August 19, 2014

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 ›
1:00 PM | Sharkageddon may be the worst Shark Week show *ever*
Thursday night, I sat down with more than 15 scientists to watch Shark Week. Most of them don’t watch the annual spectacle—they’ve become embittered after years of Discovery’s fear mongering, mockumentaries, and lies. But this particular episode was different—it was all about our home, Hawaii. We all wondered how the sharks that roam our islands’ […]The post Sharkageddon may be the worst Shark Week show *ever* appeared first on Science Sushi.
10:27 AM | True facts about anglerfish | @GrrlScientist
To the female anglerfish, the human male is a very loud, annoying and unnecessarily complicated pair of gonads.Caturday has arrived once again, so it is time to watch some animals doing stuff! Today's caturday animal is the anglerfish, an ancient taxonomic order of bony fishes that arose sometime between 100 and 130 million years ago. (In contrast, humans are mere evolutionary babies, having appeared sometime between just 2 and 6 million years ago.)Anglerfishes got their name from their method […]

Miya M., James W Orr, Rachel J Arnold, Takashi P Satoh, Andrew M Shedlock, Hsuan-Ching Ho, Mitsuomi Shimazaki, Mamoru Yabe & Mutsumi Nishida (2010). Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspective, BMC Evolutionary Biology, 10 (1) 58. DOI:

Widder E.A. (2010). Bioluminescence in the Ocean: Origins of Biological, Chemical, and Ecological Diversity, Science, 328 (5979) 704-708. DOI:

2:50 AM | From the Russian wilderness to the big city!
Guest Blogger: Sarah Frederick (’15) Arriving in Moscow was a sharp return to reality. Suddenly all of the things that had come to feel normal while we were in Kamchatka – the winding gravel roads and little towns with random meandering livestock that would peek in your windows – were replaced by traffic jams and […]

August 15, 2014

9:21 PM | How to conquer the world
Our species Homo sapiens has been around for some 200 000 years, and is generally thought to have evolved from older human species present in eastern and sub-Saharan Africa (University of Utah, 2005). But how did we come to be global (and even lunar) mammals? Debate still rages over how long ago H. sapiens left […]
7:59 PM | AAAS and SnapChat collaborate to develop SnapScience to publish scientific papers transiently
Just got this in an email and thought it should be shared.Washington, DC. August 15, 2014.Kent Anderson, the newly appointed Publisher of AAAS (see has announced his first action as Publisher - a partnership between AAAS and Snapchat ( said "Although I will not officially assume the role of Science publisher until 3 November, this was too important a task to not carry out immediately. AAAS has always […]
3:19 PM | Problematic Humour In Academic Talks
I recently attended a large academic conference, and I had an excellent time—I met fantastic colleagues, learnt a lot of state-of-the-art science, and heard some wonderful senior scientists talk about their decades of work. But there were a few moments … Continue reading →
2:07 PM | New Books Party: books received this week | @GrrlScientist
What good is a weekend without a good book to read? Take a look at these books -- hot off the presses -- that you may enjoy!When I get new books, I like to share them with people. Unfortunately, since you all are so far away, I cannot host a book party in my crib where you can look over them, so Ill do the next best thing. Ill host a book party on my blog each Friday of the week when I either purchase books, they are given to me or when review copies arrive in the mail. In this New Books Party, […]
2:01 PM | Botanical Geek Tour in Florence - Giardino dei Simplici
Chronological order is just so demanding, so let's back up a few days. Veronica (a very botanical name) works here at the villa and as a natural history student she recommended, once she discovered our botanical interests, that TPP visit the Giardino dei Simplici in the center of Florence. Florence is a lovely old city on the Arno River filled to the brim with Renaissance art and architecture that is presently under an assault by hordes of tourists.  And therein […]
2:01 PM | Today's YAMMM (Yet Another Mostly Male Meeting) Brought to You by CIFAR & NAS
Well, just got an invite to this meeting: Symbioses becoming permanent: The origins and evolutionary trajectories of organelles.  The topic seems of direct interest to what I work on.  And, it is relatively close (Irvine is a short hop away).  So this could be a way to go to a meeting without having to travel too far.  And maybe I could see my younger brother Matt who lives in LA and just graduated from UC Irvine's Masters program in Sound Engineering. Then I looked at […]
1:00 PM | Stuff online, leftovers and lactation edition
This week, at Nothing in Biology Makes Sense! The natural history of Ebola. Guess I need a “sunrise lamp.” How to make yourself a morning person. Search me. When everyone can have a blog, why does anyone need a comments … Continue reading →
1:00 PM | What we’re reading: Selection for heterozygosity in threatened seals, testing Fst outlier tests, and …?
In the journals Forcada J and Hoffman JI. 2014. Climate change selects for heterozygosity in a declining fur seal population. Nature. 511:462–465. doi: 10.1038/nature13542. Variation in SAM [Southern Annular Mode of the Antarctic atmosphere] significantly affects most of the life … Continue reading →
12:57 PM | Giardino di Villa Camberaia - Botanical Geek Tour adventures in Tuscany
Some guide book somewhere mentioned that the garden of the Villa Camberaia perched high in the hills above Florence as a great destination for garden lovers.  Well, you know the botanical geek tour squad will try their best to get the straight dope for our faithful readers. Without any particular agenda today, the villa's location was easily found on Via del Rosselino outside of the little town of Settignano. What better than a little botanical adventure a bit off the beaten […]
9:27 AM | Is Oil Responsible for Norway’s Wealth?
Most Americans assume Norway’s prominence in wealth and world affairs to be directly related to her discovery and refinement of oil. But are they?
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