, Wyss JM, Nagy TR, Kesterson RA & Yoder BK (2007). Disruption of intraflagellar transport in adult mice leads to obesity and slow-onset cystic kidney disease., Current biology : CB, 17 (18) 1586-94. PMID:

Keryer, G., Pineda, J., Liot, G., Kim, J., Dietrich, P., Benstaali, C., Smith, K., Cordelières, F., Spassky, N., Ferrante, R. & Dragatsis, I. (2011). Ciliogenesis is regulated by a huntingtin-HAP1-PCM1 pathway and is altered in Huntington disease, Journal of Clinical Investigation, 121 (11) 4372-4382. DOI: 10.1172/JCI57552

Miyoshi, K., Kasahara, K., Miyazaki, I. & Asanuma, M. (2009). Lithium treatment elongates primary cilia in the mouse brain and in cultured cells, Biochemical and Biophysical Research Communications, 388 (4) 757-762. DOI: 10.1016/j.bbrc.2009.08.099

8:00 AM | Charts that don’t seem quite right – organ donation edition
Organ donation rates are an often used example of the power of defaults. Take the following passage by Dan Ariely, explaining this (also often used) chart from Johnson and Goldstein (2003) (ungated pdf): One of my favorite graphs in all of social science is the following plot from an inspiring paper by Eric Johnson and Daniel Goldstein. This […]
2:36 AM | Biological Warfare: Parasitic Wasp Uses A Virus To Control Its Host
Any depth of understanding of biology and ecology is accompanied by this inevitable conclusion: parasites rule the world. They're the "man behind the curtain" as fans of Oz would put it. They are the directors and stage managers of the grand production that is life on this Earth, nature's finest puppeteers, and that we think we have any modicum of control over any species' physiology in comparison (including our own) is downright laughable. The latest reminder of our inadequacy when it […]
12:41 AM | Brian J. Ford’s Aquatic Dinosaurs, 2014 Edition
Via bizarre and unexpected circumstances I recently* found myself secretly and furtively attending a lecture by Brian J. Ford. Ford is a British author and researcher who dabbles widely in matters of... -- Read more on

February 10, 2015

9:54 PM | One last thing (2015)
That’s a rainbow unicorn. And some lollipops. Hello, lovely readers. This isn’t a proper post, as I am, after several promises to the effect, winding the blog down. Not because I’ve given up - more because I’ve run out of stories to tell, and because the new posts were taking ages to research and write, and weren’t […]
9:31 PM | Harry Smith, the founder of Molecular Ecology, has died
We’ve received word that Harry Smith, the founder of Molecular Ecology, passed away yesterday. Smith had a prolific and well-regarded career studying the molecular basis of plants’ responses to their environments. In particular, he helped to demonstrate how plants perceive … Continue reading →
3:24 PM | How to Get Into Graduate School
I am often asked by undergraduate students for advice about how to get into graduate school. In the continuing spirit of recent “how to” posts on this blog (listed at the end of this post), it seems timely to collect these thoughts in one place. I will start with the obvious stuff, where I nevertheless hope to provide some novel insights, and I will then move to the less obvious, but perhaps just as important, ideas.1. GradesLet’s get this obvious one out of the way first. […]
12:36 PM | THREAT DOWN! Gene flow from polar bears into brown bears
What do you get when you cross a male polar bear with a female brown bear? Trick question: Nothing, because it doesn’t really happen!* But seriously, folks. A new Molecular Ecology study from James Cahill, Ed Green, and Beth Shapiro … Continue reading →
2:57 AM | How Parents’ Ideologies Affect Children
First, this is not a psychological study. It’s fr […]

February 09, 2015

9:40 PM | Erotic garden in northern Thailand
Sorry TPP missed this erotic garden on his last visit to Thailand, but it's newly opened. Not sure this is quite TPP's cup of tea, but it does have a tea house. To be sure, this is not the first place featuring numerous phalli that TPP has visited; one temple in southern India had thousands. That the owner of the garden looks like a very nice lady only demonstrates how differently different cultures perceive such imagery. In the USA you'd probably get arrested for […]
8:58 PM | Breaking free of the guide tree: two new species delimitation methods
A couple of weeks ago I wrote about a new method to incorporate morphology and DNA sequences into species delimitation. Including both data types improved the results but a couple of tricky spots remained: 1) correctly assigning individuals to putative species and 2) estimating … Continue reading →
6:30 PM | Slime mould and researcher set to play piano duet
SUMMARY: A single-celled organism will perform a piano duet with a computer musician at Plymouth University on 1 March 2015. The public is invited. A scientist and a single-celled organism will perform a piano duet at Biomusic, the 10th Peninsula Arts Contemporary Music Festival. Professor of Computer Music, Eduardo Miranda, and a slime mould will premiere Professor Miranda’s new composition, Biocomputer Music, on a musical bio-computer that he and his team designed. Professor Miranda is […]

Nakagaki T., Yamada H. & Tóth Á. (2000). Intelligence: Maze-solving by an amoeboid organism, Nature, 407 (470) DOI: 10.1038/35035159

Saigusa T., Toshiyuki Nakagaki & Yoshiki Kuramoto (2008). Amoebae Anticipate Periodic Events, Physical Review Letters, 100 (1) DOI:

Miranda E.R., Adamatzky A. & Jones J. (2011). Sounds Synthesis with Slime Mould of Physarum polycephalum, Journal of Bionic Engineering, 8 107-113. arXiv:

5:59 PM | Slime mould and researcher set to play piano duet | @GrrlScientist
A single-celled organism will perform a piano duet with a computer musician at Plymouth University on 1 March 2015. The public is invited.A scientist and a single-celled organism will perform a piano duet at Biomusic, the 10th Peninsula Arts Contemporary Music Festival. Professor of Computer Music, Eduardo Miranda, and a slime mould will premiere Professor Miranda’s new composition, Biocomputer Music, on a musical bio-computer that he and his team designed.Professor Miranda is Head of the […]
5:29 PM | Sciencespeak: Cricoarytenoideus
American alligators are chatty reptiles. They start out their lives chirping for their mother’s help as they push …
3:58 PM | Lincolnland's science deniers in Congress
Actually Lincolnland only has 5 hard-core science deniers, and all things considered that ain't bad, but sadly, disturbingly, one of them represents TPP's district.  And somehow having elected "leaders" who prefer Biblical prophecy to science when it comes to making policy is something TPP does not find comforting at all. Here they are, complete with quotes, thanks to Bill Moyers.  Go to that link and look up your own state, readers, and for my foreign readers, just snicker away […]
3:52 PM | Duelling Genitals
Although chastity belts are a fixture of the popular conception of medieval Eu...
3:46 PM | Another "Yet another mostly male meeting (YAMMM)" from BGI
Well just saw an announcement for this meeting on Twitter: The First Announcement of The Tenth Annual Meeting of the International Conference on Genomics (ICGAnd I hoped beyond hope that they would have a decent representation of women speakers at the meeting.  Why did I hope this?  Well, in the past, BGI run meetings have had incredibly skewed gender ratios of speakers.  See this post for a discussion of their past record: Kudos to the DOE-JGI for organizing a genomics […]
1:00 PM | National Darwin Day? (Yes, please.)
Charles Darwin is great, isn’t he? I mean – he discovered the theory of natural selection and by doing so, created an eloquently beautiful framework for studying and understanding the living world around us. He wrote On the Origin of Species (free text here!). He drew this: Every year on February 12 (Darwin’s birthday), evolution […]
12:28 PM | Birdbooker Report 353-9
SUMMARY: Books, books, beautiful books! This is a list of biology, ecology, environment, natural history and animal books that are (or will soon be) available to occupy your bookshelves and your thoughts. “Words in leather and wood”. Bookshelves in the “Long Room” at the old Trinity College Library in Dublin. Image: Nic McPhee from Morris, MN, USA. 2007. (Creative Commons.) Books to the ceiling, Books to the sky, My pile of books is a mile high. How I love them!... Read […]
8:43 AM | New “Problem of the Week” Posted
The third problem of the week is now up at the big website. I’ve also posted the official solution to Problem Two. So go have a look and let me know what you think. Feel free to present solutions in the comments. Unless, of course, you just want to pick micronits with the problem statement.…
8:37 AM | Darwin Day Approaches!
I will be in Baltimore at the end of week to give a couple of talks in honor of Darwin Day. On Thursday, February 12, I will be speaking to the Baltimore Ethical Society. Pot luck dinner at 6:30 pm, with the talk beginning at 7:30. I will give a talk entitled Among the Creationists;…
8:00 AM | The death of defaults?
Late last year I went to a presentation by Schlomo Benartzi on how people think differently when they are using a screen. The punchline was that many of the classic behavioural biases do not play out as expected in digital mediums. (Benartzi has a book on this topic, co-authored with Jonah Lehrer, coming out later this year.) […]

February 08, 2015

10:35 PM | Sunday Chess Problem
It’s time to take a break from helpmates and return to selfmates. This week’s problem was composed by Andrey Selivanov in 2014. The stipulation is selfmate in three: Recall that in a selfmate, white plays first and forces black to give checkmate in no more than the stipulated number of moves. Black, for his part,…
8:24 PM | Mid-winter garden status report
So far the winter of 2014-2015 has been fairly mild.  Some unseasonal cold during the late fall to winter transition. Some snow, but nothing unusual. A night or two of deep cold, around 0 F, but not prolonged or severe cold. And now following some a couple of modest snow events, a mid-winter thaw. This provided an opportunity to have a look around at the gardens, an inspection of sorts. There be lots of limbs and twigs to pick up, the result of having had a couple of fairly wet, heavy […]
4:50 PM | And the Little Child Will Lead Them: Has an 8 Year-Old Girl Discovered a Treatment for Cancer?
There are times in Medicine when an idea seems so simple, so obvious, that it couldn’t possibly work. Except when it does. Husband and wife cancer research team, Drs. Michael […]
2:27 PM | Strong AI, utilitarianism and our limited minds
There is a fascinating discussion happening across a few of my favourite blogs, it is about the moral implications of the hypothetical emergence of strong artificial intelligence: should we grant rights to sentient machines? How will we ever be able…Read more ›
10:36 AM | You Should Know: Dr J Marshall Shepherd, host of the The WxGeeks Show
Welcome to the twenty-second installment of You Should Know, where I give my own #ScholarSunday salute to Science Bloggers and the Blogs you may not yet know about. Introducing…Dr. J. Marshall... -- Read more on

February 07, 2015

10:40 PM | New Books on Dinosaurs 1: Matthew P. Martyniuk’s Beasts of Antiquity: Stem-Birds in the Solnhofen Limestone
Recent months have seen the publication of several new dinosaur-themed books, and in this and several future articles I want to share brief thoughts on them. This article represents another effort to... -- Read more on
9:31 PM | Most Useless Superpower
A long time ago, my friends and I were geeks. One day, […]
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