September 12, 2014

1:00 PM | What we’re reading: The phylogenomics of peanut allergens, saving the world with (and from) evolution, and how to make better figures
In the journals Ratnaparkhe MB, T-H Lee, X Tan, X Wang, J Li, C Kim, LK Rainville, C Lemke, RO Compton, J Robertson, M Gallo, DJ Bertioli, and AH Paterson. 2014. Comparative and evolutionary analysis of major peanut allergen gene … Continue reading →
9:33 AM | A week of links
Links this week: An excellent Econtalk podcast with Jonathan Haidt. Just don’t buy his lines about group selection – my reasons here. Steven Pinker’s amusing article on the Ivy League. Pinker also pointed out this oldie but goodie – Bell Curve Liberals. Greg Clark applies his work on social mobility to immigration. Reihan Salam comments. […]
5:53 AM | Wooster’s Fossils of the Week: The mysterious Paleozoic encrusters Ascodictyon and Allonema
  The above pair of fossils are small sclerobionts commonly found on hard substrates in shallow marine sediments through much of the Paleozoic, especially the Silurian and Devonian. Paul Taylor and I have been studying them for a few years now and our first paper on them was published this summer (Wilson and Taylor, 2014). […]

September 11, 2014

7:14 PM | The New Spinosaurus
Spinosaurus has changed dramatically since I was a kid. The model I used to terrorize my other toys …
6:25 PM | Ice Cream 101
Can any university claim to be a distinguished, quality institution of higher learning if they do not have decent ice cream in their student center/union?  Clearly an absurd question to which the answer is equally clear; no. A few universities of the ag/tech sort have dairy science departments where students in ice cream (DS 101) plus advanced studies where less common flavors as well as frozen chunks are explored, sell the products of this academic endeavor with excellent […]
2:32 PM | Kudos to Tedmed for the gender ratio of speakers for this year's event
Well done Tedmed.Here are the speaker pages below.  Notice anything?The gender ratio of speakers is actually well balanced.  Well done Tedmed.  Well done. -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. --------
2:01 PM | Emily Who???
Hi, folks. This is just a quick update to let all my readers know that I’m getting married next week. More importantly for Science Over a Cuppa, my last name […]
12:00 PM | Diversity in STEM: it matters
Diversity in the sciences is a recurrent topic on this blog (and – well – basically everywhere). Scientific American has an excellent overview on what “diversity” is and why it matters to the STEM fields. So whether you think about these issues a lot or a little, I highly recommend reading “Diversity in STEM: What […]

September 10, 2014

9:17 PM | Soggy September weather
Usually September is a fairly dry, fairly nice weather month. August had above average rainfall, so things entering September were not too dry. TPP made the observation 3 days ago that some rain would be nice or a few things would need some watering.  Hoo boy!  With a total rainfall approaching 4" in the past 48 hours, everything is well watered now OK. Usually this time of year the lily pond needs some topping up, but now a couple of inches will have to be drained off. […]
2:39 PM | Bacteria Can Really Get Around
Biology concepts – motility, microbiology, bacteria, evolution, gliding, twitching, flagella, pilusThe Giant Devil Ray, or mobula ray (Mobula mobular) can reach 18 ft. (5.4 m) wide. It’s not so much that they fly or glide, they just breach the waves and look like they are trying to flap wings. They were almost fished to extinction in the 1970’s. Their meat was sold as scallops after they cut it out with a round cookie cutter!How many different ways can humans move about? Walk, […]

Balish MF (2014). Giant steps toward understanding a mycoplasma gliding motor., Trends in microbiology, 22 (8) 429-31. PMID:

Kinosita Y, Nakane D, Sugawa M, Masaike T, Mizutani K, Miyata M & Nishizaka T (2014). Unitary step of gliding machinery in Mycoplasma mobile., Proceedings of the National Academy of Sciences of the United States of America, 111 (23) 8601-6. PMID:

Jin F, Conrad JC, Gibiansky ML & Wong GC (2011). Bacteria use type-IV pili to slingshot on surfaces., Proceedings of the National Academy of Sciences of the United States of America, 108 (31) 12617-22. PMID:

Stocker R (2011). Reverse and flick: Hybrid locomotion in bacteria., Proceedings of the National Academy of Sciences of the United States of America, 108 (7) 2635-6. PMID:

Editor's Pick
2:00 PM | Don’t Pet the Fuzzy Caterpillar
Keeping up my posting of interesting organisms, this little guy has been getting a ton of press lately. Adorable, looks like a tribble, and makes you want to cuddle them. But these little guys might be the most venomous insect in the US. So don’t pet the fuzzy caterpillar.    
9:43 AM | Footless urbanite pigeons
Foot deformities are ubiquitous in urban pigeons – why? As you’ll know if you’ve spent any time watching the pigeons of towns and cities, something like one in every ten (or more) has missing or... -- Read more on
9:12 AM | Nudging citizens to be risk savvy
I should start this review of Gerd Gigerenzer’s least satisfactory but still interesting book, Risk Savvy: How to Make Good Decisions, by saying that I am a huge Gigerenzer fan and that this book is still worth reading. But there was something about this book that grated at times, especially against the backdrop of his other fantastic work. […]

September 09, 2014

9:47 PM | MYScience: A newer faster cheaper easier BETTER open access journal
Tired of being rejected from PLoS ONE, PeerJ, and Arxiv?Don’t want to reformat for the next journal?Annoyed by referee and editor comments?Irked by suggestions that your paper is better suited for some other journal?Bothered by arguments to reduce text and transfer things to supplementary appendices?Wearied by having to select only a few relevant references?Irritated at having to submit your data to an online database?Chuffed to say what you want how you want as long and as often as you […]
7:16 PM | Biological research funding
This AM on public radio there was a story about the lack of research grant money and what a difficult time biomedical researchers had keeping their research labs going. Now here's the thing, these are biomedical researchers, and they've always had access to more research money than any other part of biology to the point that we like to say the human bio-medical tail wags the biology dog. The hunt for grant money shapes many hiring decisions at research […]
5:46 PM | International Symposium on Subsurface Microbiology - where men tell us about deep things
Just saw this Tweet: ISSM, a conference with no female plenary speakers. #fail cc @phylogenomics @pgirguis— Jen Biddle (@subsurface_life) September 9, 2014 This refers to this meeting: Call for Abstracts for 2014 Ninth International Symposium on Subsurface Microbiology, Pacific Grove CaliforniaThe plenary speakers for this meeting are all menPeter GirguisTerry HazenRainer MeckenstockLars NielsenAaron PackmanKarsten PedersenTimothy ScheibeJack SchijvenThe last […]
2:15 PM | Different Views of the Bog
Dr. Anderson describing the moisture gradient measured from the bog to the crest of the kame where the old growth remnant oak forest resides.   Our Climate Change visited Browns Lake Bog with the Plant Communities and Ecosystems class from Ohio Weslyan University’s Biology class taught by Dr. Laurie Anderson. Dr. Chuck Goss, a stream […]
12:51 PM | Report on Cultural Evolution for the National Humanities Center, Revised Edition
Back in 2010 I wrote a piece for the National Humanities Center (USA), Cultural Evolution A Vehicle for Cooperative Interaction Between the Sciences and the Humanities, which is online at their Forum along with comments. I have since revised it to include a section on Jockers, Macroanalysis: Digital Methods in Literary History (2013). You can […]

September 08, 2014

9:29 PM | The Last Phytosaur
Leaving the field is always bittersweet. After a week scrambling over rocks in search of fossils, a warm …
6:49 PM | More on Basic and Extended Syntax
Question pronouns are important but hard to visualize. Yesterday I posted a notice about a review article by Heather K.J. van der Lely and Steven Pinker titled "The biological basis of language," that reports the brain supports two separate syntax...
2:59 PM | Birdbooker Report 337
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 […]
9:56 AM | How Some Critters Evolved to Eat Poison
Since plants generally can’t move around, they have to rely on other strategie...
5:01 AM | Ancient Whale Provides an Early Glimpse into the Evolution of Echolocation
The author of a Nature study details the discovery of Cotylocara macei, a 28 million-year-old species of fossil whale, and its importance for the evolution of echolocation.
4:20 AM | Sunday Chess Problem
I’m feeling a bit bereft now that the Sinquefield Cup is over. Fabiano Caruana won his first seven games, and then drew his last three, to win the tournament by a ridiculous three points (ahead of World Champion Magnus Carlsen). This is certainly one of the great tournament performances in chess history, worthy of mention…

September 07, 2014

11:03 PM | Extracting High Quality Mud from Cedar Creek Bog
Tom Lowell and graduate student Stephanie Allard from Cincinnati and Jacklyn Rodriguez from the University of Illinois made the trip to Morrow County to core mud from a bog adjacent to the Cedar Creek Mastodon site. We will be working with the cores in Climate Change over the next several weeks and collaborating with this team. Extracting […]
9:21 PM | The Science of Paris
My fiancé and I have been in France since August 30th, enjoying a combination of early honeymoon and a Brain Disorders conference. This post, rather than offering anything innovative and […]
6:57 PM | A Breakthrough Paper
Sophie's Story looks at the strengths and limitations of Specific Language Impairment. The story of language and its origins that has been emerging on this blog is fairly simple: Members of the human lineage began using words when a population...
6:32 PM | New POTW Posted
The second POTW has now been posted, along with one possible set of solutions for the first problem. This week’s problem has a similar flavor to last week’s, so if you liked that one you’ll like this one.
4:00 PM | Story behind the paper: Bonnie Baxter on "A tale of salt and gender" #STEMWomen #Halophiles
After posting A tale of salt and gender: participation of women in halophile research I sent the post to Bonnie Baxter, one of the authors of the article I discussed and I asked if she would be interested in writing a guest post about the "Story Behind the Paper" (for which I have a whole series).  I am so so pleased that she said yes.  I have followed Bonnie's work for many years but this is her first guest post here.  I hope there will be more.  She is a […]

September 06, 2014

7:20 PM | Understanding 3-way interactions between continuous and categorical variables: small multiples
It can be pretty tricky to interpret the results of statistical analysis sometimes, and particularly so when just gazing at a table of regression coefficients that include multiple interactions. I wrote a post recently on visualising these interactions when variables are continuous; in that instance, I computed the effect of X on Y when the […]
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