Whalefall

"Life for these Fir seedlings began in unfortunate circumstances. Perhaps they germinated underneath..."

earthlab — Wed, 22 May 2013 15:00:42 -0400

“Life for these Fir seedlings began in unfortunate circumstances. Perhaps they germinated underneath power lines, or in lots slated for development. These youths sprout as wayward and neglected weeds. They are highly at-risk for future delinquency: blocking views, disrupting power lines, and worse. Society generally chops them down before they have a chance. These yearlings must be rescued and nurtured.”

- Unsanctioned Restoration | forest habitat restoration, eco-artwork

"Here, we use the concept of “citizen science” to quantify taxon-specific contributions..."

earthlab — Tue, 21 May 2013 18:11:34 -0400

“Here, we use the concept of “citizen science” to quantify taxon-specific contributions to dung decomposition at the level of a nation.”

- ESA Online Journals - Using citizen scientists to measure an ecosystem service nationwide

ESA Online Journals - An invasive species facilitates the recovery of salt marsh ecosystems on Cape Cod

earthlab — Tue, 21 May 2013 18:10:30 -0400

ESA Online Journals - An invasive species facilitates the recovery of salt marsh ecosystems on Cape Cod:

With global increases in human impacts, invasive species have become a major threat to ecosystems worldwide. While they have been traditionally viewed as harmful, invasive species may facilitate the restoration of degraded ecosystems outside their native ranges. In New England, overfishing has depleted salt marsh predators, allowing the herbivorous crab Sesarma reticulatum to denude hundreds of hectares of low marsh. Here we show that the subsequent invasion of green crabs, Carcinus maenas, into heavily burrowed marshes partially reverses decades of cordgrass die-off. By consuming Sesarma, eliciting a non-lethal escape response and evicting Sesarma from burrows, Carcinus reduces Sesarma herbivory and promotes cordgrass recovery. These results suggest that invasive species can contribute to restoring degraded ecosystems and underscores the potential for invasive species to return ecological functions lost to human impacts.

"Prey species with anti-predator defences, such as wasps and sticklebacks, were sometimes eaten in..."

earthlab — Thu, 14 Mar 2013 08:55:21 -0400

“Prey species with anti-predator defences, such as wasps and sticklebacks, were sometimes eaten in abundance.”

- Stomach contents from invasive American bullfrogs Rana catesbeiana (= Lithobates catesbeianus) on southern Vancouver Island, British Columbia, Canada - Pensoft

(via » Press Release – Larger Pacific Striped Octopus)

earthlab — Tue, 12 Mar 2013 09:15:38 -0400

(via » Press Release – Larger Pacific Striped Octopus)

Mind, Brain and Big Science

earthlab — Thu, 07 Mar 2013 08:58:13 -0500

Comment on What’s Wrong with the Brain Activity Map Proposal:

Fascinating read. BAM struck me as problematic from the beginning; not that it shouldn’t be done, necessarily, but it seemed like the wrong choice for a Big Science project, especially one with an ostensible public health goal.

I’d argue that BAM proceeds from the possibly faulty assumption that it’s possible to understand mind by partitioning brain at ever more discrete levels. Not that “mind” and “brain” are separate, but the distance between them is filled by as-yet-undetermined processes more likely to be understood by looking at circuitry and psychology.

(Mithra gets at that with “the authors imply that this correlated or collective behavior cannot be deduced from other levels of observation,” though with some reservations about the troublesome nature of ‘emergent.’ FWIW, I’d embrace the idea; the problem is the fuzzy nature of emergence, but the idea of studying it at the wrong scales. You don’t understand the forest by looking at each tree with ever-larger magnifying glasses.)

There are also just too many differences between the brains of model organisms and our own, especially when it’s unlikely the BAM methods will ever be used in a human. Add the hype-machine circumstances — billions of dollars, Presidential promotion — and there will be enormous indirect pressure to skew the science, or at least its public communication.

Or, to make an analogy to the genome efforts, tagging every SNP won’t teach you about network structures or chromosome geometry. Moving one scale up, epidemiology gives us far more meaningful information about common disease than GWAS have, and likely than even large-scale rare variant surveys will. But at least the genome efforts have been tremendously beneficial in many other ways. The BAM efforts are far more speculative.

And, again, there’s nothing wrong with speculation. In an ideal world, we’d take our military budget and use it to fund speculations of all sorts. But putting an amount equivalent to nearly half the National Science Foundation’s yearly budget into something like BAM should happen after, not before, an open and public discussion of the science.

"The problem isn’t solely that self-appointed scientists often jump to faulty conclusions about..."

earthlab — Fri, 22 Feb 2013 08:45:10 -0500

“The problem isn’t solely that self-appointed scientists often jump to faulty conclusions about neuroscience. It’s also that they are part of a larger cultural tendency, in which neuroscientific explanations eclipse historical, political, economic, literary and journalistic interpretations of experience.”

- Neuroscience - Under Attack - NYTimes.com

"We were told we had to sacrifice nature for the economy. In fact, we sacrificed both. We were told,..."

earthlab — Wed, 20 Feb 2013 17:14:34 -0500

“We were told we had to sacrifice nature for the economy. In fact, we sacrificed both. We were told, if everyone maximized their profit we would all gain. In fact, we all lost.”

- Life at the End of the World: PW Talks with Andri Snaer Magnason

(via The funny way we communicate « Pennsylvania Echoes)

earthlab — Wed, 20 Feb 2013 14:37:09 -0500

(via The funny way we communicate « Pennsylvania Echoes)

"Our results for P. ornata suggest that males carrying a wrapped prey increase their probability of..."

earthlab — Tue, 12 Feb 2013 12:28:28 -0500

“Our results for P. ornata suggest that males carrying a wrapped prey increase their probability of mating in the first sexual encounter compared with those presenting unwrapped gifts,”

- ScienceDirect.com - Animal Behaviour - Nuptial gift-giving behaviour and male mating effort in the Neotropical spider Paratrechalea ornata (Trechaleidae)

"Today we know that the Milky Way is a galaxy a hundred thousand light-years wide and that it..."

earthlab — Thu, 31 Jan 2013 10:38:30 -0500

“Today we know that the Milky Way is a galaxy a hundred thousand light-years wide and that it contains more than two hundred billion stars, including our sun. Our galaxy is shaped like a flat, spiraling disk, with a bulge at the center where the density of stars is greatest (there’s a black hole in there, too); we live more than halfway out, on one of the spiral arms. When you view the Milky Way, you are gazing through the plane of this disk and at the universe around and beyond—which, astronomers report, is imponderably vast and contains billions of other galaxies. Are there other sentient beings out there? Who knows. On Earth, at least, humans suppose that we alone seek out the sweep of our own galaxy. But we’re wrong. Late last week, in a paper in Current Biology, Marie Dacke, a biologist at Lund University, in Sweden, and her colleagues revealed that at least one other species takes guidance from the Milky Way: the dung beetle.”

- Dung Beetles, Dancing to the Milky Way : The New Yorker

H5N1 demoratorium p.s.

earthlab — Fri, 25 Jan 2013 17:10:00 -0500

Re: conversation at https://twitter.com/carlzimmer/status/294927572532359169

Would have been nice to see more of the older journalists distinguishing themselves, too. But just tracking down a critic isn’t enough in itself. There were plenty of pro-forma, down-at-the-bottom single-critic quotes in coverage. One has to make a judgement call about weighting the criticisms, and whether the stock narrative (transmissibility-enhancing H5N1 research to begin again; many top flu virologists say benefits outweigh risks; no need to talk more about it) was the right one. And there wasn’t time for that in the three or four non-press conference hours most daily journalists had to report on this story, especially if you hadn’t been following the story, the politics and the science fairly closely — which from questions asked at during the press conference seemed to be the case for most of us.

Some Thoughts on H5N1 Moratorium Lift

earthlab — Thu, 24 Jan 2013 15:56:00 -0500

Results of unscientific survey of mainstream H5N1 moratorium-lift stories near the top of Google News:

Number of stories: 21

Stories in which top quote has a direct interest in continuing H5N1 transmissibility enhancement: 19 (nearly all Kawaoka or Fouchier)

Stories in which top quote is critical of the research: 1

Number of quoted pro-transmissibility enhancement sources: 42

Number of critical or skeptical quoted sources: 12

***

Notes from an email ramble:

Reporters were told at 1pm yesterday about the big announcement, with embargo lift scheduled for 1pm today and a press conference at 10am.

The dynamics of this profession being what they are, this meant that daily journalists had part of an afternoon to report and several hours to write. In a situation like this, you either publish within a couple hours of embargo, or not at all. Obviously that’s not the case for publications hooked to weekly or longer news cycles, but the first wave of coverage, and arguably the most important from a public relations perspective, will come from the dailies.

Typically embargoed stories go out to reporters at least four or five days ahead of time. Even last-minute stories go out a couple days ahead. There was absolutely no reason not to inform reporters late last week. Arguably reporters (including myself) should be following the issue so closely that more time isn’t needed, and certainly some articles reflect that expertise, but most daily reporters in this situation are going to be generalists without a deep understanding of the material, who by default will give their imprimatur to whatever’s said at the press conference.

Looking at the stories out now, there’s clearly a lot of that. At best, the NIH, journals and virologists handled the situation badly. At worst, they manipulated it cynically. As Kawaoka said during the press conference, “We need the media’s help.” That might be true — I’m not in a position to quantitatively judge disputes over the necessity of their methodologies or value of their transmissibility insights — but however much they need our help, they certainly don’t have my trust.

"The shared responses in the evolutionarily ancient mesolimbic reward system suggest that birdsong..."

earthlab — Mon, 14 Jan 2013 12:27:21 -0500

“The shared responses in the evolutionarily ancient mesolimbic reward system suggest that birdsong and music engage the same neuroaffective mechanisms in the intended listeners.”

- Frontiers | Birdsong: Is It Music to Their Ears? | Frontiers in Evolutionary Neuroscience

"The algorithm for building an organism is therefore not only stored in a linear digital sequence..."

earthlab — Mon, 07 Jan 2013 21:59:05 -0500

“The algorithm for building an organism is therefore not only stored in a linear digital sequence (tape), but also in the current state of the entire system (e.g. epigenetic factors such as the level of gene expression, post-translational modifications of proteins, methylation patterns, chromatin architecture, nucleosome distribution, cellular phenotype and environmental context). The algorithm itself is therefore highly delocalized, distribu- ted inextricably throughout the very physical system whose dynamics it encodes.”

- The algorithmic origins of life

"Eels—with their simplicity of form, their preference for darkness, their gracefulness—have helped me..."

earthlab — Tue, 18 Dec 2012 16:06:49 -0500

“Eels—with their simplicity of form, their preference for darkness, their gracefulness—have helped me embrace the unnameable and get to the essence of experience, that which cannot be cataloged or quantified.”

- James Prosek in National Geographic Magazine - NGM.com

Holy eye candy.

earthlab — Mon, 17 Dec 2012 15:27:19 -0500

Holy eye candy.

(via Hive Plots - Linear Layout for Network Visualization -...

earthlab — Mon, 17 Dec 2012 15:21:20 -0500

(via Hive Plots - Linear Layout for Network Visualization - Visually Interpreting Network Structure and Content Made Possible)

(via James Prosek / James Prosek: Ocean Fishes)

earthlab — Thu, 13 Dec 2012 09:44:59 -0500

(via James Prosek / James Prosek: Ocean Fishes)

"DuPont, based in Wilmington, Delaware, says that it carried out over 400 field trials of Imprelis,..."

earthlab — Thu, 06 Dec 2012 15:26:16 -0500

“DuPont, based in Wilmington, Delaware, says that it carried out over 400 field trials of Imprelis, yet only a few months after Imprelis hit the market, complaints – and lawsuits – about dead trees from Iowa to New Jersey came rolling in.”

- Controversial weed-killer to be pulled from market : Nature News Blog