August 21, 2014

1:26 AM | More passerines as seen from the peripheries (part III): Great tits!
Welcome to another of my articles on passerines from the peripheries. As before, the idea here is that we’re looking at passerine bird groups as seen ‘from the fringes’ – from an obscure, maritime... -- Read more on

August 20, 2014

10:05 PM | Temperature Key to Crocs in the Sea
Evolution is great at producing novelty. Every organism that has ever lived – from the first cell to …
7:28 PM | Today's YAMMM (Yet another mostly male meeting): pharma-nutrition #PN2015
Just got pointed to (by Elisabeth Bik) an announcement for a meeting: Home : Pharma-Nutrition 2015 with a focus on "Linking the Microbiome with Nutrition and Pharma".  And alas, the list of confirmed speakers is as follows:Keynote SpeakerMartin J. Blaser, NY University Medical Center, New York, NY, USASpeakersGregor Reid, University of Western Ontario, London, ON, Canada Alain van Gool, Radboud University, Nijmegen, The Netherlands David Hafler, Yale, New Haven, CT, […]
4:46 PM | Deacon’s Neo-Aristotelian Complication of Simple Action/Motion
Jared Diamond: We Could Be Living in a New Stone Age by 2114
4:00 PM | Nice Art and Science example - UC Davis Medical School molecule sculpture
Quikc post here.  A month or so ago I went to the UC Davis Medical School in Sacramento for a meeting and got to see this amazing new sculpture for the first time.For more about this and the Artist Roger Berry see this article.  It is always inspiring and uplifting to see nice architecture and nice art in a science building.  -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, […]
2:50 PM | In vino veritas
Italy makes a whole bunch of wine, a bundle bunch, and most of it is quite good, and astoundingly quite reasonable in price. To investigate the Tuscan wine scene a bit more thoroughly, a field trip was organized to a family run boutique winery called Campo del Monte ( near Terranuova Bacciolini, about 50 km away. Images of pineapples kept intruding, but a wine tasting was arranged for our party of six. This family makes some very good wine, and who […]
2:00 PM | What’s wrong with peer review? Us. The reviewers.
Peer review is often criticized for it’s lack of efficiency and frequently for making a paper… worse. An article over at Code and Culture does a good job of summarizing the issue, complete with cool little videos that aptly describe how I think peer review feels.
12:00 PM | Because He Is The One
Biology Concepts – ommatidia, reflex, fly, arthropod, sensory receptors, sensilla, metabolic rate, life spanNeo (Keanu Reeves) learned that he could dodge bullets at one point in The Matrix. This was before he learned he didn’t have to. Was he speeding himself up so the bullets looked to be going slower, or was he actually slowing down time?Neo from the Matrixfilms had the ability, once he learned to accept it, to react so fast that everything around him seemed to be moving slowly. […]

Muijres FT, Elzinga MJ, Melis JM & Dickinson MH (2014). Flies evade looming targets by executing rapid visually directed banked turns., Science (New York, N.Y.), 344 (6180) 172-7. PMID:

Healy K, McNally L, Ruxton GD, Cooper N & Jackson AL (2013). Metabolic rate and body size are linked with perception of temporal information., Animal behaviour, 86 (4) 685-696. PMID:

Jumpertz R, Hanson RL, Sievers ML, Bennett PH, Nelson RG & Krakoff J (2011). Higher energy expenditure in humans predicts natural mortality., The Journal of clinical endocrinology and metabolism, 96 (6) 6. PMID:

12:26 AM | Reading Macroanalysis 6.1: Theme–Dogs, Gold, Slavery, and Awakening
Over at New Savanna I’ve been blogging my way though Matthew Jockers, Macroanalysis: Digital Methods & Literary History, University of Illinois Press, 2013. I figured this particular post would be of interest here. If you’re not familiar wiht topic analysis, there’s some links below that’ll help you out. Chapter 8 of Macroanalysis is about “Theme.” […]

August 19, 2014

9:54 PM | Which Came First, the Word or the Gesture?
I got a good laugh out of this cartoon on Alex Baker's Cake or Death cartoon file. And it fits in with this post's point: gestures have their limits. Susan Goldin-Meadow is a hero on this blog because her work...
8:36 PM | Skeptical that PMS is an adaptive response designed to break up your relationship? Me too.
In a pleasantly surprising turn of events, this week a take-down of some dubious evolutionary psychology was published by the popular media!  The original article, a perspective piece published in Evolutionary Applications, claims that moodiness associated with PMS may have historically served an adaptive role by driving infertile couples apart.  Premenstrual syndrome (PMS) affects up to […]
8:11 PM | You can evolve there from here. And from here. And here …
If evolutionary history somehow reverted back to the “warm little pond” in which life began, and started over from almost-scratch, would the re-diversification of life end up, four billion years later, pretty much as we see it today? I think … Continue reading →
10:07 AM | The amazing world of flyingfish by Steve Howell – review
SUMMARY: Written by a professional pelagic birding tour guide and photographer, this book presents a popular account of what is known about the enigmatic flyingfishes, and it’s illustrated with an abundance of breathtaking full-colour photographs. After browsing through shelves and shelves of field guides in a typical nature bookshop, you might suspect there’s a field guide for absolutely every group of anything you can find on the planet -- birds, mammals, reptiles, amphibians, […]
8:35 AM | Functional trade-off between lexical tone and intonation
Languages can use pitch to make lexical contrasts (so called tone languages) or to mark contrasts at the utterance level, usually called intonation, such as using rising pitch to indicate a question as opposed to a statement.  In fact, a language can use pitch to do both by various means such as changes in pitch […]

August 18, 2014

10:49 PM | The Mammals Who Lived
When the asteroid slammed into prehistoric Mexico and drew the curtain on the Cretaceous, dinosaurs did not fare …
8:10 PM | The Gelato Challenge
As a partial compensation for having dumped on Italian bread, TPP will admit that gelato is great stuff. Personal challenges can be highly motivating, so far be it for TPP to ever suggest that Mrs. Phactor's gelato challenge is anything but a righteous endeavor. So here it is: 30 different flavors of gelato in 30 days, hey, and licks or tastes don't count. The effort involved cannot be diminished, nor can the sacrifice.  Her major problem is that our Tuscan residence is quite a ways […]
6:09 PM | Mendelian-Mutationism (II): The Fluctuation-Mutation Distinction
As discussed in my last post, the mutationist/Mendelians (defined below) have mostly been sidelined in the history of biology. The claims used to justify this argument make up what Arlin Stoltzfus and I call “The Mutationism Story.” While Arlin first discovered this in the scientific literature, we found that scientists were getting many of these mistaken […]
3:12 PM | AAAS - Blocking Access to the Scientific Literature Even When They Say It Is "Free"
Today, I wanted to show someone a PDF of a paper of mine that I co-authored in 1999.  The paper was, I think, kind of cool.  It reported the sequencing and analysis of the genome of Deinococcus radiodurans, an incredibly radiation resistant bacterium.  Alas, I did not have a copy on me, and the only electornic device I had with me was my phone.  The person I wanted to show the paper to had their computer, a device with a strange little red trackball and running some sort of […]
1:41 PM | The LonCon3 Speculative Biology event
I’ve just returned from LonCon3, the 72nd World Science Fiction Convention, held at the enormous ExCel Exhibition Centre in east London. Yeah, I know, sci-fi isn’t exactly a normal part of the Tet... -- Read more on
12:00 PM | The 3 Dumbest Products Sold By Whole Foods Market
Whole Foods "Whole Body" products.I have a love-hate relationship with Whole Foods Market. On the one hand, I love their fresh produce, their baked goods, and many other food choices there. On the other hand, they seem to have embraced anti-science positions in the interest of keeping everything “natural.”Before describing what they do wrong, let’s start with some things they get right. Their seafood sustainability policy supports fishing practices that allow wild […]
11:33 AM | The amazing world of flyingfish by Steve NG Howell | review | @GrrlScientist
Written by a professional pelagic birding tour guide and photographer, this book presents a popular account of what is known about the enigmatic flyingfishes, and its illustrated with an abundance of breathtaking full-colour photographs.After browsing through shelves and shelves of field guides in a typical nature bookshop, you might suspect theres a field guide for absolutely every group of anything you can find on the planet -- birds, mammals, reptiles, amphibians, fishes, insects, plants, […]
11:33 AM | How Tibetans' Ancestors Adapted to High Altitudes
In response to low oxygen conditions, our body produces extra red blood cells in...
2:15 AM | Neither rain
Fresh summer rain. Marathon in six weeks. Gotta do the miles. Running shoes squish and suck all the way down the empty trail to the lakes. The few other runners wave in solidarity. One reaches out for a high-five, shouts … Continue reading →

August 17, 2014

8:11 PM | Schizophrenia, Autism, and Sensory Processing
“During the last while back I have noticed that noises all seem to be louder to me than they were before. It’s as if someone had turned up the volume. […]
5:04 PM | What the hell is “Information” anyway?
DNA, ideas, knowledge, books, computations, schedules, job descriptions, money(!), bank accounts, music, culture, beliefs and every last thing that has some importance in our lives has something to do with “information”, but still, all my attempts to find a no-nonsense,…Read more ›
3:29 PM | The time the cops pulled their guns on me
This post is not about science.I'm writing this because the horrific news out of Ferguson, Missouri—the killing of an unarmed man and the subsequent assault on the populace and media—has been bringing back memories an experience I had with the police ten years ago in Chicago.I should be clear about why I'm choosing to share this. It's not because I think my own problems are particularly deserving of attention in comparison to the violence done to Michael Brown, Eric Garner, and […]
6:31 AM | Bread - most disappointing thing in Italy
Bread is great, and TPP has always been a big fan of it. Mrs. Phactor bakes a mean loaf of French bread for which she has some renown. The bread in Italy looks fantastic, and we've sampled a good bit of including a small local bakery, both flat and poofed up bread. It also smells good, but the taste is rather bland. It took some thought to figure out why the flavor seemed to be missing - no salt. It doesn't even help to butter the bread, although that is decidedly un-Italian, […]

August 16, 2014

11:03 PM | A week of links
Links this week: An awesome looking conference – Complexity and Evolution: A New Synthesis for Economics Hybridisation – what does it mean for conversation and the future of species? Picking up in a Lamborghini Status wars How far are we from designer babies? Neuroscience and marketing
4:29 PM | The Divide: a survey about interactions between theoretical and empirical researchers
What is the proper role of theoretical versus empirical work in biology?  I self-identify as a theorist, and I do pretty much all of my work sitting at my Mac Pro.  However, I did my Ph.D. in Andrew Hendry’s lab, surrounded by empirical biologists working on stickleback, guppies, salmon, and other slimy real-world critters.  This was somewhat of an accident; initially, I was interested in doing an empirical Ph.D., but my past as a software engineer meant that I soon shifted […]
2:20 PM | Random thoughts on Antifragility (Part 2): the role of heuristics
How can we prepare for the unexpected? One of the central features of Nassim N. Taleb book “Antifragile: Things That Gain from Disorder” is that the great big world is essentially (?!?) unpredictable, and that most attempts to tame it…Read more ›
201 Results