December 11, 2014

11:10 AM | Natural causes of language
Natural causes of language by Nick Enfield discusses theories behind cultural transmission of language.  From the blurb: What causes a language to be the way it is? Some features are universal, some are inherited, others are borrowed, and yet others are internally innovated. But no matter where a bit of language is from, it will […]
8:00 AM | My year
In the day job, for most of this year I was seconded onto the Australian Government’s Financial System Inquiry. The Inquiry was established to provide a broad review of the Australian financial system, looking at system stability, competition, consumer protection, technological change and whether the system was serving the needs of users. The Inquiry’s final report is now out […]
7:06 AM | Insect Biodiversity: Unknown – a status report
Nature published an article this week with some nice infographics that illustrate the astonishing number of species considered threatened by the International Union for Conservation of Nature, which is pretty depressing, at least if you look at the vertebrates. In what was a nice surprise, they actually included data on insects in addition to the [...]

December 10, 2014

11:36 PM | Wordless Wednesdays: here, have a science cookie
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7:32 PM | Birth of a lichen
Lichens are symbiotic organisms consisting of a highly organized fungal mycelium enclosing algal cells. What's strange about lichens is that without the algae, the fungus just looks like a fungus. Without the fungus, the algae is just algae. They only take on the form recognized as a lichen when the two organisms are in that symbiotic association, and of course, the term itself means "living together". This presents some interesting aspects of reproduction. This illustration is from the […]
7:00 PM | C.L. Gloger’s favorite owl
Biologists love clines. We’ve been mentally masticating on clines for decades. Clines in body size. Clines in color. Clines in heart size! Clines that go in circles! Recognizing clinal patterns in phenotypes or genotypes is fun, but discovering the mechanisms behind … Continue reading →
6:20 PM | DNA can survive atmosphere re-entry
On March 29, 2011, a TEXUS-49 rocket took off from northern Sweden for a short trip into space and back …Continue reading →
3:39 PM | New lab paper: The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types [PeerJ]
A new paper out from my lab (with Jenna Lang as the 1st author and in collaboration with Angela Zivcovic from the UC Davis Food For Health Initiative and the Department of Nutrition):  The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types.  The work in the paper focuses on characterizing the abundance and taxonomy of microbes in food from three model diets. Basically, Angela prepared meals for these three […]
1:26 PM | Increase your broader impacts with Data Nuggets
  This week we have a special guest post by Elizabeth Schultheis, a PhD candidate at Michigan State University and the Kellogg Biological Station, to describe her Data Nuggets project. Previous guest posts have discussed other great projects happening in the … Continue reading →
1:00 PM | Christmas Trees Have Trouble Seeing The Light
Biology concepts – photoprotection, photosynthesis, non-photochemical quenching, reaction center, yule, evergreen, chlorophyllYule was/is a pagan celebration in midwinter. Krampus was the spirit who came during Yule to punish children who had misbehaved. Yule celebrations used evergreens (note his headdress) and this has continued in the modern Christmas celebration, but the Krampus became paired with good Saint Nicholas, so they kind of went the other way with that one.Christmas trees […]

Lysenko EA, Klaus AA, Pshybytko NL & Kusnetsov VV (2014). Cadmium accumulation in chloroplasts and its impact on chloroplastic processes in barley and maize., Photosynthesis research, PMID:

Demmig, B., Winter, K., Kruger, A. & Czygan, F. (1987). Photoinhibition and Zeaxanthin Formation in Intact Leaves : A Possible Role of the Xanthophyll Cycle in the Dissipation of Excess Light Energy, PLANT PHYSIOLOGY, 84 (2) 218-224. DOI: 10.1104/pp.84.2.218

Ottander C, Campbell D, Öquist G (1995). Seasonal changes in photosystem II organization and pigment composition in Pinus sylvestris. , Planta , 197 176-183. Other:


December 09, 2014

11:05 PM | Confirmation Bias Stories
Confirmation bias is when you read or hear (or search out) things (people, research, etc) that agrees with what you say or rejects what someone else says. We are all guilty of this at some point or another. It’s hard to stay on top of it and really read stuff you disagree with. I wanted […]
9:54 PM | Christmas present for a cat
All cat people know that the only thing to get a cat for a present is a catnip toy. Here's another of those terribly clever animations of Simon's cat.  It perfectly captures the usual reaction of a cat to a new catnip toy. The animation is a present to us from the cartoonist. Enjoy.
8:08 PM | Winter survival supplies - fresh batteries
The Phactors were just sitting around the other evening reading the Sunday papers and assorted other periodicals, and eventually it came to their attention that they were cold. Say what?  Yes, the temperature in the house was several degrees below what is considered comfortable. Sort of reminded TPP of the story about putting a frog in a pot of water and warming it so slowly such that the frog never jumps out and just gets cooked. Might the same thing happen to a couple of senior citizens […]
7:58 PM | Neighborhood vandalism
Vandalism just about tops the list of urban dwellers pet peeves, so when a neighbor reports being the target of vandalism, everyone gets concerned. When the vandalism kept occurring they called the cops. Someone was cutting branches off their little newly-planted redbud at night. Sigh. How well TPP knows the repeated and wanton vandalism the neighbors were talking about because you would not believe how many shrubs and small trees have to be fenced in our gardens to protect them from vandalism […]
7:48 PM | Hawaiian shirts making a come back
What?? Hawaiian shirts are making a fashion come back.  When did Hawaiian shirts ever go out of style? Certainly none of the tropical biologists TPP associates with have ever stopped wearing them, and hey, who gets to dictate tropical style if not tropical botanists. It was many years ago now that TPP got to thinking about professional attire, and the basic premise was that neckties were truly stupid, although to be fair, TPP was gifted a couple of Jerry Garcia ties […]
7:28 PM | Missing the Mastodon
When I look out my front window to the Wasatch Front, I can’t help but feel that there’s …
7:09 PM | Lamarck & the Epigenetic revolution in evolution (Press Release) Available from Amazon in paperback & all major book outlets from 20th Dec 2014
PRESS RELEASE “LAMARCK was RIGHT as seen in the SILENT EPIGENETIC REVOLUTION IN EVOLUTION” Dig-Press (contact Maria B. O’Hare) E-mail: Website: New Paperback Book entitled: THE EPIGENETIC CATERPILLAR: AN ALTERNATIVE TO THE DARWINIAN VIEW OF THE PEPPERED MOTH PHENONMENON by MARIA B. O’HARE (PHD). ISBN: 978-1-78280-388-1 (Launch date: 20th December 2014) will be […]
5:53 PM | Why Facebook can be toxic for relationships
I have noticed that many people are involved in quarrels on Facebook, in the way they would have never quarreled during any tete-a-tete conversation. Quarrels caused by trifles, by words said hastily, by small misunderstandings. Quarrels caused by a routine exchange of words and by an outburst of emotions which, once written, exercise their toxic […] The post Why Facebook can be toxic for relationships appeared first on Social Ethology.
12:24 PM | Identifying and correcting errors in draft genomes
Over the past decade we have seen an exponential increase in the number of sequenced, assembled, and annotated genomes. These these genomes are essential for pretty much any genomics research. If you want to sequence the genome, transcriptome, epigenome, or … Continue reading →

December 08, 2014

7:11 PM | What have we learned from the recent spate of incidents of police violence on black victims?
What have we learned from recent spate of incidents of police violence on black victims?  Tom Tomorrow has the answers, at least from one perspective. All of this seems to be symptoms of a much more serious, troubling, and deep-seated problem in our culture, in our country. Did all of our city police departments use training films taken in Selma during the 1960s? And even in a "nice" Midwestern college town minorities are subject to unjustified profiling and harassment […]
4:22 PM | Et tu, Brute? Black-legged ticks use genes co-opted from bacteria to fight bacterial infection
Horizontal gene transfer occurs when genes are passed between individuals by mechanisms other than reproduction. It is common in bacteria and occasionally happens between highly divergent groups (for example, monocot genes transferred to eudicots, fungal genes transferred to aphids, bacterial genes transferred … Continue reading →
4:00 PM | “Hurrah! Hurrah!” DNA barcoding and the lost story of Darwin’s meadow
Five years ago, I was a co-author on a consortium paper in PNAS that recommended two genes to serve as universal markers for DNA-based identification (DNA barcoding*) of plants. Five years ago, the world celebrated Charles Darwin’s 200th birthday. You … Continue reading →
2:00 PM | Different approaches to causality in linguistics
Damian Blasi and I are organising a workshop on Causality in the language sciences (call for presentations now open!). As we were talking about the themes, we realised that there are multiple ways that a causal mechanism may manifest itself in the real world, and that very different statistical approaches may be applicable to each. […]
10:42 AM | Why Do Mosquitoes Bite Humans?
The mosquito Aedes aegypti , which preys on humans in tropical and subtropical ...
8:00 AM | We need more complicated mathematical models in economics
I am half way through David Colander and Roland Kupers’s book Complexity and the Art of Public Policy: Solving Society’s Problems from the Bottom Up. Overall, it’s a good book, although the authors are somewhat slow to get to the point and there are plenty of lines that perplex or annoy (Arnold Kling seemed to […]

December 07, 2014

11:00 PM | Experimental Failures in Baking
Today I did something horrible… almost unimaginable. I took a 30 year tradition in my family and stomped it flat… and was punished for it. Let me explain. There is a particular cookie that my mother made for me every holiday season for the past 30 years or so. I get one batch of these […]
4:44 PM | Do Disturbances to Neuronal Maturation Lead to Autism?
A few weeks ago I summarized the findings of our latest study in Frontiers. Unfortunately, I gather as there was almost no interest in the blog that I did a […]
3:43 AM | Some history of hype regarding the human genome project and genomics
Just taking some notes here - relates to a discussion going on online.  Would love pointers to other references relating to hype and the human genome project (including references that think it was not overhyped).Here are some things I have found:White House press conference on announcing completetion of the human genomeGenome science will have a real impact on all our lives -- and even more, on the lives of our children. It will revolutionize the diagnosis, prevention and treatment of […]
12:30 AM | Old Dates Pose Problems for Old Theories
One of the running quarrels on this blog concerns the age of language. I think it began about 1.8 million years ago while a great many linguists and archaeologists date it, at most, as 0.1 million years ago. The main...

December 06, 2014

9:53 PM | December GENETICS Highlights
The  December issue of GENETICS is out now! Check out the highlights below or the full Table of Contents here. Ectopic centromere nucleation by CENP-A in fission yeast, pp. 1433–1446 Marlyn Gonzalez, Haijin He, Qianhua Dong, Siyu Sun, and Fei Li … Read MoreThe post December GENETICS Highlights appeared first on Genes to Genomes.
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