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Archive for February, 2011

Bloomberg: Altered switchgrass has less lignin, makes more ethanol – plus, it’s cheaper

Tuesday, February 15th, 2011

This week the Oak Ridge Nat’l Laboratory and a large family fortune-based ag and health fund, the Samuel Roberts Noble Foundation in Oklahoma, jointly sent out an  interesting press release announcing their researchers have bred and engineered a new kind of switchgrass. It’s also topic of a paper in PNAS. This is interesting. Not splashy front page news, but it’s good to see somebody covered it:

Lopatto adds background info on ethanol production and the history of the great plains to what is in the press release. She quotes from the paper. The led calls switchgrass the fuel for the buffalo herds that the US westward expansion encountered. I wondered about that – really? Switchgrass just sounds so prickly and coarse. But I changed my mind after riffling through the Noble Foundation’s annual report to see who funds it (looks like self-endowed by Lloyd Noble, the philanthropic oil driller who set the foundation up 60-some years ago). I saw a reference to a test in which foundation-funded researchers counted the bites of cattle in a field of mixed forage. They liked switchgrass best.

More interesting to me, maybe worth more reporting and quite aside from the primary significance for biofuel production, is that these genetically altered crop plants are modified to change their structural nature -  to have less lignin -  and are not in the parade of GM crops that resist herbicides such as Roundup or  contain Bt or other pesticide genes. Those latter ones are not new or remarkable or very inspired. This new one (as would be examples of food crops with better nutrients) appears from here to be more in line with what a well-regulated exploitation of genetic engineering in ag ought to be doing.

Another suggestion – would somebody ask these people at ORNL or the Noble Foundation whether their more easily digested  and distilled, lower-lignin grass is, um,  floppier?

Grist for the Mill:

ORNL Press Release ; Noble Foundation Press Release (same as ORNL) ; Noble Foundation homepage ; Annual Report ;

- Charlie Petit

Short Note on the Two men with HIV, each “The German Patient”

Tuesday, February 15th, 2011

Last week I posted on news reports of  the remarkable, if nascent, efforts to create a new HIV treatment. The proposed therapy is inspired by a man treated in Germany and apparently cured by stem cell transplant – and who, while now identified, has been called “The German Patient” by doctors treating him. Two reporters took issue with my declaration they fell significantly short by not including word that there was a somewhat similar case, and also called  “The German Patient,” in AIDS history.

I’ve amended the post – scroll down, or go directly to it to read more.

- Charlie Petit

NYTimes, AP: Rep. Giffords’s progress shown in her conversations

Monday, February 14th, 2011

The progress by badly wounded Gabrielle Giffords, shot in the head by a would-be assassin whose bullet passed through a portion of one frontal lob  in Arizona last month, gave the public a lift in the last day or so. Several news reports described improvement if not full recovery in her ability to speak.

None of these quite qualify as technical medical writing. Reports come second and third hand from friends and relations, and public word that she has spoken with her astronaut brother in law by phone call to orbit.

The public is following this news with great interest. The AP story, by one report, ranked number one for awhile on the list of most-read stories.

Stories:

  • NYTimes – Marc Lacey, James C. McKinley Jr. (with Denise Grady) : Word and Lyric, Giffords Labors to Speak Again. The news, plus a good sense of the atmosphere in the hospital .
  • AP – Malcolm Ritter: Doctors work to help Giffords’ brain rewire itself ; Ritter wisely turns quickly from the scant details on the Congresswoman’s clinical condition to an explanation in general terms of how injured brains may partly or even wholly heal themselves. He also gently tip toes up to an implied speculation that  few want to discuss quite yet: whether she will be able to continue her work in Congress.
  • ABC News – Bob Woodruff: Arizona Rep. Gabrielle Giffords Lip-Syncs Lyrics to Songs ; Interesting. While the story does not say she understands detailed political briefings she is getting, people attending strongly believe that she does. Woodruff, with personal experience with head injury, gives the story extra impact just by putting his byline on it. He wrote a recent, more general piece: Gabrielle Giffords: Recovery From Brain Injury.

- Charlie Petit

BBC, NYTimes, LATimes, AP, etc: In ‘bonus mission,’ a second look at comet Tempel 1 coming up

Monday, February 14th, 2011

Seven years ago NASA’s Deep Impact probe zipped past comet Tempel 1, shooting a barrel-sized slug into it to see what splashed out. A  second spacecraft, the well-traveled, 13-year-old  Stardust Mission with its primate aims already achieved will, following further orders, is about to  come near Tempel 1. Perhaps its photos will reveal Deep Impact’s scar or other recent changes.

If the advance stories from several major outlets  are any clue this may get substantial coverage . It does not hurt that NASA put out a press release on the rendezvous  calling attention to this not only happening, but being a Valentine’s Day rendezvous – even if it’s more miss than tryst.

Advance Stardust NExT Mission Stories:

Grist for the Mill:

NASA JPL Press Releases One, Two, Three ..

- Charlie Petit

Kodiak Daily Miner, AP: On Kodiak Island, an eagle electrocuted on power pole. Was very old bird.

Monday, February 14th, 2011

Never one to riffle past a wildlife story if there’s time to stop, The Tracker paused today at an AP piece, filed Friday by Dan Joling, noting that the oldest confirmed bald eagle in Alaska, at age 25+, was found dead recently in downtown Kodiak under a town power pole. The bird had evaded the devices meant to prevent just such mishaps. It landed on a powerline believed to be too hemmed in by other lines for an eagle to land on it. The large female, it says here,  wore a leg band affixed a quarter of a century ago. Even though the town is home to flocks of eagles, few of whom have happy deaths in any case one presumes, that’s a sad read.

What is good is that the AP acknowledged that while Joling expands on the news, the little Kodiak Daily Mirror reported it first. There one finds it datelined Feb. 4, by Drew Herman . He does a nice job with it. . Herman’s piece is not overtly sentimental, a good move as the facts alone provide the needed element of pathos. He id’s it as male, and one is unsure which report is correct. One also learns that for this paper EVOS is an acronym (read it to see what it’s for).  One also learns that Herman is among other things the paper’s sports writer.

Bonus – looking around for info on the paper and Mr. Herman I discovered and present as a little gift for other ink stained wretches of a certain age who started at small papers:  a nostalgic video. It shows the press room chunking out papers from the web (not as in www, but as in newsprint off a big roll) to folder on the Daily Mirror’s ground floor.

- Charlie Petit

La Nación (Costa Rica): ciencia y polémica con la visita de James Watson

Monday, February 14th, 2011

(English intro to Spanish lang. post) James D. Watson was surely surprised during his first visit to Costa Rica by a committee from the University of Costa Rica that disrupted his talk at a conference. His detractors argued that he has made racist and sexist public statements. According to the good coverage in La Nación, it caused just a 30 min delay. But he gave a great lecture. La Nación also includes an exclusive, deep, and very well documented Q&A interview with him. It indeed merits reading.  Jim Watson was also present last Friday at NIH during the symposium to discuss the strategic plan “Charting a course for genomic medicine” presented in Nature on Thursday. Certainly the plan is unspecific and it doesn’t say anything new, but we are surprised that only El Mundo seems to have reported about in in the Spanish-speaking media landscape.

Pequeño altercado hace unos días durante la visita a Costa Rica de James D. Watson; premio Nobel por el co-descubrimiento en 1953 de la estructura del ADN. Minutos antes de impartir su charla en la Universidad de Costa Rica, el consejo universitario estuvo a punto de boicotear el acto argumentando que en el pasado Watson había realizado declaraciones de carácter racista y sexista, y la Universidad no debía cederle espacio. Como explica Alejandra Vargas “UCR intentó vetar charla del premio Nobel James D. Watson” en La Nación, al final el acto sí pudo realizarse y la conferencia resultó ser un éxito rotundo. Destacamos cómo la nota de Alejandra no se quedó sólo en la anécdota, sino que aprovechó para recoger opiniones de los involucrados, destacar los mensajes más relevantes de este ciertamente polémico pero emblemático científico, e insertar videos de la conferencia en la versión online.

Muy completo trabajo, cuya guinda la aporta la excelente y profunda entrevista que en exclusiva le realizó Debbie Ponchner. Debbie exprimió a Watson combinando anotaciones de carácter científico -como los fracasos de la terapia génica o la función del mal llamado genoma basura-, con opiniones más controvertidas -como su peculiar distinción entre ganadores y perdedores, la importancia de secuenciar el genoma a una edad temprana, o su sutil desprecio a Craig Venter-. Lectura muy recomendada, que no busca aprovechar alguna de las conocidas salidas de tono de este personaje, sino dar una imagen fidedigna de su persona y pensamiento. Una muestra más de la solidez y bien hacer de la sección Aldea Global en La Nación.

Desde aquí incidimos en que Aldea Global puede ser tomado como un ejemplo de espacio para cubrir noticias de ciencia, tecnología, salud y medioambiente; que tiene en cuenta las principales noticias internacionales, pero presta siempre muchísima información a las informaciones científicas de su país. El éxito de Aldea global y el prestigio que le da a La Nación, puede inspirar a más publicaciones. Sólo se necesita el apoyo del periódico, un liderazgo inicial de un/una periodista especializada, y la apuesta por formar, constituir y dar continuidad a un grupo de periodistas con interés por la ciencia. Estos requisitos confluyen para permitir que -por ejemplo- Pablo Fonseca esté escribiendo de manera prolífica desde un congreso tecnológico en Barcelona. Gran trabajo de este equipo de redactores (no olvidamos a Irene en Salud) que – como vimos por su implicación en el TEDxPura Vida- tiene un rol muy activo en el compromiso con la difusión de la ciencia en Costa Rica.

Sin abandonar el tema de la genética, Nature presentó el jueves pasado el plan estratégico del NIH “trazando el camino hacia la medicina genómica” que pretende marcar las pautas de la próxima década en materia de investigación en genética humana y su aplicación clínica. Cierto que el plan es  poco específico, y no aporta nada revolucionario. Dice que se debe buscar la transferencia de la ciencia a la práctica clínica, pero al mismo tiempo advierte que no debemos esperarlo en esta década. El plan no tiene gancho y más bien parece un recordatorio; pero es un documento importante dentro de la comunidad científica, y nos sorprende que sólo El Mundo haya reportado sobre él. Lo hizo Isabel Lantigua en “La nueva era del genoma”. Una pieza muy documentada, con gran diversidad de fuentes (quizás falta alguna referencia al estado de la genómica en España), y que refleja muy bien la idea de que la implantación definitiva de la genómica en los sistemas sanitarios todavía es lejana. “Utópica” escribe Isabel. Iremos viendo si es así, pues la genómica es uno de los campos más candentes de la ciencia actual.

- Pere Estupinyà

(UPDATED*) Lots of Ink: A. afarensis, aka Lucy, had an arched foot. Walk? She could strut!

Friday, February 11th, 2011

We all know people with flat feet, and most of them walk pretty well and most probably do so very well. But news that a #4 metacarpal bone recently found in Africa is consistent with an arched foot, and that it belonged to a specimen of Australopithecus afarensis, is getting good play. The species was proclaimed after discovery in 1974 of a small female that paleontologists named Lucy, after the Beatles tune they had on their tape player in their camp in the Afar desert of eastern Ethiopia. An arched foot, reported today in Science,  means not only bipedal, but evolved so as to be efficiently bipedal and hence, much more like us than if she waddled like a chimp keeping it’s knuckles out of the dirt. Interesting is that one of the famous Lucy’s discoverers, Donald Johanson at Arizona State, is among the paper’s authors, and his longtime colleague at ASU, William Kimbel, found the bone. The paper’s first author is at U. of Missouri.

Stories:

  • Time Magazine – MIchael Lemonick: Found: Ancient Bone That Let Humans Walk Upright ; Whoo, forget Lucy. Get a load of Ambam. Lemonick smartly leads with video of a gorilla in a UK zoo who spends a lot of time standing or walking around on two legs. Forget too my waddle talk above. The ape’s posture is superb. It gives the piece a gentle, and thoroughly engaging, introduction to what we are now learning about A. afarensis and other early hominids (or hominins. I can’t keep straight what is the preferred term or why. I think I”ll look it up, later). One might also wonder, sympathetically for the guy, whether Ambam has a touch of Stockholm Syndrome. Another thought:  if wild gorillas did this enough to notice, Darwin’s The Descent of Man would have long ago reduced anti-evolutionist clamorers to a much fainter grumble.
  • New York Times – Sindya N. Bhanoo: Lucy Walked Tall, a Foot Bone Suggests ;
  • BBC – Jonathan Amos: Fossil find puts ‘Lucy’ story on firm footing ;
  • Fox News – Jennifer Welsh: Ancient Foot Bone Proves Prehuman Lucy Walked Tall ; That the second hed with “walked tall” in it. Not to be excessively and numbingly punctilious about it, but how does this make the walk any taller? Bouncier maybe.
  • Kansas City Star: Alan Bavley : Lucy the ape-woman walked much like modern humans ; Bavley, I find, is the paper’s health reporter. He slides out of the niche well, covering this in good fashion. The paper’s lead author tells him, of Lucy, “I bet she could dance.” Maybe that’s an assignment for Ambam’s keeper’s in England – show him how to dance. The story also quotes the papers lead author as saying that such feet started with Lucy and her kin. One would like to know more about that. How did Ardipithecus walk? Or other earlier species?
  • Daily Mail (UK) David Derbyshire: The most important metatarsal in history: Fossil shows many walked tall 3 million years ago ; A claim too far, that scientists have pinpointed the moment when our ancestors abandoned the trees. Good illus, but one caption puts the discovery site in the wrong nation (Egypt, not Ethiopia). If you want a real deep illus mystery, how to explain what the Independent in the UK put with this story, which it picked up from the Daily Mail? It’s a pic of men dancing in African-looking feathers, made up with beetling brows, probably in a Rio samba parade at my guess, and their feet aren’t even visible. What was the art editor thinking?

* UPDATE

  • USA Today ScienceFair blog – Dan Vergano: two items. First is Reaction round-up: Lucy’s feet made for walking,  from Saturday, a solid compilation of opinion from other paleontologists, including one who argues persuasively (to me) that one bone does not a generality make – only that some A. afarensis members may have been flat-footed just like people, and some had good arches. But that does leave Lucy and kin, by implication, with an understanding as good as ours (which is, yes, an allusion to L. Frank Baum’s Oz series).  Second, Vergano reports that  USA Today had an Ambam story, too, two weeks ago, with a similar collection of expert reaction.

Grist for the Mill:

Univ. of Missouri Press Release ; Arizona State University Press Release ;

Note: Had today’s post (scroll down) on a possible HIV treatment not taken so long to sort out, I’d have also tracked the news in Science of an equally interesting paleontology story, on dinosaur and avian forelimb digits 1, 2, and 3. Perhaps Monday.

- Charlie Petit

(UPDATED and Amended*) Bloomberg: “The Berlin Patient” redux, a tale of HIV immunity and perhaps, confusion

Friday, February 11th, 2011

On the Bloomberg wire and at its partner, Business Week, Rob Waters introduces maybe you and certainly me, unless I’d heard of him and forgot, to a remarkable man who had AIDS but no longer does. He calls him the Berlin Patient.

This is a straight business story, focussing on a company with an idea, and thus as are many business stories, largely a piece that takes at face value the company’s business plan. Not exactly an unpaid ad, but close to it. It is a remarkable business plan, even accounting for the lack of any discouraging word in the piece. The news is that a San Francisco man, after a stem cell transplant in 2007 in Berlin in which he received cells from another person with natural resistance to HIV, seems to be cured. And not merely of HIV infection but of AIDS. And that  a California company called Sangamo BioSciences is aiming for a commercial, mass market version using an occasionally reported technology, involving “zinc fingers” that alter DNA, to tweak stem cells to generate immune systems resistant to HIV infection.

Which, if it works, and even if it’s colossally expensive when imagined as a mass treatment, is colossal news.

I am also colossally confused. Waters reports explicitly that this 44-year-old San Francisco man who now seems clear of the virus had, until recently, been known in medical circles only as ‘the Berlin patient.”

If so, he may be Berlin patient #2. The first one is described well in this 1998 New York Times story by Mark Schoofs, headlined The Berlin Patient. My guess is that The Berlin Patient of that story is the source of the transplant to our San Francisco patient with the apparent cure, and that the Bloomberg/BusWeek story gets mixed up on who the near-fabled Berlin Patient is. And it’s not the first report to do so:

*UPDATE – See comments below to see why, but in writing this I got a little carried away on the idea that these two surprising, seemingly fully-cured “The German Patient” examples in the history of HIV and AIDS treatment are somehow intertwined. I withdraw the implication that reporters on the recent episode had significant holes in their stories due to omission of the earlier one. I apologize to Waters and Sheridan, who resented  implications of oversight I made as result of  my delight with myself on learning there was a German Patient #1.  It remains a curious thing.  And now to return to the original post….

There probably are others. But if it took me only a moment to search out “The Berlin Patient” and the term’s history, the exact meaning of the term ought to have been explored and, if there is more than one of them, explained in print. In an email exchange, Rob Waters assures me that at least since a 2009 paper in the New England Journal of Medicine, the title “The Berlin Patient” has been on the patient in his story.

A search for a good technical description of Sangamo’s zinc fingers strategy reveals:

Thus, the Bloomberg/BusWk story has been building, and has been reported in bits and pieces, for years. It merits update. But it also could have used more history, and some perspective. A cure for AIDS is a huge claim. Any  hint of such a thing ought to include an explicit recognition of the long list of astoundingly hopeful ideas and initial results that have, so far, fallen short of fulfilling those hopes.

Grist for the Mill:

Sangamo Feb 7 Press Release ; Sangamo 2008 Press Release ;

- Charlie Petit

Lots of Ink: House Republicans go after EPA, clean energy, and other restrictions on business as usual

Thursday, February 10th, 2011

struggling for composure

Where ought one go for real insight into events? Just to the news as reported in traditional and deliberately dispassionate mainline journalism style, or to wade into the blogosphere – and if one chooses blogs, which kind?

I’ll get to that latter question in a moment. Let’s start with some news reports on an event that got wide coverage – a hearing before the House Energy and Commerce subcommittee in Washington yesterday in which the Republicans in charge lambasted, and threatened to eviscerate via funding cuts, the EPA’s ability or authority to regulate CO2 as a pollutant. Pictured is the latter’s administrator, Lisa Jackson, the designated piñata in the hot seat.

Sample Stories:

That’s enough. These read, in quick scan, as solid pieces of breaking news reports. I am hastening on to another topic however – how to get a deeper, if narrower, slant on things from blogs. The question was prompted this morning by, appropriately, a blogpost:

  • Collide-a-Scape – Keith Kloor: The gang that can’t talk intelligibly ; His topic is the same as led to yesterday’s hearing, with reference to other stories on the run-up to that hearing. His thesis is that newspaper blogs are not all the different from newspaper stories, but at some magazines one finds the sort of stories that have “color and verve” and provide readers a deeper sense of the absurdism that may underlie a Congressional hearing.

To filch one link from Kloor’s piece, here is his fave example of the sort of blog that, after one has read the news, provides value-added focus:

- Charlie Petit

AP, BBC, Brit Press: Prince Charles rallies to climate science

Thursday, February 10th, 2011

England’s Prince Charles yesterday blasted, rapped, criticised, and otherwise took to task the UK’s (and world’s) ranks of climate change contrarians, skeptics, sceptics, deniers, and rejectionists or whatever you want to call those who think the IPCC has been hoodwinked or is part of a conspiracy or is just thick.

These remarks, at a European Union meeting in Brussells, unavoidably generated some press. His words of encouragement for the main bloc of scientists are no doubt welcome among them. They might also be more weighty if he were not also a stout advocate for homeopathic medicine. Oh well. Desperate circumstances are not a wise time to fine-toothed-comb one’s allies for nits.  (Snarkiness over such external matters aside, after watching a clip or two, one must concede he makes a very solid declaration, with appropriate remarks on the plausibility of a world wide conspiracy among scientists.)

Stories:

Grist for the Mill:

Office of Prince of Wales Press Release ; Text of Speech ; Article by Prince Charles ( Times of London published it, but put it behind a subscription wall).

- Charlie Petit

(UPDATED* w/USA Today) Nature News: Gender gap in science real, and its root not just the old boys club.

Thursday, February 10th, 2011

Hypatia, Mathematician of Alexandria

In Proceedings of the National Academy of Sciences is a study from two  Cornell researchers that says yes, women are underrepresented in science. It also says don’t blame it these days on overt or even unconscious discrimination that tilts the playing field on hiring, publication, and promotion. Yet it does not provide ammo for those who surmise, as Lawrence Summers forever will be remembered for offering as (he says) a talking point, that underlying ability in math and other rigorous skills is less common among women.

Rather, it’s …. complicated and hard to pin down. But in general it appears, after a quick riffle through the study, the lower overall achievement and advancement rate among women is not imposed by institutions so much as by their own choices to spend significant time as parents or to fit other lifestyle modes around their careers.

The only news outlet I could find that ran with this is the rather specialized NatureNews, from the publisher of Nature. There Gwyneth Dickey Zakaib writes it under the snappy lede: Goodbye glass ceiling ; so long old-boys club. She characterizes the reasons as “the invisible web. Its multiple strands – some social, some biological, some institutional – can make it significantly harder to females researchers to achieve as much, as fast, as their male counterparts.”

*UPDATE:

  • USA Today ScienceFair Blog – Dan Vergano: Family choices challenge careers for women scientists ;

There is, by the way, an apparent balancing yin elsewhere for this yang in science. It is seen in the core audience for this here ksjtracker operation. It is no secret that science journalism, which as long as I can remember has had plenty of women, has for at least the last ten years tilted more toward the distaff side of membership. Pulling down the nearest-at-hand issue of ScienceWriters, the NASW’s magazine (Summer 2010 number), I just scanned through its listing of 50+ new members of the association. If I sorted the names right, 65 percent are women.  There are no numbers to back it up, but I’ll bet a large and perhaps controlling fraction are people with training in science and who had expected careers in science, not science journalism. We are getting, perhaps, a welcome tide of refugees.

This is no new trend. A dozen years ago I wrote an essay on this, after noting back then the pronounced shift toward women in science reporting. It’s in the ScienceWriters archive somewhere but I can’t find it on line. Here’s the draft I sent in. It was written mainly as an amusement, Its stats seem to be representative still.

A wonderful lot of talented people trained to think as scientists are joining the science journalism trade. If it’s partly because more women than men tend to regard 12 to 18 hours a day in a lab through one’s younger years as not a real life (ie, if the dork factor among women is  less prominent), and if they are looking for a way to use their science sense in other ways, our guild is a beneficiary.

Grist for the Mill:

Cornell Press Release ; PNAS Understanding current causes of women’s underrepresentation in science ;

- Charlie Petit

Miami Herald, etc: Florida’s cold snap no match for alien encounters of the constrictor kind

Thursday, February 10th, 2011

Yikes!

Hopes were high in Florida for a silver lining to bouts of frigid weather in the last year or so: fewer exotic, slithering, and very large serpents. That goes especially for the Burmese pythons that have found the Everglades and other broad wetlands a fine place to live and multiply.

Wildlife managers say however that while some natives, including manatees and sea turtles, suffered and a significant number perished, exotic snakes and most other invasive species seem not to have taken a satisfactory hit. Whatever short term reduction occurred they appear to have rebounded.

I cannot resist news about pythons in Florida. Just so … weird.

Stories:

Photo source Palm Beach Post.

- Charlie Petit