a citizen’s journal by Thomas Nephew


Posted by Thomas Nephew on 29th July 2008


Scientific American
Nature: Science Update
Proceedings of the Natl. Academy of Sciences
American Scientist
New Scientist
Technology Review
National Geographic
Smithsonian Magazine



* Hubble Space Telescope
* Earth Observatory
* Exploring Mars
* Galileo mission

National Air and Space Museum
* Center for Earth and Planetary Studies

Astronomy Picture of the Day
SETI@Home: Search for Extraterrestrial Intelligence At Home



IPCC (Intergovernmental Panel on Climate Change)
NOAA (Natl Oceanic & Atmospheric Admin.)




* Education
* WaterWatch
* Maryland geologic maps


Latest earthquakes, magnitude 4+
USGS Earthquake Hazards Program

Life sciences

National Museum of Natural History
* Explore a Topic
* Research and Collections
* Naturalist Center (Leesburg)
* Plant Image Collection
* Current greenhouse highlight

National Zoo
* Backyard Biology
* Conservation and Science: the hidden zoo

U.S. Botanic Garden
Native Plants for Wildlife Habitat and Conservation Landscaping: Chesapeake Bay Watershed
Missouri Botanical Garden
CONE WELDER: observe and report birds via webcam

Human Genome Project, The Genome Channel, International HapMap Project
Information Systems for Biotechnology

The Scientist

Blogs: The Panda’s Thumb


Public health

CDC; Pandemic Flu
Schaffer Library of Drug Policy

Blogs: Effect Measure


Click for larger map of
Confirmed H5N1 cases

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Cool stuff

Posted by Thomas Nephew on 6th April 2006

# Wikocracy — Sick of the same old boring Digital Millennium Copyright Act? USA Patriot Act? U.S. Constitution? Rewrite your own, wiki-style! “Over time, this platform could reflect a collaborative statement of what we think the law should be. Or it could reflect a moment-by-moment statement of the most recent editor’s views. This will be as bloody or as civil as you make it… This is only a test.” — There are four new amendments to the Constitution so far.

# Connexions — Possibly more of a future in this Wiki-like collaboration system for writing textbooks. “Our Content Commons contains small “knowledge chunks” we call modules that connect into courses. “

# Antarctic ice collisionIn 2000, several large pieces of the shelf broke off and wandered around in the Ross Sea, breaking into several smaller bergs over the next few years. Among the survivors of the initial calving event is piece C-16. In late March 2006, C-16 worked its way northward along the coastline and plowed into the tip of the Drygalski Ice Tongue. The collision knocked loose a chunk from the tip of the ice tongue.

# Self-propelled liquid droplets“This phenomenon is called the Leidenfrost effect (or film boiling) and occurs beyond a surface temperature called the Leidenfrost point (about 200 – 300 C for water on flat surfaces, depending on surface quality). … We discovered that film-boiling droplets move at speeds of several centimeters per second when placed on asymmetrically structured surfaces (movie), such as a piece of brass with periodic, saw-tooth shaped ridges (see highspeed movie).” — The author thinks pumps and other devices could be powered by the effect.

# Tune in and prosper — unusual Star Trek footage over at Gary Farber’s “Amygdala.”

# Estimate the effect on North America of a 7m rise in sea level. — Things get even more exciting when you zoom in. You can switch to other parts of the world. Elsewhere, a 3/24/06 Scientific American article warns:

Experts predict that at current levels of greenhouse gases–carbon dioxide alone is at 375 parts per million–the earth may warm by as much as five degrees Celsius, matching conditions roughly 130,000 years ago. Now a refined climate model is predicting, among other things, sea level rises of as much as 20 feet, according to research results published today in the journal Science.

NOTES: Liquid droplets via sofa. rites de passage; Connexions via Savage Minds, sea level simulation via Making Light “Particles”.

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New dawn for oldest profession

Posted by Thomas Nephew on 7th June 2005

During the chaos in the monkey cage, Chen saw something out of the corner of his eye that he would later try to play down but in his heart of hearts he knew to be true. What he witnessed was probably the first observed exchange of money for sex in the history of monkeykind. (Further proof that the monkeys truly understood money: the monkey who was paid for sex immediately traded the token in for a grape.)

…from “Monkey Business,” by Stephen Dubner and Steven Levitt (the authors of “Freakonomics”) in the New York Times, via Savage Minds (“Notes and Queries in Anthropology”), where co-blogger Kerim adds:

I have long believed that humans place too much stake on language in evaluating the cognitive abilities of our fellow creatures, and I hope that experiments like these serve to broaden our understanding of the multiple intelligences required for linguistic communication.

The story reminds me of my “Kinsley’s conjecture” and “What do you believe is true even though you cannot prove it?” posts, with Kerim’s statement serving as one response to Dennett’s assertion. Of course it took the specific prompts and environment of the laboratory to make it happen, but it makes me wonder whether monkeys do anything like this in the wild. You can imagine the research leading to some prototype “uplift” experiments — so to speak.

At any rate, go to the Times story for the facts and to the Savage Minds link for better informed speculation, and generally for a very interesting blog indeed. I discovered it via a typically fascinating Timothy Burke reflection on a different Savage Minds post (one that Burke ultimately disagrees with) about military consumption and generation of anthropological research.

The monkey research is done by Yale economist Keith Chen, who figured that capuchin monkeys — each one a “bottomless stomach of want” in his words — might be interesting subjects for modeling a number of economic theories and/or irrational human behaviors. He may be on to something. For example, it turns out that capuchins much prefer gambling for a small potential gain than for an equally small potential loss, a.k.a. “loss aversion.” The conclusion rings true:

The data generated by the capuchin monkeys, Chen says, ”make them statistically indistinguishable from most stock-market investors.”

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What do you believe is true even though you cannot prove it?

Posted by Thomas Nephew on 19th January 2005

That’s the question posed by John Brockman, the publisher of the scientific website, to 120 scientists and thinkers. As Brockman writes, many answers have to do with the nature (and even the primacy) of consciousness, but even within this topic there are a number of interesting variations and contrasts. For example:

Joseph Ledoux (neuroscientist, New York University)

For me, this is an easy question. I believe that animals have feelings and other states of consciousness, but neither I, nor anyone else, has been able to prove it. We can’t even prove that other people are conscious, much less other animals.

Daniel C. Dennett (philosopher, Tufts University):

I believe, but cannot yet prove, that acquiring a human language (an oral or sign language) is a necessary precondition for consciousness–in the strong sense of there being a subject, an I, a ‘something it is like something to be.’ It would follow that non-human animals and pre-linguistic children, although they can be sensitive, alert, responsive to pain and suffering, and cognitively competent in many remarkable ways–including ways that exceed normal adult human competence–are not really conscious (in this strong sense): there is no organized subject (yet) to be the enjoyer or sufferer, no owner of the experiences as contrasted with a mere cerebral locus of effects.

That’s very hard for me to believe about many dogs and cats I’ve known, but I can’t prove Dennett wrong, either, so let that go. I’ll be back to look at more answers, this is one of the more interesting sites I’ve run across lately. Via a great “Links Dump” post by Chad Orzel; see other finds of his there, especially “Read Your Signature on the Scattered Ashes,” about the stories that your possessions tell about you, and particularly the ones intentionally kept items tell about you.

NOTE: 08/30/10: see also “New Dawn for Oldest Profession“, and this “Followups” item mentioning the assertion that prairie dogs have a language.

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Followups department

Posted by Thomas Nephew on 12th January 2005

Stories touching on various posts on this blog, including…

  • Time shaving: a shameful pattern of corporate theft

    Wal-Mart lawsuit certified in Cambridge, MA (2005/01/08): “The lawsuit alleges that Wal-Mart managers deleted hours from workers’ payroll records, and did not provide meal and rest breaks. The suit is among a flurry of legal complaints brought against Wal-Mart in recent years.”

  • German prosecutors seek greater U.S. cooperation in Motassadeq 9/11 case

    9/11 Cases Proving Difficult in Germany (2004/12/13): “Prosecutors and the five-judge panel overseeing the trial said they still hope U.S. officials will provide fresh evidence or allow Mohammad and Binalshibh to be questioned directly. The German federal prosecutor, Kay Nehm, said Tuesday at a news conference in the city of Karlsruhe that U.S. officials had agreed to provide more information for the Motassadeq trial that he hoped would pave the way for a conviction.

    Nehm did not give details about the information being sought. Spokesmen for the U.S. Justice and State departments did not respond to requests for comment.

    The court has also sent invitations to members of the Sept. 11 commission to testify about the report they issued last summer, which described the formation and inner workings of the Hamburg cell in detail.”

  • Kinsley’s conjecture

    Prairie dogs appear to have their own language (2004/12/06): “They have different ‘words’ for tall human in yellow shirt, short human in green shirt, coyote, deer, red-tailed hawk and many other creatures.

    They can even coin new terms for things they’ve never seen before, independently coming up with the same calls or words, according to Con Slobodchikoff, a Northern Arizona University biology professor and prairie dog linguist.”

    (via Eric Muller, who asks the really important question)

  • Tsunamis

    How Scientists and Victims Watched Helplessly (2004/12/31), describing scientists at the Pacific Tsunami Warning Center, unclear on the danger at first — and then unable to do anything about it once the danger was apparent: “Their instinct was to somehow tell more, to warn the region that it would continue, to reach people who could clear beaches. But how? Mr. Hirshorn recalled a tsunami expert he knew in Australia, called and got an answering machine. He left a message. Someone phoned the International Tsunami Information Center, asking if they knew people in the stricken region. The center simply had no contacts in this distant world.”

EDIT, 1/12: Cambridge, MA, not Boston

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Looking for chameleons? Use a satellite

Posted by Thomas Nephew on 3rd July 2004

inset from figure on NASA Earth Observatory site

To me, this is extremely, triumphantly, hopping-up-and-down cool: scientists from the American Museum of Natural History used archived museum records, satellite imaging, computer mapping (a.k.a. GIS), and genetic algorithms to discover unsuspected chameleon habitats in Madagascar. From NASA’s “Earth Observatory” web site, Madagascar’s Chameleons:

Raxworthy and his colleagues have been developing predictive models that are based on a combination of satellite observations of environmental characteristics — such as land cover from NASA’s Moderate Resolution Imaging Spectroradiometer and topography from the Shuttle Radar Topography Mission — and museum records of locations where biologists and naturalists have spotted different chameleons over the years. […]

The scientists were initially surprised that for four species, the models predicted that the species lived in areas where no specimens had ever been documented before (bottom row, colored ovals). … [and] eventually discovered that far from being a mistake, these overlapping “over-predicted” areas actually pointed to locations where new species of chameleon were likely to be discovered.

(The “overpredicted” areas are circled in the figure above.) In the accompanying article Uncovering Chameleons, writer Rebecca Lindsey explains:

To come up with ecological niche models for Madagascar’s chameleons, Raxworthy and his colleagues [used] a genetic algorithm nicknamed GARP (which stands for Genetic Algorithm for Rule-set Prediction).

GARP evaluated the models based on the number of chameleon location points from the original museum records it correctly predicted, as well as by its ability to identify places where the species would not be found. GARP kept evolving the mathematical rules of the survivors and deleting the losers until it produced a single model that it couldn’t improve upon—survival of the fittest.

The real world soon provided confirmation — of a sort — for the satellite image-museum data-GARP process:

“At the time this modeling project was going on, we were also identifying chameleon specimens we had collected on previous expeditions to Madagascar,” explains Raxworthy, “so the discoveries were going on in parallel universes, so to speak. Then one day I realized that one of the new species we had discovered actually came from an over-predicted area on one of the model’s maps. It finally occurred to me that maybe each of those areas that we thought were model foul-ups could actually be the location of new species”.

As the team identified more of the specimens, the number of newly identified species began to mount. In all, the over-predicted areas identified by the models were home to seven new species of chameleon that had never been documented by scientists before. (emphasis added)

My rudimentary evolutionary theory suggests to me the newly identified species occupy ecological niches that might well have otherwise been occupied by those Raxworthy et al focused on (e.g., Brookesia stumpfii, see figure above). It would be interesting to know just how divergent — genetically and phenotypically — the newly discovered species are from those ‘erroneously’ predicted to be there by the GARP process: close cousins? Convergent evolution?

The method Raxworthy et al developed (or at least convincingly demonstrated, I’m not up on this) has obvious applications in ecology and conservation biology at minimum. But it might have applications in sociology and political science as well — I imagine the thing being modeled doesn’t absolutely have to be an evolving entity of its own for GARP etc. to be worth a try. At any rate, an article about all this has been published in Nature,* and I may actually make my way to some university library or other to xerox it.

Waah. Those are the toys I want to play with. Hmmm… maybe I can.

* Christopher J. Raxworthy, Enrique Martinez-Meyer, Ned Horning, Ronald A. Nussbaum, Gregory E. Schneider, Miguel A. Ortega-Huerta2 & A. Townsend Peterson. Predicting distributions of known and unknown reptile species in Madagascar. 2003. Nature 426, 837-841.

UPDATE, 7/6: More genetic algorithms in the news: a German-American team used the technique to optimize network server performance. Via Gary Farber.

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Well, I’m sold

Posted by Thomas Nephew on 24th May 2003

Nature Science Update reports that CalTech astronomer David Stevenson wants to explore the interior of the Earth by melting thousands of tons of iron, cracking the Earth’s crust with a nuclear explosion, putting a probe in the molten pool of iron, and letting it all sink towards the Earth’s core.

Leaving aside what the probe could report (“Still in a molten pool of iron”) there’s a problem:

“Frankly, I would be surprised if this really works,” he admits.

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Present at the creation: M17 “Swan” Nebula

Posted by Thomas Nephew on 29th April 2003

Present at the creation: M17 “Swan” Nebula

Department of Unprovable Assertions

Flying home from my dad’s birthday (75!), I picked up a “Scientific American” in the news kiosk, intrigued by the “Parallel Universes” cover story. Among the simpler arguments presented was that (1) the available evidence apparently supports the intuitive notion that space is infinite (not “curved” so that a latter-day Magellan would return to his starting point), (2) there seems no reason to suppose the space beyond our viewing horizon (speed of light * age of universe) isn’t full of stuff, too, so that (3) there’s enough stuff to eventually make a duplicate galaxy with a duplicate you sitting in it reading a duplicate blog post by a duplicate me. This is called a Level I parallel universe (where “universe” is actually just “everything you can see,” which is much less than “everything there is.”)

Looking at that image above, or just at ants making their way across my lawn, I have trouble believing in that: there just seems too much detail, whimsy, and beauty for anything so vast as my universe to be repeated. On the other hand, it might be comforting to believe the whole universe is so dumb it would allow a parallel “Survivor” show somewhere 10^(10^28) meters away. At that rate, my own dumb habits would be a little easier to put up with.

But the idea seems seems to imply that once you’ve arranged all the atoms etc. identically, the whole process leading to the arrangement and the whole process following it must be identical. Otherwise, what accounts for the difference before or after the moment when the two universes are identical? Yet if the two universes are in different places, that can’t be. So something seems wrong to me, and it’s probably that I’ve stayed up too late again.


UPDATE, 10AM: OK, thinking about it a little more, there’s no need to assume two identical universes got identical the same way, any more than two paintings had to be completed with the same series of brushstrokes to be identical. So Level I universe cosmology is safe from my late-night criticism. I’m also not sure the two identical universes would have to stay identical once they got that way: at the periphery of the two identical universes, observers would see different things, and would thereby become different: different memories, science, etc. This would work its way to the center of each identical universe. Therefore: never mind.

UPDATE, May 14: I just noticed that Chad Orzel discussed the article and my questions yesterday. Thanks!

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Von Karman Vortex street

Posted by Thomas Nephew on 24th January 2003

I got curious about the picture below, and found this nifty item, courtesy of Brazilian fluid dynamicist Dr. Cesareo de La Rosa Siqueira. I now know that a regular pattern of vortices is called a “vortex street.” From the web site:

Since ancient times, it has been known that wind causes vortex induced vibration of the wires of an Aeolian harp. According to Rabbinic records, King David hung his kinnor (kithara) over his bed at night where it sounded in the midnight breeze. In the fifteenth century, Leonardo da Vinci sketched a row of vortices in the wake of a piling in a stream. In 1878, Strouhal found that the Aeolian tones generated by a wire in the wind were proportional to the wind speed divided by the wire thickness. He noticed that the sound greatly increased when the natural tones of the wire coincided with the Aeolian tones. In 1879, Lord Raleigh found that a violin string in a chimney draft vibrated primarily across the flow, rather than with the flow. The periodicity of the wake of a cylinder was associated with vortex formation by Benard in 1908 and with the formation of a stable street of staggered vortices by von Karman in 1912. (ref.: Flow-Induced Vibration, Robert D.Blevins).

I added the da Vinci link. There you go.

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Terraforming Today

Posted by Thomas Nephew on 20th October 2002

NASA SeaWiFS image: chlorophyll concentrations in NE Pacific, 7/29/2002
Image via NASA Earth Observatory: “Sea-viewing Wide Field-of-view Sensor
(SeaWiFS) image shows chlorophyll concentrations in the N.E. Pacific Ocean.
Note the patch of high chlorophyll concentration (yellow and red pixels)
toward bottom center of the image. This patch was created by the SERIES Project
(Subarctic Ecosystem Response to Iron Enrichment Study).

“Terraforming,” for readers who avoid the science fiction shelves in their local bookstores and libraries, is the word coined to describe changing another planet’s characteristics wholesale, obviously with the goal of making that planet more habitable for humans.* The photo to the right might be considered experimental terraforming of our own planet.

As the photograph’s NASA link explains, the image depicts a patch of sea off the Alaskan coast with strikingly different chlorophyll concentrations than the surrounding ocean:

By “seeding” the seawater with trace amounts of iron—the equivalent of one geritol tablet per hundred tons of sea water—scientists stimulated a fairly large phytoplankton bloom. In this patch, the chlorophyll levels are elevated from mid-ocean values of near 0.3 milligrams per cubic meter (blue pixels in this image) to more than 3 milligrams per cubic meter (yellow and red pixels)…

Similar experiments have occurred in the South Pacific; taken together, they largely validate the so-called “iron hypothesis” advanced by Dr. John Martin, which asserted that the “desolate zones” of the open ocean where next to no phytoplankton (microscopic chlorophyll-based life) is found can be explained by these regions’ near-complete lack of dissolved iron, rather than by predation or the lack of other trace elements.

How does this relate to terraforming? Because, as Dr. Martin put it, “Give me a half tanker of iron, and I will give you an ice age.” Inevitably, the surge of biomass produced by iron fertilization of a desolate zone will first remove carbon dioxide from the atmosphere and surface water, and then, upon death, settle into the deep ocean. This net removal of carbon dioxide from the atmosphere would contribute to global cooling, just as net additions of carbon dioxide contribute to global warming.

Personally, this seemed like a pretty cool (no pun intended) idea to me: if global warming ever gets too far out of hand, we may have an ace in the hole with Dr. Martin’s suggestion. As the linked biography suggests, though, the idea was quickly controversial; it is also clear that Dr. Martin himself was not advocating the immediate start-up of an iron fertilization program. Rather, he just wanted more research done, and the photo above is a tribute to his success on that score.

What are the possible drawbacks? Some of the experiments have shown less than expected carbon flow to the deep sea, so that the method’s efficacy is not always high; it would take more iron to work, with whatever drawbacks (beyond sheer cost) there are to iron level “spikes” in the upper ocean. Perhaps more importantly, the deep sea environment could change drastically; removing enough carbon dioxide to reverse historical industrial carbon dioxide additions to the atmosphere might well raise deep sea pH (acidity) levels by 0.1 pH,** and deep sea organisms are very sensitive to such changes. As Richard Monastersky of Science News writes in his 1995 account of the “IRONEX” experiment off the Galapagos, the decay of plant matter would rob the upper ocean of oxygen, and might release significant amounts of methane, an even more potent greenhouse gas than carbon dioxide. Even good friends of John Martin like Sally Chisholm of MIT are among the leading skeptics of the “geritol tablet” option to fighting global warming.

So now I’m not sure about it, except as an emergency measure. I suppose the controversy may someday be, is the emergency already severe enough to warrant trying mass iron fertilization as a last-ditch way out, and who pays for it, and who approves doing it. It was interesting to read about, though. For me at least.

* Among the foremost science fiction novels dealing with the possibility are Kim Stanley Robinson’s Mars Trilogy (Red Mars, Green Mars, Blue Mars). Robinson attempts to make the prospect seem legitimately controversial even for sterile Mars, and largely succeeds; as the titles indicate, that controversy is won by the terraformers.
**It’s been a while, but I believe this equates to about a 25% increase in acidity; not a gargantuan increase, but not as negligible as “0.1” looks at first glance. As the link indicates, “reverse” means to return atmospheric carbon dioxide to twice the pre-industrial level, and not the attempt to return all the way to that level.

UPDATE, 3/24/06: broken link at “occurred” edited to point to “SOIREE: A Phytoplankton Party in the South Pacific.” SOIREE stands for “Southern Ocean Iron Enrichment Experiment.”
EDIT, 12/3/12: new photo image uploaded to, linked from Photobucket account, captioned.

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