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Archive for January, 2009

ABC (Australia): Lizard-like fossils may force revision of New Zealand’s paleohistory

Wednesday, January 21st, 2009

The Tracker had never heard of the tuatara before last August, and here they are in the news again. They are large reptiles native to New Zealand and, as one learned the first time around, the last of their lineage. Not quite lizards but a clade of their own. They look a lot like iguanas – hefty and bedecked in spines and other eyecatching decor. The latest, from ABC’s Carmelo Amalfi, is that recent discovery of fossils of their ancestors of several million years ago forces revision of the geological presumption that what is now mountainous New Zealand was then a submerged chunk of continental crust. Forget the image from the article (and from the press release), reproduced here. That is a photoshopped (or the equivalent) mashup to match its imaginative hed: Fossil reptile remains keep NZ afloat. The creatures are not and were not aquatic. As a pithy source tells Amalfi, if there is water in the way, “Tuatara are not good at dispersing.” Which is to say, if parts of the NZ landmass were dry all the way through, that solves the problems of figuring out how their ancestors reached the islands. They were already there a great deal earlier. The formal report is in Proceedings of the Royal Society B.

Grist for the Mill:

University College London Press Release ; the web page for the post-doc lead author of the research ;

-CP

Fortune Magazine: Laser mapping, rock gardens, and the tumultuous history of Easter Island

Wednesday, January 21st, 2009

In the Jan. 13 issue of Fortune Magazine is a piece with engrossing, current, in-depth science news from Easter Island. Many people who keep track of the writing world know that Jared Diamond, in his book Collapse of a few years ago, wrote of that island’s ecosystem ruination, after people arrived, as a cautionary tale for the world. In Fortune’s current issue is another, tighter kind of report from there by writer Jeffrey M. O’Brien. It keeps the spotlight more narrowly on the island’s archeology in itself, and on a remarkable self-taught local woman who gave the pros a lesson in how to look at a landscape clearly (and how to not be completely mesmerized by the big, famed, carved-basalt moai heads).

This is recommended reading. It has a heroine, and a hero too in a tourist who showed up and realized his business’s main products – a laser mapping system and ways to digitize 3-D data – could do wonders for the lady with the keen eye, perceptive brain, and too many data on paper to digest easily. These two main elements, perhaps, ought to have been employed solo. But there is also a large, third element devoted to plans by the island’s government to develop the place for tourists. It didn’t, at first, seem to fit in the piece. As a narrative tale, the new ways to literally visualize of how this island also called Rapa Nui was settled, farmed, developed, and eventually ruined is exceedingly effective on its own. But, one speculates, to get this tale in a money magazine like Fortune requires a good dose of business and development pertinence. So, in that context, the tale makes sense as published. Plus, the biz digression has a bit on a generous, progressive-minded billionaire who showed up aboard his own private cruise ship.

And maybe this is extra news in the story. The Tracker does not recall learning previously that not all traces of Easter Island’s original palm tree forests were cut down by desperate, warring tribes centuries ago. The writer is taken by his guide to see, in a rocky alcove, “six stout palms in hiding. The biggest is about ten feet tall with a trunk like a wine barrel.”

Grist for the Mill:

Autodesk Corp.  Press Release (2007) ; Image Gallery ; Diary Samples ;

p.s. Is it just me and the week of inaugural news, but if the rapanui had put big ears on that moai up there, wouldn’t it look just like guess who?

-CP

(UPDATED*) Los Angeles Times: What happens when a family unravels the tapestry of its ancestry – the one woven from DNA

Tuesday, January 20th, 2009

With so much written these days about the commercialization of genomic analyses it’s not easy to find a new angle for describing this brave new world’s thrills and perils. At the Los Angeles Times Alan Zarembo on Sunday provided one. He interviewed the organizer, a man named Kincaid, of what he’s calling the Kincaid surname project. Scores of people with that name or its variants have gotten genes tested to learn more of the shared, and non-shared, portions of their ancestries. The revelations of, he writes, “war heroes, survivors, .. bastards, liars and two-timers…” and more haven’t all brought hurrahs. Some of this, especially about revelations of paternity, might in coarser hands be fodder for a confrontational TV reality show – the ones where she learns where he’s been spending his free time (or vice versa) and all hell breaks loose. Zarembo however handles like a grown up the pain and embarassment and shocked surprise that may emerge when a big clan gets some discomfiting, as well as enlightening news, about what its collective genome comprises.

The sober tone of the piece breaks down a bit when looking at the graphic. It’s accurate but its hed is a slap: Who’s your daddy?

*UPDATE – Grist for the Mill: The project’s manager provides this spread sheet, rather interesting to scan, showing the data’s essentials as they now stand.

-CP

NYTimes, SF Chronicle, etc: Moon’s heart has held a hot secret…

Tuesday, January 20th, 2009

On Friday last week a tsunami of news of methane on Mars distracted The Tracker from another surprising piece of solar system discovery and that received appreciable coverage: The Moon had a molten core for more than a few moments during its birth – some say, congealing from a splash of Earth’s crust blown into orbit by a Mars-sized impactor. To catch up: in Science on Friday an MIT and Berkeley Geochronology Center team published a paper based largely on proof that those old Apollo missions did more than wave the red white and blue over the lunar regolith. It brought some chunks of that soil back that tell a powerful scientific tale. One pale, greenish stone nicknamed “the trocto” (mineralogically, it is a troctolite) in particular appears to have been left somehow more or less pristine by billions of years of impacts on the moon’s surface. Its surviving magnetic imprints strongly imply it hardened from lava while soaked in the influence of a churning molten iron dynamo within the moon far smaller and weaker than, but perhaps in many ways similar to, that in Earth today. Reporters tended to hew to the message in the paper and press release, but a few went beyond it.

Notably in the latter group is NY Times‘s Kenneth Chang, who in the Science Times section today ties the paleomagnetic analysis of the moon rock with signs from seismometers left on the moon by America’s visits there nearly 40 years ago. The implication, he writes, is that the moon’s core may be molten yet. That is not news, but provides a good additional perspective on the latest about the young moon’s core. Chang does not address one peculiar and pertinent factor: the moon’s low density compared to Earth. It virtually rules out a large nickel and iron core (and feeds the hypothesis that it’s essentially a ball of displaced Earth crust, blown off after our world had differentiated most of its heavy metal to its middle). It may have a simple answer, but how much iron or other conductor would need be inside the Moon to sustain a dynamo effect?

Other stories:

Grist for the Mill:

MIT Press Release ;Plus, one happens across this PDF of a presentation by Harrison Schmidt of his sojourn and geologizing on the Moon including a map (slide 8 ) that shows where he picked up Troctolite 76535.

-CP

NYTimes (and more): Perils and science of avalanches; plus more in Science Times

Tuesday, January 20th, 2009

This has been a banner year for avalanches and that’s not good for winter sports. The Tracker had noticed a great deal of attention lately in the Rockies and coast ranges of the west to worsened dangers from unstable snow packs and to deaths from these white slides – even inside the supposedly safe, patrolled zones at ski resorts and snowmobile recreation areas. For a change, this post will therefore go beyond it’s expected main topic when I started it, the NYTimes Science Times, and round up some notable stories from other outlets. The lead story in the section today is a detailed explainer on avalanches and on research into them by Jim Robbins. It’s smart, opportunistic feature writing. It fills a need by answering:  ‘what’s up with all the avalanches?’ His lead zeroes in on one way to do science: build a sturdy shack, make sure the doors and windows are well-shut, check a few sensors to be sure they’re up and running, and tell a colleague uphill to let that avalanche come roaring on down. Or … just model the thing in a nice, clean, controlled lab.

Other recent avalanche stories:

ELSEWHERE IN SCIENCE TIMES TODAY:

Natalie Angier makes sure there’s an Obama-hooked story in this section too for inauguration day. A source gives her the pithy lowdown on gender in science: “Men can have it all but women can’t.” The story’s hook is the failure, so far, to include any women scientists in the Obama adminstration’s “geek chic” appointments to high cabinet and advisory posts. It quickly turns to deeper worries over the extraordinary sacrifices of family time needed to succeed in science’s top tiers and the tougher time that women – you know, the ones that actually have the children – face when they climb the academy’s heights. A second theme is that it’s not so easy for the men, either, and whether anything can be done about letting top scientists have real lives, too.

Other headlines to note:

Lots more in the whole section ;

-CP

Genes, India, and Heart Mutation Hell

Tuesday, January 20th, 2009

(Note: Welcome to an additional tracker, Julie Robotham, a science and medical writer based in Australia. She’ll be providing closer and more expert looks at health and medical science journalism than we’ve had. Julie was a Knight fellow last year – see her short bio here.  Hurrah – CP)

Genes don’t get more simple than this, at least to hear most news reports tell it.Normal proteins (top). Proteins with newly-identified deletion (bottom)

A 25 base-pair deletion in a gene that regulates the production of heart-muscle forming proteins sends the process awry and weakens the muscle instead, causing heart failure, according to a research letter published in Nature Genetics.

In a much more straightforward case of cause and effect than you find in most genetics discoveries, having the misfortune to inherit the deletion on the MYBPC3 gene increases seven-fold your chance of developing cardiomypoathy. What’s more, the mutation is carried by as many as 1 per cent of the population, including about 4 per cent of people living in or hailing from the Indian subcontinent. Large effect, high prevalence equals massive impact.

The main source (if you’re being generous) or just about the only source (if you’re being accurate) on this story was a press release from Britain’s Wellcome Trust Sanger Institute, one of four collaborators in this international project.

And a fine release it was too, including as it did a plain-English definition of an odds-ratio, and the images Tracker has reproduced here, though it seems no-one else used them. (After three days in culture, you can see normal muscle striations in the top set of images from the normal form of the gene, and the mess the deletion makes of muscle tissue in the lower set).

It also included a statement on funding (Indian government, Wellcome Trust and a few other grants) that others would do well to replicate, lots of colourful but on-message quotes that diplomatically placed the Indian scientists – led by Kumarasamy Thangaraj from Hyderabad’s Centre for Cellular and Molecular Biology – first.

And don’t forget the agonisingly British quote from the Institute’s Chris Tyler-Smith that the mutation was, “simply terribly bad luck,” for those who carried it.

Just about all news media led on the line that carrying the mutation “almost guaranteed” heart disease.

What no-one does is set into perspective what this actually means for people’s health. What proportion respond well to treatment, versus those who die early? What is the range of age of onset? And what does “almost guaranteed” to develop heart failure actually mean in terms of percentages?

Though one or two outlets seem to have spoken to the scientists in person, they really haven’t pinned them down on these questions or others that might spring to mind. Nor is there much evidence that any media – with the exception of the LA Times – have been through the actual Nature Genetics publication. (The journal, which published it online-first, did not itself issue a press release.)

At the LA Times, Thomas H. Maugh II offers a version that will be more pleasing to those who know their genetics. His is the only report that names the gene (cardiac myosin binding protein C) in full, and the only version to describe how the scientists nailed the prevalence of the mutation in the wider community, having defined the deletion with an initial case-control study that followed investigations in a single affected family.

Canada’s CBC News usefully emphasises up-front how the discovery might improve the lives of those affected. Like others it mentions that people with the gene might be advised to live a healthier lifestyle (though no mention that the things such people need to avoid may be different than for others whose heart disease is not linked to the mutation). Along with many other outlets, CBC says there is potential to develop a drug targeting the faulty protein, which people appear to eliminate less readily as they age. But no-one mentions the obvious possibility that people with the mutation may respond differentially to heart failure treatments – regular beta blockers, for example – already on the market. Far short of a protein-busting wonder-drug, there may be many options to refine treatment protocols.

Agence France-Presse picks up a detail that most others skip over: the exact geographic distribution of the gene (as well as India it is also highly prevalent in Pakistan, Sri Lanka, Malaysia and Indonesia.)

Pakistan’s Daily Times reprises the AFP copy, but also gives an assessment of the contribution of the mutation to the burden of heart disease on the subcontinent: about 5 per cent. However, it’s unclear where that statistic comes from as it is not attributed to any of the individual scientists. Maybe it’s a misreading? The headline reads “Faulty gene causes heart diseases in 5% Indians”. But that of course is different from the total proportion of heart disease the mutation bears responsibility for.

Only the Times of India broaches the fraught topic of the possibility of selective abortion for foetuses diagnosed as carrying two copies of the mutation, who it says have a high chance of dying in childhood. It also offers a perspective on MYBPC3 within the wider field of cardiac genetics. While about 20 cardiac disease genes have so far been identified, the report claims, mutations on MYBPC3 account for almost half of all sudden heart death.

Over in the United Kingdom, the Guardian has more detail on the study’s history and its methodology while the BBC does a straight-up-and-down version. It does one thing, though, that other reports consicuously fail to: seeks a comment from outside the inner-circle of the scientists involved in the discovery, in the shape of Professor Peter Weissberg from the British Heart Foundation, who said the study, “provides good grounds for screening people of South Asian origin with unexplained heart failure and screening their families if positive.”

OK, as a comment it’s not going to set the world alight, but at least the BBC made a phone call. That’s journalism, right?

But the prize for report most true to media type must go to Britain’s The Sun rag, which dispatches the entire topic in fewer than 100 words under the fabulous tabloid headline “Heart mutation hell hits 60 million”.

Grist for the mill: Wellcome Trust Sanger Institute press release

-JR

See you all on Tuesday…

Sunday, January 18th, 2009

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.Tracker’s taking Monday, January 19 off for Martin Luther King Day, a US national holiday. Be back on Tuesday with as much as possible among sneaked peeks at the enormous hullabaloo in DC for the inauguration.

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-CP

Orange County Register, NYTimes, etc: Frostbite may have killed all those west coast brown pelicans

Friday, January 16th, 2009

Discovery of hundreds of sick and dying pelicans from Mexico up into Oregon last month may have been the aftereffect of severe frost bite, investigators from an animal rescue operation and from the California Dept. of Fish and Game report. We had a post on this last week. The new analysis, reports the OC Register‘s Pat Brennan, points blame at a wave of bitterly cold storms off the Washington and Oregon coasts in the second week of December. Sores on the dead birds’ feet and discoloration of their pouches look like the aftereffects of frostbite, a source told Brennan. If the theory is right, the birds were able to migrate south to warmer areas before succumbing to their injuries. Some experts, it says here, still suspect a different or at least additional cause: domoic acid poisoning from ingesting algae.

The NYTimes‘s Jesse McKinley also had much the same news this week. He filed it yesterday, citing an advanced copy of the report released today. He gets a vivid, maybe exaggerated, but powerful quote to back up the hypothesis. The frostbite was severe – “There were legs, toes, and pouches frozen off,” a source told the Times.

Grist for the Mill: International Bird Rescue Research Center Update Report ;

-CP

Raleigh News & Observer: State gives permit for mining a wetland. That still happens?

Friday, January 16th, 2009

Along and under the Pamlico River in North Carolina, it appears, are deep, dark sediments loaded with phosphate. They are in a part of the country that provides most US phosphate for agricultural fertilizer and similar uses.  Miners have been digging it up for decades, the News & Observer‘s Wade Rawlins reports. And now the state has given its preliminary okay for an enlarged operation that, Rawlins calmly reports, will bring “massive damage to wetlands and creeks”  – on the largest scale ever permitted in the state. You can still do that in the 21st century? Even one state official says it’s a very large impact: “There is no way to sugarcoat that one.” These, it appears from glancing through the EIS (see Grist) are deep mines – pits may go 130 feet below sea level, excavated by drag lines like the one shown. Must be quite a sight.

The Tracker suspects that this story is one of many in the region covering this application. One does imagine that, somewhere, are long time residents and a few enviros furious over the deal. But it does mean jobs, maybe this particular wetland type is dime-a-dozen down there (maybe), and from space one would probably never notice a little 3,000 acre+ parcel that went from swamp to strip mine.

Grist for the Mill: At an Army Corps of Engineers site, the company’s original EIS and application ;

Pic source (where one learns that these mines are great for fossil hunting) ;

-CP

Wall St. Journal: Legal system starts taking neuroscience, and the circuitries of guilt, of judgment, and of punishment, seriously

Friday, January 16th, 2009

The Tracker thinks of memories and thoughts as skeins of synaptic circuits, almost randomly assembled, that tickle our sensory pathways in a fashion to give a sense of feeling to things past or imagined in the future. Which is to say, a big soupy mess of happenstance brain connections distinct to each of us. Now along has come neuroscience with rumors of mind-reading, of mood-reading, and of hints that most people thinking the same things are probably using their brains in mappable, similar ways. In today’s Wall Street Journal Robert Lee Hotz, who has made brain science one of his specialties, brings an enlightening visit to legal scholars who wonder whether direct monitoring of brains can help the courts decide who is guilty. It is, as one source tells him, “baby science, first-step science, like genetics in the 1950s.” The latter of course led to DNA matching, so it’s a potent simile. But Hotz finds disturbing examples of some courts that have leapt far ahead of the science when using wired-up brain waves as guides to who to throw in the pokey. Reasonable doubt remains a pillar of US law. Judging from this, there is much in brain activity monitoring that is unreasonable to trust – but it is getting there.

See Also: About two years ago in Technology Review Richard Brandt summarized efforts to map brain activity differences between normal and criminal minds.

Pic source ;

-CP

Wires: Pile of dung evidence – a Malaysian park has world’s largest concentration of Asian elephants (But what’re odds it’s 631 of them??)

Friday, January 16th, 2009

Who says enviro activist groups are addicted to providing only dire news for animals, climate, pollution, etc? The Wildlife Conservation Society reported this week that a census in Malaysia’s Taman Negara National Park performed by statistical extrapolation from piles of dung  implied it has many more elephants than had been expected. AP‘s Michael Casey reports that the estimated 631 animals live in what Malaysians just call their nation’s “green heart.” His lede, to his credit, puts it simply as more than 600 animals, with the suspect 631 figure a bit deeper. Reuters‘s Julie Goh picks it up too and dittos it as – and taking the figure right off the press release – 631 elephants. C’mon now. Reporters don’t have to be ace crackerjack and cynical old science writing specialists to figure out that if one is using piles of crap to estimate a species’ local presence, one thing you can count on: there are NOT precisely 631 of them out there. The fault originates with the press release writer who should have queried the researchers with the improbability that their algorithm is accurate to three significant figures. Both reporters give the park’s area as 4,343 square kilometers (or 1,676 square miles), and that’s a figure one needn’t suspect.

Also on this list is the San Francisco Examiner‘s Meg Marquardt, who writes in spritely fashion that “The precise number of elephants (631) was determined by an unappealing yet scientifically sound method…”. Oh, sigh.

Grist for the Mill: WCC Press Release (via ScienceDaily) ;

Other Elephant News: At BBC Amirtharaj Christy Williams, a biologist with WWF, reports in a long “viewpoint” the bloody results, mainly bloody for the elephants, when they run into conflict with people.
Pic source ;

-CP

Lots of Ink: Finally. A clue to maybe possibly perhaps there’s life on Mars, and it’s not ’cause it was wet!

Friday, January 16th, 2009

If memory serves – which it rarely does – NASA has discovered water, icy or otherwise, on Mars a zillion and ten times. And each time, it’s more evidence that life once may have evolved there. Not that each further discovery didn’t advance the scientific ball down field a bit and sometimes a lot, but some reporters (and many of the press releases they feed off) seemed to have no angle with each episode other than by golly it’s LIFE!!!  Thus the welcome flood of news reports today reacting to a distinctly new and tantalizing clue to Martian astrobiology, or perhaps to just some active geological processing (or both), in the form of intermittent wisps of methane gas in the air. CH4 has so much more novelty than that ubiquitous H2O that was pretty much nailed with the first photos of giant braided outflow channels from Mariner 9 in 1971.

Whew. Venting is now complete at Tracker central.

The straight news from NASA, published in Science and propelled by a press conference, is that several regions on Mars seem to be seeping significant methane into the air in distinct plumes – and it varies by season. Signs of methane have been collected for about six years. Now, heavy scrutiny of the evidence makes it look certain. Three ground-based telescopes collected the spectroscopy (not easy, as the Mars methane signature must be sifted from that of Earth’s own gases). Because methane is not very stable and breaks down quickly, any steady supply to Martian air implies there either are microbes or other life forms producing it, or active geological processes at work. And even if it’s the latter, methane itself is a nutrient for many other kinds of microbes here on Earth so maybe there too. Already, there is talk of sending NASA’s next big lander mission, the Mars Science Laboratory in 2011, to one of the regions seen to be emanating what on Earth is sometimes called marsh gas.

The report is generating about as near the high end for herd journalism by different outlets as The Tracker ever sees. The news’s headlines range from bonkers, to restrained. In the latter category is, over the NYTimes‘s piece by Kenneth Chang, “Paper Details Sites on Mars With Plumes of Methane“. That’s sober. His second graf gets into the what-belched question in lively fashion with “Subsurface Martian cows are highly unlikely. But scientists are seriously considering the possibility of bacteria.” At the playful end on hed writing, one submits “More proof that men are from Mars” in the Everett (WA) Herald by Jon Bauer. Get it? – the planet is belching, farting, etc. Smartest hed for its history sense is “NASA finds next clue to life on Mars” at ABC News, Australia, using a shorty BBC story (also see below for more Beeb).

Other stories, by headline:

See Also:

  • Scientific American put up this week a May, 2007 story from the printed magazine, by JPL scientist Sushil K. Atreya, that provides deep background on methane’s significance in planetary atmospheres.

Grist for the Mill: NASA Press Release ;

-CP