Posts

September 26, 2014

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1:00 PM | What we’re reading: A guide to Bioconductor, Latin American admixture, and the sordid truth about academic job hunting
In the journals Lawrence M., M. Morgan. 2014. Scalable genomics with R and Bioconductor. arXiv:1409.2864. This paper reviews strategies for solving problems encountered when analyzing large genomic data sets and describes the implementation of those strategies in R by packages … Continue reading →
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5:52 AM | Wooster’s Fossil of the Week: A crinoid calyx from the Upper Ordovician of southern Ohio
This week’s contribution from the Wooster collections will be short. If all is going well, as this is posted I’m on my way to the Fourth International Palaeontological Congress in Mendoza, Argentina. I hope to have a few posts from that exotic place! The fossil above is the crown of a monobathrid crinoid called Xenocrinus […]
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2:50 AM | Thanks, Bush and Obama!
President Obama is expanding the Pacific Remote Islands Marine National Monument today from the wonderful 86,888 square miles President George W. Bush set up in 2009, to about 490,000 square miles. I gotta love anything involving ocean conservation. Thanks, Bush and Obama! “This is a great moment,” said Greg Stone, chief scientist for Conservation International. […]

September 25, 2014

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7:32 PM | Ziapelta – New Mexico’s Newest Dinosaur
Another day, another dinosaur. The last to trundle out into public view was Rhinorex, a shovel-beaked herbivore that …
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6:35 PM | TALL grass prairie vegetation
One obvious aspect of field research is that you cannot apply treatments or gather data if you cannot find your permanent plots. Now least you think TPP is careless or an amateur, several precautions were taken this spring, and in prior springs, to mark and map the 100 or so meter square plots out there on our research prairie. There is a permanent spike in the SE corner and smaller markers in the other corners, and in the late spring a 30" piece of white pvc pipe is pushed in over the […]
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6:27 PM | The American White Pelican
The American White Pelicans (Pelecanus erythrorhynchus) are in the midst of their southerly migration from their breeding grounds in the Dakotas and Minnesota. I saw some myself at Long Meadow Lake near the Mall of America two weekends ago, in which 15-20 were participating in this slightly discomforting but elegant synchronized fishing/swimming activity: Seeing them, I decided to take some time […]
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4:22 AM | #YAMMM Alert: Drug Discovery and Therapy World Congress, a meeting made for @realDonaldTrump & other men
Elizabeth Bik sent me a link to this meeintg: DRUG DISCOVERY & THERAPY WORLD CONGRESS 2015 with a comment about the ratio of males to females in the keynote speakers.  And it is painful.  Of the plenary and keynote speakers, 15 are male and 1 is female.  Below I show pics of the plenary and keynote speakers:Plenary and Keynote Speakers at Drug Discovery and Thearpy World CongressFemale Plenary and Keynote Speakers at Drug Discovery and Thearpy World CongressTwo […]

September 24, 2014

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9:46 PM | Sex, the Early Years
Sex is an ancient tradition. It’s older than today’s continents, older than dinosaurs, older than trees, dating back …
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5:38 PM | Aren’t Adaptations Special?
We just passed the 35th anniversary of the publication of Gould and Lewontin’s classic, highly cited, highly controversial essay (diatribe?), “The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme.” The 21st of September 1979 was the fateful date. Every PhD student in biology should read it (you can find […]
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4:27 PM | Postdoc: Aspergillus Pathogenesis and Immune Activation Dartmouth
A postdoctoral position is available to study the molecular mechanisms of pathogenesis and host defense during Aspergillus fumigatus infection. The project will focus on fungal and host factors that are responsive to in vivo oxygen levels which subsequently modulate virulence and host inflammatory responses in clinically relevant models of aspergillosis. Two years of initial funding are guaranteed for generating […]
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4:15 PM | Job: Assistant Professor of Plant Pathology, Tenn State Univ
Assistant Professor of Plant Pathology at Tennessee State University. The position is a 12-month, tenure-track position and includes a technician and internal funding.  The position is located at the Otis L. Floyd Nursery Research Center, McMinnville, TN (http://www.tnstate.edu/agriculture/nrc/). Applicants interested in applying for the position should visit jobs.tnstate.edu and enter the position description number 092775, which will take […]
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3:53 PM | Back from Bayes IV
As announced a while ago, we had moved our now already traditional summer school in Bayesian Statistics to Bergen, Norway this year. Maybe fitting for such a course, the weather turned out to be very different from the long-term frequency, in what must be the upper 1% quantile of sun intensity for the region at…
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2:53 PM | 2014, an amazing year for pterosaurs
I’m still not sure whether I blog about Mesozoic archosaurs – specifically dinosaurs and pterosaurs – too often, or too infrequently. As I always say, the problem as I see it is that dinosaurs and... -- Read more on ScientificAmerican.com
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2:50 PM | Poor taste marketing
TPP is late to this issue; so what?  In one sense Urban Outfitters marketing a bloodied Kent State University sweatshirt almost deserved no comment, so utterly tasteless is this idea. Who in bloody hell would order one?  If you actually remember the event at Kent State that spurred this product then you are over 60, and if you think such a shirt if clever, then you never gunna grow up. It does occur to TPP that all discussion about militarization of the police, Kent State is what […]
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2:00 PM | Grumpy Cat: Frog Version
If there is one internet meme that I’d like to see last forever it’s grumpy cat. And, as WTF Evolution has noted, if we dream it up, evolution can provide. I give you: grumpy frog. Not only are these guys adorably grumpy (new meme anyone?) but they are also have a really interesting physiological traits! […]
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11:22 AM | Kahneman’s optimistic view of the mind
In the Gerd Gigerenzer versus Daniel Kahneman wars, most of the projectiles seem to fly one way. Gigerenzer attacks directly, Kahneman expends little effort in defence. As one test of whether my impression was correct, I searched Kahneman’s Thinking, Fast and Slow for how many times Kahneman directly mentions Gigerenzer. The answer is six, once […]
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10:00 AM | Chase The Good, Evade The Bad
Biology concepts – motility, flagella, bacteria, chemotaxis, magnetotactic, monotrichous, amphitrichous, lophotrichous, peritrichous, run and tumble, coccusThe Princess Bride had everything – good guys, bad guys, rodents of unusual size, ex-professional wrestlers. Vizzini was supposed to be brilliant, so why didn’t he cure his own speech impediment? Inconceivable!Proximity is a good relative indicator of danger or benefit. As Vizzini said to Wesley in The Princess Bride, […]
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1:36 AM | Triassic Bites and a Carnivore Conundrum
The Triassic was one of the strangest times in the history of the planet. Rebounding from the worst …

September 23, 2014

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3:35 PM | Spurious correlations at Occham’s Beard festival
Mark Dingemanse and I will be appearing the Discovery Festival in Amsterdam on Friday.  We’ll be talking about spurious correlations in language and culture as part of the Occam’s Beard symposium. The idea is to take some real data, then throw away Occam’s razor and go after the most complicated explanation possible. I foresee no […]
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2:09 PM | Snake poop and the adaptive ballast hypothesis
Click here to read this post in SpanishHaga clic aquí para leer este blog en españolAlternate title suggested by David Steen: Why snakes might benefit from holding it Most people probably spend as little time as possible thinking about poop, especially snake poop. Some animals produce enormous amounts of poop, like dairy cows. Others make lots of little poops - up to 50 a day in small birds.  In contrast, snakes don't poop much at all. In fact, because they eat […]
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9:39 AM | The Direction of Cultural Evolution, Macroanalysis at 3 Quarks Daily
As soon as I finished up my series of posts about Matt Jockers, Macroanalysis: Digital Methods & Literary History, I set up a file on my Mac for further thoughts, knowing full well I’d keep thinking about the book. I’ve now posted the first of those continuing thoughts at 3 Quarks Daily: Macroanalysis and the […]
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9:29 AM | Triclosan in toothpaste: potential risks are not a "rumor" as arrogant Colgate official argues, but are something to worry about
Triclosan in my toothpaste (and maybe yours too)I was reading some posts of a friend and went down a bit of a rabbit hole that led me to a place that did not make me happy.First I saw a post about some issues with Crest Toothpastes containing polyethylene: Dentist calls Crest toothpaste dangerous; Now P&G changing ingredients.  This seemed a bit disturbing.  But then I saw a "Related Link": Shoppers Ditching Colgate Total Amid Triclosan Fears.  And I thought - holy […]
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7:57 AM | Story Behind the Paper: Comparative Analysis of Functional Metagenomic Annotation and the Mappability of Short Reads (by Rogan Carr and Elhanan Borenstein)
Here is another post in my "Story Behind the Paper" series where I ask authors of open access papers to tell the story behind their paper.  This one comes from Rogan Carr and Elhanan Borenstein.  Note - this was crossposted at microBEnet.  If anyone out there has an open access paper for which you want to tell the story -- let me know.We’d like to first thank Jon for the opportunity to discuss our work in this forum. We recently published a study investigating direct […]
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12:55 AM | Dating Houses and Reconstructing Climate
The Wooster Geology Climate Change class spent a beautiful fall day in Stony Creek, Ohio coring beams in three structures of historical significance. They will determine the cut dates (calendar dates when the timber for the houses were felled) for the homeowners and then examine the tree-ring data that results to help reconstruct drought for […]
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12:05 AM | The green wine bottle challenge
Somehow over the past several decades the Phactors have accumulated 300 or so green wine bottles of the standard type with shoulders. All of them have been cleaned of labels and there are a variety of green hues from dark green to pale green. Now having expended this much energy just recycling these bottles into more glass seems a waste. What the Phactors want is a thing of beauty and a joy forever, something fanciful and perhaps aesthetically pleasing, perhaps whimsical, perhaps […]

September 22, 2014

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5:38 PM | Those who do not learn from history.....
Here the USA goes again. You think this country would learn, but noooo-oooh.  Once again Tom Tomorrow nails it.  What can possibly go wrong? 
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4:25 PM | 3 Quarks Daily Science Prizes have been announced!
The 3 Quarks Daily Science Prizes have been announced. Top Quark went to the ever-amazing Eric Michael Johnson for his deeply-researched and thought-engaging post on how Promiscuity Is Pragmatic. The second place slot, The Strange Quark, went to… ME! I’m honored to be chosen for this award, judged by none other than the esteemed Frans B. […]The post 3 Quarks Daily Science Prizes have been announced! appeared first on Science Sushi.
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11:55 AM | Beyond species: why ecological interaction networks vary through space and time
Poisot, Stouffer, & Gravel. bioRxiv DOI: http://dx.doi.org/10.1101/001677. Beyond species: why ecological interaction networks vary through space and time Welcome back to PEGE! We’ve taken a break over the summer, but we are hopefully back fully revived for the new season. We decided to pre-pick a bunch of papers so that we are not scrabbling for […]
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9:00 AM | The evolution of human facial diversity
We all rely on our ability to recognize other people’s faces to get along in the world. Most people don’t think too hard about this, it’s so fundamental to our existence. But it turns out that in order to stand out in the crowd, you need to be, well different. A recent study shows that […]
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6:46 AM | From chimps to chickens: how a little DNA can make a lot of difference
I've written before about how epigenetic differences enable very similar genome...
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