"Our sense of wonder grows exponentially; the greater the knowledge, the deeper the mystery."

-- E.O. Wilson

Web scienceontap.blogspot.com

Thursday, December 31, 2009

Good Readin'

Utne Magazine lists their top-rated magazines from the last decade:


Statins, Side Effects

Just one anecdotal report (out of many):


Planning For Earth's Future

Russians are making tentative plans to 'deflect' an asteroid, 99942 Apophis (estimated to be 3 times larger than the famous 1908 Tunguska meteorite), headed toward earth on a 20-year timetable. I don't expect to still be around at that point, so not too concerned about it, but for those who are, read all about it:


Wednesday, December 30, 2009

Frank Wilczek Interviewed

NY Times interview with Nobel prize laureate (physics) Frank Wilczek of MIT:


Owl Pellets

And now for something totally different --- an owl pellet dissected:


Tuesday, December 29, 2009

And This is News???

Weakness reported in FDA approval system for new cardiovascular devices HERE.

The drug approval path has always had such weaknesses, as well. Indeed it would be cost-prohibitive to conduct and await truly strong scientific analyses/screens of products in the medical pipeline. The pressure to opt for speed (and profit) in the process will always overwhelm the emphasis on safety. The solution is not to spend more time on better science, but to better communicate the potential risks and negative outcomes of treatments to consumers, moving toward an improved system of informed consent (medicine ought be consensual, not brow-beaten).

Science's Role

The place of science in society from Rachel Carson, and Chet Raymo:


Quantum Mechanics Redux

Latest book from science writer Jeremy Bernstein, "Quantum Leaps," on quantum mechanics for the lay reader, here:



The LHC -- What Good Is It

The latest from David Overbye (NY Times), explaining why the Large Hadron Collider is important:


Monday, December 28, 2009

10 Posts From 2009

Bloggers often do year-end lists of favorite posts from the previous 12 months, so without further ado, 10  S.O.T. posts I especially enjoyed from 2009 (most are either book reviews or videos):

1. "The Inner Feynman"
2.  "Martin Gardner"
3. "Alex, Wesley, and Love"
4. "Wingsuit Flying"
5. "The Canon and Scientific Literacy
6. "Embracing the Wide Sky
7. "Amazing Sea Creatures
8.  "Dawkins On Display"
9. "Believe It Or Not"
10. "Huhhh?"

Underpinnings of Science

Good piece on the nature of experiments, anomalies, and belief from Jonah Lehrer in Wired Magazine here:


Sunday, December 27, 2009

Digital Technology and the Future

 "The internet devalues everything it touches" :

A view of where digitalization is leading...

Speaking of Benzene...

Incredibly, a molecular transistor has finally been achieved, involving benzene:


Kekule's Snake

Friedrich August Kekule's benzene ring... brought to life:


(check out the rest of the photos here as well, by clicking directly on each pic to load the next one!)

Saturday, December 26, 2009

No Backup Plan?

If the Large Hadron Collider DOESN'T find the Higgs Boson, physics will go back to the drawing board:


"a hundred years of scientific theory" and "the Standard Model" will be "undermined" if the LHC fails to confirm the Higgs, resulting in bitterness and infighting among the physics community, according to former Harvard professor Shahriar Afshar.

Just For Fun

Back-to-back videos this week:

(hat tip: Blog Around the Clock)

Friday, December 25, 2009

California Condor

 Friday video... the California Condor Comeback:

Thursday, December 24, 2009

More Year-end Best Book Lists

The best science books of 2009 as picked by...

Physics.com :


The Washington Post :


and Amazon.com :


New Math Book

New math book, "The Princeton Companion to Mathematics," reviewed very favorably here:


"Rain Man" Dead

Before there was savant Daniel Tammet, there was Kim Peek, "Rain Man." Now dead at 58.:


Wednesday, December 23, 2009

Powers of 10

Jennifer Ouellette's latest on the cosmos here:

Godel, Escher, Bach

A video introduction to Douglas Hofstadter's classic "Godel, Escher, Bach" begins here:


Physics Wannabes Take Note

Finally a physics book for the rest of us:


....arf, arff

Clinical Trials... Issues/Concerns

Review below of 3 recent books addressing ethical and empirical aspects of clinical research on humans:


Tuesday, December 22, 2009

The Secret Life of Plants

Vegans still hold the ethical high-ground, but the always-interesting Natalie Angier reports on the 'sensitivities' of plants here:

Epigenetics, DNA Methylation, Lupus, and Twins

Accounting for lupus in one of a pair of identical twins via epigenetics:


Top 10 Science Books from Amazon

Amazon.com lists their Top 10 science books for 2009 here (nice mix of choices):


Cool Illusion

An illusion of (color) perception:


(for 30 seconds of dot-staring, cursor must be off the picture, then move on to picture)

Monday, December 21, 2009

The Golden Ratio

Human affinity for the 'Golden Ratio' of mathematics now explained by an engineer in terms of unification of "vision, thought and movement under a single law of nature's design":


Dawkins' Life and Times

Long autobiographical piece, "Growing Up In Ethology," by Richard Dawkins here:


Deep Paradox

The paradox of prolific lifeforms but little food at the bottom of the seas discussed here:


A quote from one researcher, just to peak your interest ;-) :

“It’s a constant snow of detritus at the bottom,” McClain said, “And most of it has passed through the rectum of at least two different organisms as it traveled down the water column. What arrives to the seafloor is a mixture of carbon, inorganic carbon, and other ’stuff’.  The carbon material passes through a lot of guts which both reduces the quantity and quality of the material.”

Sunday, December 20, 2009

Genomics and Nanoscience

DNA sequencing sped up using nanotechnology:


Ecological Developmental Biology

Review of "Ecological Developmental Biology: Integrating Epigenetics, Medicine, and Evolution" by Scott F. Gilbert and David Epel, here :


Friday, December 18, 2009

The Intelligence of Crows

Friday video: a popular TED talk on the high intelligence of crows, and how we can use it:

Thursday, December 17, 2009

Opportunities In 'Citizen Science'

 You don't have to be an expert:


Burial, Cremation, or ....

 Learned another new word this week: "resomation"




Wednesday, December 16, 2009

Random Subject Samples, Not So Random

Article points out that subject samples in most behavioral and social science research studies are not truly randomly chosen as would ideally be called for. What isn't mentioned is that subject samples in biological and medical studies (which also generalize results to entire populations) are also not random, and thusly flawed (indeed, the entire notion of "randomness" is almost undefinable, even in math, let alone in other sciences):


Tuesday, December 15, 2009


In the following sentence, the number of occurrences of 0 is 1, of 1 is 7, of 2 is 4, of 3 is 1, of 4 is 1, of 5 is 1,of 6 is 1, of 7 is 1, of 8 is 2, and of 9 is 1.

In the prior sentence, the number of occurrences of 0 is 1, of 1 is 8, of 2 is 2, of 3 is 1, of 4 is 2, of 5 is 1,of 6 is 1, of 7 is 2, of 8 is 1, and of 9 is 1.

Quality In Genomic Sequencing

As newer sequencing technologies allow for "quick and dirty draft genomes," article HERE raises concerns about the quality of genomic sequencing and recommends standards for future reporting.

Monday, December 14, 2009

Intro to "Chaos" and More

From SEED Magazine, "Chaos" theory as applied to the quantum level:


Junk DNA Revisited

A new look at introns, at least within the Daphnia pulex (water flea) here:


Whether the findings can be extended to other species, including humans, is being further investigated.

Sunday, December 13, 2009

Toxin Exposure

Hooray, I'm over 50....

Mercury and other chemicals in us:


The LHC Proceeds

Old news (...well, 4-day old news anyway), but the NY Times' Dennis Overbye reports on the new record finally set by CERN's Large Hadron Collider here (much more to come):


Still, the success is limited, as Overbye notes:
"Testing revealed that the collider is riddled with thousands of defective electrical joints and dozens of underperforming magnets that will keep it from reaching its full potential until an overhaul scheduled for 2011. When it starts doing real physics after the holidays, the collider will be running at half power."

Saturday, December 12, 2009

Sky Gazing

Look, see....

The Geminid Meteor Shower peaks this Sunday night in North America:


Friday, December 11, 2009

Predator and Prey

Friday video: Young ibex eludes a fox and certain death:


Thursday, December 10, 2009

Information Consumption

How much data do you gobble up each day? Some folks are trying to measure it:


(p.s. I learned a new word today: "zettabyte") 

Putting Bioinformatics In It's Place

Interesting take on what bioinformatics is... and isn't here:


Wednesday, December 9, 2009

An Oxymoron Perhaps

 A new "giant virus" (large enough to be seen through a conventional light microscope) has been discovered by French scientists. It is the fifth largest virus thus far found, and a "completely new viral form" at that:


Technology and the Life Sciences

Top 10 innovations in the life sciences in 2009 reported by The Scientist Magazine:


Tuesday, December 8, 2009

Cosmos Courtesy of Hubble

Deep space elicits deep thoughts.....

More wonder from Hubble here:


A Wild Rumor... or Not

Has dark matter been discovered...? :


(I'm guessin' not, but we'll know more come December 18th.)

Monday, December 7, 2009

A 2009 Best Books List

An eclectic list of the "best" science-related books from 2009 as picked by SEED Magazine:


Sunday, December 6, 2009

Music - Speech Linked

Research finding underlying link between human speech and music reported here:


Friday, December 4, 2009

Spiders On Drugs

Friday video:

This piece of science/humor has been circling the Web for quite awhile but still worth a gander, and based on some actual research:

Thursday, December 3, 2009

Of Nematodes and Men

Chet Raymo amuses again:


Plants as Air Purifiers

Household plants that remove pollutants from indoor air here:


The Science of Reading

Jonah Lehrer reviews Stanislas Dehaene's fascinating new book "Reading In the Brain," on how the human brain pulls off the amazing (yet routine) practice of rapidly and systematically acquiring meaning from squiggles on pages.

Wednesday, December 2, 2009

Feynman Recommended...

"...He is by all odds the most brilliant young physicist here, and everyone knows this..."

An old letter, recently disclosed, from the late Robert Oppenheimer highly recommending a young Richard Feynman for a position in the physics dept. of UC Berkeley back in 1943 (Feynman opted to go elsewhere):


A Classic

 Classic Eugene Wigner paper here on the "unreasonable effectiveness of mathematics":


Tuesday, December 1, 2009

Consciousness Cont'd.

And much much more about consciousness, compiled by David Chalmers here:


New Ideas On Consciousness

Consciousness and the brain, from John Brockman's "Edge" site:


Monday, November 30, 2009

Neuroscience Breakthrough

In a major brain chemistry finding, Nature reports that the glutamate receptor in the brain has now been characterized:


On Becoming a Naturalist

Chet Raymo muses on ditches and children:


And a slightly related post (on nature in our lives) from ThisLivelyEarth blog here:


Sunday, November 29, 2009

Science, String Theory, and the Public

Physicist Peter Woit on science, string theory, pseudo-science, and religious thinking here:


Minimal Cell and Complexity

Complexity of a minimal cell studied... Report from several research groups on the bacterium Mycoplasma pneumoniae indicates this prokaryote cell operates in many ways like a eukaryote.


Friday, November 27, 2009

Neuronal Wiring

Friday video:

The human brain -- machine... or miracle:

Wednesday, November 25, 2009

Pinker-Wright Discussion

Robert Wright and Steven Pinker in an interesting hour-long dialogue from a recent "Bloggingheads.TV":


Tuesday, November 24, 2009

The Polymath Project

The Polymath Project uses the 'Net to prove complex mathematical theorems (faster than they could be solved by individuals working apart). Fascinating concept... read all about it:


Monday, November 23, 2009

"A Year On the Wing" Enthralls

 Dee-licious, Dee-lightful!

"A Year on the Wing: Four Seasons in a Life With Birds" by Tim Dee

I'll cut to the chase: this is the most beautiful piece of nature-writing I have ever read. Period. There are other contenders, other great reads, but this taut, marvelous volume blew me away like no other.

I'd already been browsing this offering in a local bookstore for a couple of weeks when, serendipitously, the publisher sent along a copy for review. Brit Tim Dee is a BBC radio producer and writer, but "A Year On the Wing: Four Seasons In a Life With Birds" is his book-writing debut... And WHAT a debut!: This book sings... and soars... and sizzles, with prose that doesn't seem so much written, as poured onto each page from a wonderful carafe, like fine wine. Promotional material for the book uses words like "mesmerizing," "mystical," "moving," "gorgeous," "thrilling," "luminous," "poignant, "compelling," "poetic"... and all are apt for the rich text.  I'd additionally call this book intensely 'biophilic' --- a sendoff on E.O. Wilson's famously-coined term "biophilia," referring to the innate human need for connection with nature.

Generally, I like science books to bowl me over with empiricism, interesting facts, logic, reasoning, thought-provoking ideas. But nature books are a different ballgame... here I like to be swept away in lyricism, feeling, sentiment, connection, imagery. And Dee's book delivers in spades; a tour de force of nature-writing, reminiscent of early Annie Dillard.

Despite Dee's references being to British birds and locales, any American birder will easily follow and be swept up in the images and feelings evoked here.
The second chapter of the book narrates at length on the Woodcock, a fascinating bird familiar to both Americans and Brits. Here's a paragraph to give you the flavor of Dee's prose (if not the flavor of a Woodcock itself!!):
"Eating a woodcock, as I did once, is like eating earth. No wine has ever released its terroir to me as that bird did. It tasted like a prune, sweet and sour at once, a mixture of loam and chalk. The bird's dark purple flesh crumbled on my plate like a dried worm cast and the worms that made its meat. I had held the bird in my hand before it was plucked and cooked among the white surfaces and steel utensils of a smart London kitchen. Its cryptic moth-wing colors gave it the look of a worn fireside rug. To hold its book of browns, the wings falling open on either side of its body, was to sense the humus of dead leaves mulched into a bird over thousands of years --- the woodcock as a surviving fragment of an old earth, from a time when leaves became birds, branches grew wings, and the dark moved."

And this is the norm... There isn't a mundane page, a weak paragraph, a dull sentence in this amazing volume, as the author dances from woodcocks, to classic bird books, to swirling starlings, ravens, poetry, migration, nightjars, and other topics unforeseen, like literature, childhood escapades, and a suicide. I've always loved warblers, but I attained a new appreciation for Redstarts, in particular (another bird shared by America and Britain), from Dee's treatment of them here. And nightjars will never be the same for me again either. But every bird Dee touches turns magical and memorable. And there are dozens of species that take flight in these pages, some but briefly, some more front-and-center.

Each of the book's twelve chapters address a different month of the year and Tim's birding activities therein, but he really weaves his entire life into the narrative, sometimes hauntingly or sadly, or contemplatively or joyously. August is focused around bird banding, September on migration. The "October" chapter interestingly recounts Dee's own dual background in birding and nature-writing, telling which writers impacted him most growing up. His mini-discussions of literature, writers, and natural history are as interesting as his verbal portraiture of nature and birds.

I wanted this book to go on and on (it is only 200 pages), and was expecting some sort of profound crescendo as it did approach the end. Instead, it seemed to me to end in mid-air, a tad abruptly (the last chapters just as good as the prior chapters, but with no climactic finale), but maybe I missed something along the way. I'll be reading it again to see if the ending brings more closure, or if it simply makes you want to start over and read it again... and again.

I have to believe this volume is in line to win several awards for 2009 books, in nature writing and possibly other categories as well. And I hesitate to even look forward to Dee's next book --- I mean how could he equal, let alone top this?!! The volume is a bit reminiscent of Jonathan Rosen's wonderful work and ode to birds, "The Life of the Skies" which I previously rated a high "A-" --- what's left for me to give Dee's volume, except an A++ (...and no, I've never given that before).

Having heaped on all this praise though I must add that the potency of Dee's prose may be lost on those who lack great experience with the subjects he is addressing: nature and birds. Anyone with no interest in these topics just won't feel the power of Dee's vividness, passion, imagery. So this is not necessarily a book for everyone, or for non-nature readers, nor even beginning ones; it is for those already somewhat seasoned, even immersed... and ready, or primed, to be carried away.
But hey, I'll quit beating around the bush... I liked this book... A WHOLE... DANG... LOT!!!

Sunday, November 22, 2009

Altruism In Plants!

 Fascinating... Plants recognize, and share light/nutrients with, their own kind:


Friday, November 20, 2009

LHC Restart Begins Tonight!

 The Large Hadron Collider, under repair and preparation for the last 14 months since it's initial startup shutdown, is finally due to re-startup tonight (the beginning of a lengthy process):


Science and the Cosmos

The Friday video: Classic Carl Sagan from "Cosmos" on the triumph of science:

Thursday, November 19, 2009

Blindness and Hallucinations

Do blind people experience visual hallucinations on LSD:


Butterflies In Space

Somehow it's a lovely image; Monarch and Painted Lady butterflies are headed to the International Space Station aboard the shuttle Atlantis as part of a 'science outreach project':


Paradox of Light

 The strange nature of light:


Wednesday, November 18, 2009

Insect Brains

Pinhead-sized brains still allow for complexity:


Giant Stingray... WOW

Couple of clips of the fascinating, elusive "giant stingray":



Tuesday, November 17, 2009

Garrett Lisi Speculates

 Yo Man, surfer dude proposes 'theory of everything' (the Holy Grail of physics):



I've used this TED talk of Lisi's earlier in the year :

Wish I understood it well enough to comment... but I don't, except that the mathematics are intriguing.

Be Careful What You Wish For

 'Brain diseases' that someone says he wishes he had!:


Monday, November 16, 2009

Dawkins On Display

Dawkins Dazzles... Mostly

A brief look today at Richard Dawkins' latest two books...

First let me say that what I like best about Richard Dawkins is his British accent ;-) and his videos are all over the internet so one can partake of that... but of course his writing ain't half-bad either.

Of his last two works however, I give "The Oxford Book of Modern Science Writing," an anthology actually of other scientists' writings, the higher "A" mark. I like anthologies in general, and this is a particularly excellent volume of well-selected, modern scientific writing (in fact I'm tempted to deem it the best such anthology I've ever come across! --- an endorsement blurb from "New Scientist" on the back cover says, "A brilliant collection... If you could only ever read one science book, this should probably be it." I might agree.).

One might've expected Dawkins, a biologist, to weight biological writings heaviest in his selection, but really it is a very admirable, representative, and fair mix of scientists across a wide swathe of disciplines, including a variety of writing styles and content. Dawkins says his only regret is that so many good writers and pieces had to be left out, but his selections are superb within a 400 page framework --- the sole weakness is probably a shortage of cognitive science representation. Neuroscience has really come into its own in the last half century, but unfortunately not much of it found here. My other regret is simply that many of the pieces are so short (often 2 pages or less, and rarely more than 5) that you really wish they'd continue on. Just as you're getting some real meat to chew on, an entry is over and off to the next author. Dawkins' very short subjective intros to each writer, by the way, are also absolutely delightful gems, almost whimsical sometimes; not stuffy or mundane in the way people-introductions can sometimes be.  Also nice, is Dawkins' deliberate avoidance of very famous or well-quoted passages/essays of a given writer, in favor of pieces of lesser familiarity, but equally high caliber from said author.

 The book is organized in four parts: "What Scientists Study," "Who Scientists Are," "What Scientists Think," and "What Scientists Delight In." But it is the sort of work that can be read in any order; open to any page randomly and dive in to a fine reading experience. Indeed, I suspect I will be pulling this volume off my shelf every few months to randomly open it and re-read a few pages here and there to much satisfaction, like sipping fine wine. I highly recommend it to all lay science readers.

Moving on, I'll say up front that 'evolution' volumes in general somewhat bore me at this point (there are innumerable fine such volumes out there, and for most of us this debate was over a loooong time ago). I do still enjoy some of the anthologies in which the likes of Gould, Eldredge, Lewontin, Dawkins, Wilson, Pinker etc. wrestle the nuances and fine points of evolutionary theory through essays and excerpts, serving to show how much disagreement there is among the experts, despite agreement on basics. I'm less a fan of reading Dawkins in isolation. Having said that, it's good that he is around to keep fighting the good fight for those too tired and bored to do so.

Thusly, a brief overview of the 2009 edition of Dawkins' "The Selfish Gene".... no just kidding, rather, a look at his latest offering, "The Greatest Show On Earth"... But Dawkins has been accused from time-to-time of writing the same book over-and-over again, just changing the words around. He once responded to such criticism by saying that he HAD to keep writing the same book in different ways to try to get through to all those people who still don't 'get it.' He actually goes to pains early in this volume to maintain that this book IS different from his others because it focuses deliberately on "evidence" for evolution, whereas previous works focused moreso on the underlying theory and mechanisms of evolution.
It is true that this volume is heavy on the perceived evidence for evolution, to the point of sometimes being a tad more pedagogical than some of Dawkins' earlier writing, but only a tad. Still, he is as always a good explicator (one might almost contend he's more a writer than a scientist), even if the writing is slightly less engaging than some prior volumes.

I'm not sure though who this book is really for... Dawkins fans will of course read it, but may gain little from it they don't already know. Creationists and Intelligent Design advocates won't find it convincing (even if they're persuaded that yes, evolution happens, they won't go the extra mile of concluding that humans necessarily resulted therefrom), and there's nothing newly profound in Dawkins' arguments here that hasn't appeared in print elsewhere. It's as if he's expending his breath for a paycheck, or attempting a knock-out blow he can't achieve. I s'pose there are still some newbies out there, fresh to the whole debate who haven't made their minds up, and the book may be best targeted at them, as a good intro to the evolutionary view, but surely by now they are a small percentage.

Dawkins claims unconvincingly that there are not great gaps in the fossil evidence; that intermediate forms and 'missing links' as it were, abound. But of course there are large 'gaps' and millions of smaller ones --- he rightfully asserts that we are lucky to have any fossils at all, let alone the number we have (which is still not many) --- but for some reason he doesn't simply then acknowledge that this scarcity accounts for the large "gaps" in the evolutionary record; evolution stretches over unimaginable millions of years; there SHOULD BE millions of gaps (most transitional forms disappear, and the fossil history that does exist is often the result of concocting entire anatomies from but a very few bones or fragments and a whole lot of assumptions). Otherwise, Dawkins offers plenty of good, but always limited, examples and argumentation.

Remissfully, he doesn't even delve into epigenetics, one of the hotter topics in biology today, and one that any new book purporting to address evolution ought spend at least a few passages on, especially since it has the potential to alter some of the genetics 'facts' he is wedded to. 100 years from now we'll have a good handle on epigenetics, but by then something new, along the lines of epi-epigenetics will no doubt appear and require yet further understanding/elucidation --- that is the nature of science; peel off a layer of the onion and just as many layers still remain.

Scientists of each given age tend to think they have very advanced knowledge, just because they are on the cutting edge of science for their day --- but all is relative; in looking back, we snicker at the primitive beliefs from scientists of 1000 years ago, and similarly 1000 years from now, scientists will look back and chuckle at much of what today's Dawkinses have written (or Stephen Hawking for that matter). Some of today's inviolable "facts," in a 1000 years, will be seen as simple-mindedness and sophistry of another age; over the eons science is quite fluid; it just appears very static at any given point... and that is what Dawkins fails to comprehend, so spellbound and myopic is he on the accomplishments of present-day methods/theory/evidence/science. The variables and intervening factors on a process as broad as "evolution" are enormous, complex, and yes, still largely unknown (maybe even unknowable), but Dawkins writes with a blind acceptance and certainty of it all based on little more than 100 puny years of evidence, a miniscule blip in time and knowledge. Sometimes he reminds me of those who wrote at the turn of the 20th century that all the essential physical laws of science had been discovered and there was nothing left to learn except the application of those laws. There is likely an infinite amount left to learn.

In his final opus, "The Structure of Evolutionary Theory" Stephen Jay Gould took over 1300 pages (and probably knew he was leaving a lot out) to explain evolution. Dawkins gives us a Cliff Notes version, and seems to think it invincible, with his self-selected examples. I guess it is his tone moreso than his content that leaves me uneasy, though at the same time, I understand his frustration with the antagonists he is battling.

Having said all that, this is a very good book (Dawkins doesn't write bad books) and I give it a B+, easily recommending it as a popular science read, or as a good introduction to evolutionary theory for anyone needing such. But it does need to be read critically, not merely lapped up like honey. And for the general science reader, if I had to choose where to spend $20+ I'd spend it first on his Oxford anthology, and then maybe pick up a used copy of "The Selfish Gene" for 50 cents in the local used bookstore.

Dawkins personal webpage here:  http://richarddawkins.net/

Sunday, November 15, 2009

Golf Balls As Toxic Waste

Story with funny headline... but not altogether so funny:


The hazard of lost golf balls....