February 19, 2015

3:00 PM | Twice Mixed? Testing hypotheses of Neanderthal Introgression
Human migration in, and out of Africa was wrought with complex patterns of admixture (see my previous post summarizing the story so far). Of note were some recent findings on the disparity in amounts of Neanderthal introgression/ancestry between East Asians … Continue reading →
2:48 PM | Oxford Global Sequencing Meetings: Where MEN Tell You About Sequencing #YAMMM
Well, got an email invite to one of these Oxford Global Meetings. Sadly the gender ratio of listed speakers is awful. I highlighted the list below (men in yellow, women in green).  Ratio of 17:3.  (See below).  No thanks Oxford Global. Dear Professor Jonathan Eisen , We hope you are well and we would like to invite you to speak at our forthcoming Next Generation Sequencing (NGS) USA congress ( or […]
2:55 AM | The Role of Greenhouse Gas Emissions in Heat Waves
The summer of 2011 in Texas was pretty brutal. Some cit […]

February 18, 2015

11:10 PM | Baby Snake Shows Why The Dead Can Still Be Deadly
Remember that story from last fall about the Chinese chef that died after being envenomated by the severed head of a cobra he was cooking? (Well, if not, here's a good summary.) Many dismissed the tale outright, thinking a snake couldn't possibly be lethal if it was no longer living. But a great photo taken this week by Lee Reeve shows just how dangerous venomous animals can be, even after death: Lee found this wee western diamondback rattlesnake (Crotalus atrox) dead this morning. […]
10:06 PM | Population by age and revolution
An astonishing thing took place during the last 250 years (starting with the 18th century) – the sexual maturation of children has speeded up; it takes place 4 years earlier than the normal period. This observation was made on the ground of a pretty macabre argument – presently, the death rate curve among boys appears […] The post Population by age and revolution appeared first on Social Ethology.
6:15 PM | Dang, not a "real expert" on evolution
Right Wing Watch reports that American Family Association governmental affairs director Sandy Rios...explained on her radio show today that, “science has done nothing but disprove the theory of evolution.” “There is no scientific evidence” to substantiate evolution, she said, at least according to “the real experts”. Gee, TPP feels badly; he didn’t get that memo, and since he doesn't know about the disproof, he isn't a "real expert". How deflating. […]
5:38 PM | Please extend some sympathy
When spouse and F1 team up on you, you don't really stand a chance. In this case however they teamed up with the NSA or some other nefarious government agency to track my movements. You see, since retirement freed TPP from his academic demands and regular schedules, his where abouts have been far less certain, so in an effort to maintain communications with a this retired botanist, his significant others exercised a family plan and acquired a smart phone for him, his […]
3:56 PM | Comparing runs and counting K
If you are someone who has any interaction with population genetics, the letter K may cause you a distinct feeling of uneasiness. Identifying the number of distinct genetic clusters (often represented as K) in a data set is a primary component in … Continue reading →
12:30 PM | Space – It’ll Mess You Up
Biology concepts –  undulipodia, primary cilia, motile cilia, ependyma, spaceflight, pathology, osteopenia, radiation damage, osteoblast/osteoclast, osteocytes, No one wanted the elation of the moon visit to turn to disaster as a moon germ spread through-out the world and killed every living thing. So they moved the astronauts from splashdown to airstream. What a bummer that would have been to go all Andromeda Strain…. although it might have saved us from Watergate.Going into […]

Finetti, F., Paccani, S., Rosenbaum, J. & Baldari, C. (2011). Intraflagellar transport: a new player at the immune synapse, Trends in Immunology, 32 (4) 139-145. DOI: 10.1016/

Conroy, P., Saladino, C., Dantas, T., Lalor, P., Dockery, P. & Morrison, C. (2014). C-NAP1 and rootletin restrain DNA damage-induced centriole splitting and facilitate ciliogenesis, Cell Cycle, 11 (20) 3769-3778. DOI: 10.4161/cc.21986

Troshichev, O., Gorshkov, E., Shapovalov, S., Sokolovskii, V., Ivanov, V. & Vorobeitchikov, V. (2004). Variations of the gravitational field as a motive power for rhythmics of biochemical processes, Advances in Space Research, 34 (7) 1619-1624. DOI: 10.1016/j.asr.2004.02.013

Fitts, R., Trappe, S., Costill, D., Gallagher, P., Creer, A., Colloton, P., Peters, J., Romatowski, J., Bain, J. & Riley, D. & (2010). Prolonged space flight-induced alterations in the structure and function of human skeletal muscle fibres, The Journal of Physiology, 588 (18) 3567-3592. DOI: 10.1113/jphysiol.2010.188508

Rimmer J, Patel M, Agarwal K, Hogg C, Arshad Q & Harcourt J (2014). Peripheral Vestibular Dysfunction in Patients with Primary Ciliary Dyskinesia: Abnormal Otoconial Development?, Otology & neurotology : official publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology, PMID:

8:00 AM | Moving a nation from “Good to Great”
A PwC report and associated press release claiming that Australia could “fall from the G20″ has triggered a round of media (e.g. here and here) questioning Australia’s role in the world. There’s nothing new in the report to worry about. Under the PwC model, Australia drops out of the top 20 countries by GDP on PPP terms […]

February 17, 2015

10:21 PM | New “Problem Of The Week”
My recent travels, to Parsippany, NJ via Baltimore, MD, which involved three talks in two days, followed by multiple games of chess, bookended by two long drives, came to a dramatic conlcusion yesterday when I had to drive home in the snow. Not fun! There was so much snow on the road that you frequently…
6:45 PM | Know Your Opponents
I don’t re-post or link a lot of stuff from the official BEACON blog, but these two thoughtful commentaries, one from undergraduate Lazarius Miller and the other from grad student Carina Baskett, caught my eye.  Both of them were models of constructive engagement.  Maybe a little more earnest and serious in tone than readers will often find here, but equally honest in intent. They were particularly welcome after I spent three cups of coffee reading this […]
6:08 PM | Birdbooker Report 360
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 […]
6:04 PM | ICPhS phonetic capabilities satellite meeting – deadline extension
Re. The ICPhS phonetic capabilities satellite meeting, which has been previously advertised on this blog. We have received a number of requests for late submissions, which we have granted, and as a result, feel it fair to have the same extension for everyone. Thus, if you would like to either submit something, or would like to […]
5:34 PM | How to fly without wings?
5:24 PM | Two Eisen lab papers selected for the PeerJ 2015 Collection
Cool.  Two paper from my lab were selected as highlights of 2014 papers in the Peer J: PeerJ Collection: PeerJ Picks 2015 CollectionThe papers wereThe microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet typesJenna M. Lang,  Jonathan A. Eisen,  Angela M. Zivkovicand PhyloSift: phylogenetic analysis of genomes and metagenomesAaron E. Darling,  Guillaume Jospin,  Eric […]
4:27 PM | February - tough month for gardeners and recent retirees
The most recent snow missed us (too bad), and now another cold front has settled upon the upper midwest. It looks grimly cold outside. This is a tough month for gardeners psychologically, and physically with limited exercise, but things are even worse for non-gardeners. As a recent retiree, people keep asking if TPP is OK, enjoying retirement, and keeping busy? Yes, yes, yes. There is a great thing about being a plant-loving, gardening botanist which is that you cannot actually find […]
9:49 AM | Phylogenetic relatedness and the determinants of competitive outcomes
Godoy et al. 2014 Phylogenetic relatedness and the determinants of competitive outcomes. Ecology Letters 17 (7): 836-844 In a fantastic follow-up to the many criticisms of the community phylogenetic approach, Godoy et al. fit a form of the Chesson framework to ecological data, and find that while fitness differences are greater among distant relatives, competitive differences […]
4:47 AM | Advice for EEB Grad School Interviews: Show Interviewers How You Think!
Over the last few years, I have found myself giving quite a few prospective EEB graduate students advice on applying to graduate school. I realise this subject is rather popular with academic bloggers, and there are plenty of other places to get … Continue reading →
1:34 AM | Sciencespeak: Fossorial
Mammals have been around for a very long time. The first beasts scurried through the Mesozoic world around …
Editor's Pick
12:12 AM | Of Transcription Factors, their Evolution and Mechanism of Action
Transcription factors (TFs) play a key role in any biological system, and not surprisingly are being the centre of a continuous stream of papers. I recently covered the contrasting evidence for the role of TFs in evolution as a result of the specificity of … Continue reading →

February 16, 2015

10:59 PM | Emotional Communication Matters
Thank heavens for parents who post baby babbling videos on YouTube. The basic fact of this blog is that now the whole human species uses language, but at one time none of our ancestors did. The basic question of this...
5:56 PM | Apply for EuPathDB workshop
Dear Colleague, We are pleased to announce the 10th annual EuPathDB workshop to be held in Athens, Georgia, USA from May 31 – June 3rd, 2015. Learn how to effectively use EuPathDB resources and mine available data to help guide your research. For more information and to apply, please visit: ********************* Databases covered: EuPathDB, AmoebaDB, … Continue reading Apply for EuPathDB workshop →
5:10 PM | Mammal March Madness 2015
PhyloPic & Wikimedia Commons: Steen, Hartman, HassanPlaceholder PostThe organizing team is back- Kristi Lewton, Chris Anderson, Josh Drew & I will once again be running Mammal March Madness in 2015. The divisions are Mighty Mini Mammals (no longer will the little guys be one & done!), Mythical Mammals, Critically Endangered Mammals on the IUCN Red List, and SEXY BEASTS! Species shaped by sexual selection.The official bracket will go live on March 3rd. The Wild Card Battle starts it […]
4:25 PM | Creature Feature XIII: Two Types of Vipers
My new piece for Creature Feature is about two snakes that are a looming presence in my life in the field: the saw-scaled viper and the cottonmouth. The piece talk about research by Harvey Lillywhite and his lab on the … Continue reading →
4:08 PM | Pale blue dot
This is an interesting juxtaposition with the previous blog. That tiny blue dot is Earth seen from Voyager 1 at a distance of just 6 billion kilometers, and it was taken 25 years ago. Let TPP say now that Phil Plait's Bad Astronomy blog is one of the most consistently interesting and informative science blogs out there. Please take the time to read the essay by Carl Sagan posted there because even though our residence is part of a galaxy not unlike M106, this tiny blue dot is all we got. Wish […]
3:56 PM | WOW! Galaxy M106 poses
This is a pretty mind-blowing image of galaxy M106, and you can download an even higher resolution image. This is pretty amazing stuff. Apparently some of this composite image, the red arms, result from a massive black hole spewing out energy & hot matter across, across, hmm, no idea the scale of things here, thousands of light years?  If you look at the back ground, you see all those other things, and they be other galaxies. Just wow! 
3:27 PM | Chasing Brainbows
  Whether your computer screen displays a spreadsheet, a movie, or a LOLcat, you’re seeing  pinpoints of light in only three colors: red, green, and blue. But by varying the relative intensity of these three components, a pixel can transform … Read MoreThe post Chasing Brainbows appeared first on Genes to Genomes.
2:01 PM | The results are in for the journal selection survey
Two weeks ago I wrote a post about a recent paper by Salinas and Munch that presented a model-based method for determining to which journal an author should submit a manuscript for publication. I was curious to know how the readers … Continue reading →
12:57 PM | A really bad week for the supplements industry
If the ingredients in your pills don’t really work, does it matter if they’re correct?Well, yes. Even if that echinacea pill doesn’t cure the common cold, if a supplement manufacturer sells you an echinacea pill, they have to put echinacea in it. Supplement makers can and do make all kinds of claims about the health benefits of the stuff they’re selling you. They claim that supplements can "boost your immune system," relieve aches and pains, improve memory, and […]
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