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Yuri Wolf
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No more p-values. The Basic and Applied Social Psychology journal  (BASP) announced [1] that they are imposing a ban on most forms of the null hypothesis significance testing (p-values and their ilk).

Statistical hypothesis testing [2] and, in particular, calculation of a p-value associated with the null hypothesis [3] have long been a staple of practical statistics. As any tool, statistical or otherwise, p-value have a great potential to be misused [4]. This lead the BASP editors to a radical step of banning null hypothesis significance testing, including p-values and confidence intervals in all guises [1].

Bayesian statistical analysis [5] will be considered for publication on a “case by case basis” [1].

[1] http://dx.doi.org/10.1038/nature14180
[2] http://en.wikipedia.org/wiki/Statistical_hypothesis_testing
[3] http://en.wikipedia.org/wiki/P-value
[4] http://xkcd.com/882/
[5] https://en.wikipedia.org/wiki/Bayesian_statistics

#statistics #dataanalysis #publishorperish

Ancient Nitrogen. A recent paper in Nature [1] suggests that ~3.2 Ga sediments bear traces of biogenic nitrogen.

This is an additional piece of evidence towards establishing the timing of life on Earth [2]. Stüeken et al. [1] show that mid-Archaean sediments show nitrogen isotopic ratio characteristic of biological fixation, most probably using molybdenum-based nitrogenase.

[1] http://dx.doi.org/10.1038/nature14180
[2] http://en.wikipedia.org/wiki/Evolutionary_history_of_life#Earliest_evidence_for_life_on_Earth

Related:

https://plus.google.com/u/0/103708767238549065633/posts/ZRBsqGwZwFw
https://plus.google.com/u/0/103708767238549065633/posts/aDA7ENkJqZ8
https://plus.google.com/u/0/103708767238549065633/posts/YqViyESmx1v

#evolution #geology #originoflife

Recent news [1] on Hadal fish.

The University of Aberdeen submersible filmed fish at the depth of 8,145 m, almost half a kilometer deeper than the previous record.

It has been suggested earlier by the same authors that fish are constrained to the maximum depth of 8,200 m because of the limitations imposed by their osmolite, TMAO ([2], see also my take in [3]).

So far the theory holds.

#evolution #molecularmachinery #physiology

[1] http://www.bbc.com/news/science-environment-30541065
[2] http://dx.doi.org/10.1073/pnas.1322003111
[3] https://plus.google.com/u/0/103708767238549065633/posts/aVhYfzdTVW9

There go my 15 seconds of fame...

This morning I received the following message:

Dear Dr. Wolf,

I am the science reporter at NNN. I came across your study on cardiac macrophages and think it would make a great topic for a news story. Would you be interested in talking about your work? I can come by your office at your convenience. Thanks very much for your time.

All the best,

MMM

(the name and the email address of MMM match the staff listing of NNN, so I presume it’s legit).

Why, oh why I never wrote anything on cardiac macrophages?!

#scienceandsociety #publishorperish

The mother of all incertae sedis? A recent paper [1] in PLOS One describes two species of Dendrogramma, a new genus of animals with no clear taxonomic affiliation.

The authors describe [1] specimens, collected back in 1986 from the ocean floor of the Australian continental slope at depths of 400-1000 m and stored in bulk since then. The specimens are clearly animals (or animal body parts), but nothing definite can be said of them, hence the classification Animalia, Metazoa incertae sedis. The authors suggest that these organisms can be distant relatives of Ctenophora [2] (the latter themselves are ambiguously placed at the base of the metazoan tree).

The two Dendrogramma species share mushroom-like shape with a stalk, ending in a mouth, and a fan-like disk on the opposite end with branching gastrovascular system canals. They have peculiar symmetry (part radial, part bilateral) and resemble some ancient animals known from Ediacaran [3] fossil fauna.

The authors were unable to extract DNA from the specimens, preserved in formaldehyde and ethanol.

One of the authors, Reinhardt Kristensen, already described three new animal phyla: Loricifera [4], Cycliophora [5] and Gnathifera [6]. This could be his biggest coup.

[1] http://dx.doi.org/10.1371/journal.pone.0102976 [PMID: 25184248]
[2] http://en.wikipedia.org/wiki/Ctenophora#Relationship_to_other_animal_phyla
[3] http://en.wikipedia.org/wiki/Ediacara_biota
[4] http://en.wikipedia.org/wiki/Loricifera
[5] http://en.wikipedia.org/wiki/Symbion
[6] http://en.wikipedia.org/wiki/Limnognathia

#phylogeny #biodiversity #evolution

The mystery of sailing stones at the Racetrack Playa in the Death Valley is apparently solved. A recent paper [1] in PLOS One reports the first direct observation (using GPS tracking) of stone movements at the Racetrack Playa [2] and suggests that they are bulldozed into motion by wind-driven sheets of thin ice.

Stones on the floor of the Racetrack Playa in the Death Valley apparently move, leaving visible trails in the dried mud [2, 3]. Despite decades of observation and intense speculation [4, 5] nobody before had observed the stone movement directly [5].

Locally parallel tracks had long suggested that wind is the primary driving force for the sailing stones, although early experiments suggested that at normal conditions even the wind gusts are not strong enough to move the stones. Accumulating evidence gradually pointed to the major role of ice sheets, forming around the stones [6].

Recently a multidisciplinary group of scientists fitted GPS tracking devices to several rocks and synchronized the recorded tracks with local meteorological records [1]. Rock movement was recorded at speeds of 2-5 m/min. Nearby rocks move not only in parallel, but preserving their relative positions to each other, suggesting that the whole field moves at once. The direction of movement coincides with the locally prevailing wind direction.

The authors show that melting “windowpane” ice 3-6 mm thick breaks under the relatively light wind (4-5 m/s) into chunks of tens of meters in size. The winds drag the ice, slowly bulldozing the frozen-in stones across the wet playa floor. Unlike it was suggested earlier [6], the ice is not sufficiently thick to float the stones.

[1] http://dx.doi.org/10.1371/journal.pone.0105948 [PMID: 25162535]
[2] http://en.wikipedia.org/wiki/Racetrack_Playa#Sailing_stones
[3] http://www.yurikira.com/bin/getThree.cgi?List=DVal&Mask=14&Dirn=&Picn=04l26n4759
[4] http://dx.doi.org/10.1126/science.117.3042.438-a [PMID: 17795134]
[5] http://www.amazon.com/s?search-alias=stripbooks&field-isbn=978-0878423620
[6] http://dx.doi.org/10.1119/1.3490645

#geology

Compressed communication.@BMCBiology tweeted about our recently published paper [1] in the following form:

”Eugene Koonin examines the dynamics of gene families within prokaryotic supergenomes. And what does he find? Turmoil! http://bit.ly/1q2sZjj [2].

I am not convinced that this is the best 140-character description of the work. On the other hand @BMCBiology people are supposed to know their target audience better than I do.

On the third hand, here are two alternative outlooks on Twitter use in science: [3,4].

[1] http://www.biomedcentral.com/1741-7007/12/66 [PMID: 25141959]
[2] https://twitter.com/BMCBiology/statuses/502448613575122944
[3] http://www.nature.com/news/online-collaboration-scientists-and-the-social-network-1.15711
[4] http://phdcomics.com/comics/archive.php?comicid=1737

#publishorperish #scienceandsociety #language

Yet another great data visualization [1] from Randall Munroe, the XKCD.com author - worst hurricanes on the USA East Coast. One might possibly improve on it by gently shading the areas according to the year, using a rainbow range from 1914 to 2014.

[1] http://xkcd.com/1407/

#maps #visualization #dataanalysis

Today I Learned that woodpeckers do not violate Energy Conservation laws. A recent paper [1] analyzes energy distribution and transfer in the body of a woodpecker.

Ability of woodpeckers to sustain multiple head impacts without apparent brain injury is the subject of many decades of research [2-4]. Until recently the studies concentrated on the brain suspension system [5] that allows for safe deceleration at rates of 600-1500 g [1].

The paper by a group of researchers from Dalian University of Technology (Dalian, China) shows that 99.7% of the mechanical energy is converted into strain energy in the bulk of body and only 0.3% is dissipated in the head during successive peckings. According to the authors’ calculations, 25 peckings in one second increase the brain temperature by ~0.14°C. They theorize that to avoid brain overheating woodpecker has to take a break for heat dissipation after a certain number peckings.

Many details of the mechanical model are treated by the authors in passing, but they find it necessary to note such details as “the beaks are in front of the head where the collision happens”. This, apparently, indicates the target audience of engineers rather than biologists.

[1] http://dx.doi.org/10.1007/s11431-014-5582-5
[2] http://dx.doi.org/10.1016/S0140-6736(76)91477-X [PMID:58330]
[3] http://dx.doi.org/10.1111/j.1469-7998.2006.00166.x
[4] http://dx.doi.org/10.1371/journal.pone.0026490 [PMID: 22046293]
[5] http://en.wikipedia.org/wiki/Woodpecker#General_characteristics

#engineering #evolution
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