Dear Myles:

I truly enjoyed reading the following statements in your editorial (43:page 85) 

First…“for the parallel study of mechanisms of evolution, both the mechanisms of speciation and those operating in adaptation at the population level in the course of domestication history and agricultural improvement.” 

Second. “…we remain at heart a journal of genetic variation.” 

I admire your commitment to the above principles. 

Darwin was inspired by domestication of plants and animals by farmers and animal fanciers, and he asked how variation was molded by nature. 



The great triumvirate – Fisher, Haldane and Wright were not only inspired by Darwin, but also intimately associated with plant and animal breeding. That is why their work is so practical, meaningful, endearing and enduring. Perhaps it may not be an exaggeration if I mention that to a large extent, we are yet to transcend the limits (should we call it the Fisher-Haldane-Wright limit?) set by these visionaries.

 The later ones such as Kimura, Ohta, Nei, Mather, McClintock, Beadle to name a few, were all trained in plant breeding. Similarly, Lush, Robertson, Cockerham, Henderson et al. were animal breeders. Examples such as the origin of cultivated wheat, cotton and sunflower are exhilarating. Indeed, these discoveries absolutely dwarf the present craze in structural/copy number variation – Please don’t mention this to Evan Eichler or Jim Lupski! 



Single genes could transform and even destroy agriculture and livestock. I am sure humans are no different from these general phenomena. These views must be addressed in our own times. 

It is a pleasure to witness this wonderful progress and to see a journal committed to advance these fundamental principles of biology. 



Sincerely yours

- Raju Govindaraju

Sample lyrics:

Regenerating eyes and hearts

Engineering private parts

See Boston Globe story here.

Wheeling around his laboratory in a white lab coat and snapping his latex gloves to the beat of M.I.A.’s rap song, “Paper Planes,” Jonathan Garlick is spreading the word about stem cell research.

Garlick, a professor at Tufts University School of Dental Medicine, who normally works on tissue engineering projects and stem cells says he finds that scientific terminology lends itself to rap – and that rap is a good way of communicating science to the public.

Between Saudi Arabia, Qatar, and the UAE, the Middle East is quickly becoming home to some of the most advanced research facilities in the world. Already KAUST in Saudi Arabia has one of the world’s fastest supercomputers, and come 2012, Qatar will complete Sidra Medical and Research Center, a world class multi-billion hospital and health research institute.

With incredible facilities and large money grants, many researchers and scientists from the West are likely to be interested in coming to the region. But is the research taking place in these facilities serving the needs of the average person in the Middle East?

Researchers at Weill Cornell Medical College – Qatar, comment that the health problems that Qatar suffers are the same as any Western country, such as diabetes, hypertension, Parkinsonism. In a way that makes sense. But Qatar is a tiny country with a population of around 1.5 million people. Shouldn’t these large research institutes cater further than the borders of the country they are in?

Not all of the Middle East suffers from the same problems as Western countries. While the Gulf States are well-off, many countries in the region are quite poor, and thus suffer from a different set of problems. For example, a recent research published on PLoS shows that member states of the Organization of Islamic Countries (OIC) are disproportionately affected by neglected tropical diseases (NTDs). For example, between 200 and 300 million people living in OIC countries are infected with one or more intestinal worms.

Sadly, there isn’t a single medical school for tropical diseases in all of the Middle East.

The bulk of the burden of these diseases falls upon the poorer people. Many of them are debilitating and cause even more poverty.

So if these new Middle Eastern institutes will continue to focus on research similar to that in the richer, Western world, who will offer research to the poorer communities back home?

The verdict is finally out. The government wants to evolve a more ‘effective, alternative mechanism’ for a science conclave that overcomes the rot plaguing the annual Indian Science Congress. Science minister Kapil Sibal has announced in a written reply in Parliament that the number of participants and topics at the science congress had increased in recent years, thereby making it ‘impossible for any organiser to hold meaningful discussions’.

We were expecting the government to take note of this malaise as reflected in this discussion in the Nature India forum.

It seems, a parallel annual meet of top scientists from across disciplines is being proposed in New Delhi to keep up with the latest in their respective fields. One just hopes that it doesn’t end up being another government exercise in Vigyan Bhavan.

Researchers probing a virtually unexplored forest on the Costa Rica-Panama border have discovered three new species of salamander.

Led by Alex Monro, a biodiversity expert at the Natural History Museum in London, the three expeditions to the La Amistad National Park recorded 5,300 plants, insects and amphibians.

“Finding so many new species in one area is exciting. Particularly as this is probably the only place in the world you can find these animals,” says Monro (press release).

Two of the Salamanders are from the Bolitoglossa genus. The Times says they were so slow-moving it was amazing they were able to find mates and too feed. However a tongue that can shoot out, catch an insect and be back in their mouths in seven milliseconds helps with the latter.

The other species is a type of dwarf salamander, measuring only 3cm in length according to the Natural History Museum. Which makes the thumb in this picture huge…

At present the species are unnamed.

Image top: dwarf salamander / A Monro

Image bottom: bolitoglossa species 1 salamander / A Monro

Cross posted from The Great Beyond UPDATED

Al Gore will share this year’s Nobel Peace Prize with the Intergovernmental Panel on Climate Change. They were awarded the prize for “for their efforts to build up and disseminate greater knowledge about man-made climate change, and to lay the foundations for the measures that are needed to counteract such change”.

The prize committee declared Al Gore “one of the world’s leading environmentalist politicians” and said the IPCC had “created an ever-broader informed consensus about the connection between human activities and global warming”.

“Action is necessary now, before climate change moves beyond man’s control,” says the committee (press release).

This may take some of the sting out of the UK court ruling Al Gore’s An Inconvenient Truth movie will have to carry caveats when shown in schools – a ruling based in part on perceived differences between Gore’s stance and the scientific consensus outlined by … the Intergovernmental Panel on Climate Change (see the updated blog posting on the ruling).

This is not the first time a prize has been won by an institution. In 2005 the International Atomic Energy Agency took half a prize, and other winners include the UN in 2001 and Médecins Sans Frontières in 1999. The real question is who will get the money at the IPCC?

The question for Gore is slightly different. The impressive Fiona Harvey at the FT has a very good piece up already, noting that the prize was perhaps unsurprising but “reinforced his reputation as the world’s foremost champion of environmental issues.” It “also added to speculation that Mr Gore would be persuaded to have another attempt at the US presidency”.

UPDATE

“It’s every scientist’s dream to win a Nobel Prize, so this is great for myself and the hundreds that worked on their reports over the years. It is perhaps a little deflating though – that one man and his PowerPoint show has as much influence as the decades of dedicated work by so many scientists,” said Piers Forster, of the University of Leeds School of Earth and Environment (via the Science Media Centre).

Cross posted by Olive Heffernan

Exactly a week ago I was on my way to O’Reilly’s Foo Camp in Sebastopol, so it’s about time I posted some notes about a few of the amazing people I met during and since that event:

• Beth Noveck told me that Peer to Patent, a wonderful project that she and others have been working on for many months, is going really well in it early days post launch. The aim is to open up patent applications to public scrutiny, which sounds like an excellent idea to me. Brady has a write-up about it on Radar.
• Manolis Kelaidis, fresh from his triumph at the TOC conference demoed bLink. I first met Manolis last September, when he came to present his invention at Macmillan (Nature’s parent company). He’s a very creative and thoughtful (but self-effacing) guy, and I’m delighted that bLink is getting the attention it deserves.
• Chris DiBona, who among many other things runs the team at Google that puts together SciFoo, was proudly showing off his iLiad, especially the Linux shell function. (Hey, this was Foo Camp.)
• Some of the science-oriented attendees — Drew Endy and Saul Griffith spring to mind — were kind enough to rave about Nature Precedings. Even at Camp, Drew was busy working away on his latest amazing project, the BioBricks Foundation. He also had a test tube of E. coli that smelled of bananas. (Hey, he is a synthetic biologist.)
• Speaking of science, I also met Marti Hearst from UC Berkeley, who’s working on BioText, figure-based searching for the scientific literature — great!
• There were plenty of other amazing people, of course, not least the O’Reilly crowd themselves, especially Tim O’R and Sara Winge, the people who make Foo Camp happen. (And SciFoo too.)

I also bumped into Ray Ozzie and told him about the great discussions we’ve been having with Tony Hey‘s group at Microsoft (known as ’Technical Computing’, they run MS’s collaborations and interactions with scientists and engineers). It was an extra delight, then, to meet Savas Parastatidis on London on my return. I can’t remember the last time I came across someone outside Nature with whom I shared so many interests and opinions. We’ll definitely be doing some cool stuff together, and we’ll keep you posted.

Last and least, I have an article in this month’s STM News (a periodical for science, technology and medical publishers). The full publication is members only, so my draft is reproduced below for anyone who’s interested. Appropriately enough, it’s basically a summary of the ways in which the O’Reilly alpha-geek crowd has influenced our activities at Nature.

(more…)

Exactly a week ago I was on my way to O’Reilly’s Foo Camp in Sebastopol, so it’s about time I posted some notes about a few of the amazing people I met during and since that event:

• Beth Noveck told me that Peer to Patent, a wonderful project that she and others have been working on for many months, is going really well in it early days post launch. The aim is to open up patent applications to public scrutiny, which sounds like an excellent idea to me. Brady has a write-up about it on Radar.
• Manolis Kelaidis, fresh from his triumph at the TOC conference demoed bLink. I first met Manolis last September, when he came to present his invention at Macmillan (Nature’s parent company). He’s a very creative and thoughtful (but self-effacing) guy, and I’m delighted that bLink is getting the attention it deserves.
• Chris DiBona, who among many other things runs the team at Google that puts together SciFoo, was proudly showing off his iLiad, especially the Linux shell function. (Hey, this was Foo Camp.)
• Some of the science-oriented attendees — Drew Endy and Saul Griffith spring to mind — were kind enough to rave about Nature Precedings. Even at Camp, Drew was busy working away on his latest amazing project, the BioBricks Foundation. He also had a test tube of E. coli that smelled of bananas. (Hey, he is a synthetic biologist.)
• Speaking of science, I also met Marti Hearst from UC Berkeley, who’s working on BioText, figure-based searching for the scientific literature — great!
• There were plenty of other amazing people, of course, not least the O’Reilly crowd themselves, especially Tim O’R and Sara Winge, the people who make Foo Camp happen. (And SciFoo too.)

I also bumped into Ray Ozzie and told him about the great discussions we’ve been having with Tony Hey‘s group at Microsoft (known as ’Technical Computing’, they run MS’s collaborations and interactions with scientists and engineers). It was an extra delight, then, to meet Savas Parastatidis on London on my return. I can’t remember the last time I came across someone outside Nature with whom I shared so many interests and opinions. We’ll definitely be doing some cool stuff together, and we’ll keep you posted.

Last and least, I have an article in this month’s STM News (a periodical for science, technology and medical publishers). The full publication is members only, so my draft is reproduced below for anyone who’s interested. Appropriately enough, it’s basically a summary of the ways in which the O’Reilly alpha-geek crowd has influenced our activities at Nature.

(more…)

A fascinating first presentation from Steve Chu, who runs Lawrence Berkeley Lab, one of the sponsors of this event, on the challenge of finding technologies for clean energy production and the possibilities that various synthetic-biology technologies offer for meeting that challenge. There was lots of talk of artificial photosynthesis, and some wonderfully far out ideas, such as redesigning plants so that their carbon-dioxide intakes and water outputs are separated, rather than being combined in the magnificently subtle mechanisms of the <a href+https://en.wikipedia.org/wiki/Stomata>stomata.

(more…)

A fascinating first presentation from Steve Chu, who runs Lawrence Berkeley Lab, one of the sponsors of this event, on the challenge of finding technologies for clean energy production and the possibilities that various synthetic-biology technologies offer for meeting that challenge. There was lots of talk of artificial photosynthesis, and some wonderfully far out ideas, such as redesigning plants so that their carbon-dioxide intakes and water outputs are separated, rather than being combined in the magnificently subtle mechanisms of the <a href+https://en.wikipedia.org/wiki/Stomata>stomata.

(more…)

OK – I know this is going to sound strange, but I really love looking at electron density… Most structural papers have a few figure panels showing some electron density (usually the active site residues), but atomic resolution structures are rare and it’s just so satisfying to see little globes of density around each atom (rather than a big blob that could represent one of several rotomers…)

If you love electron density too, there’s a recent paper from Nature Chemical Biology that might interest you: Lyubimov et al. “obtained five sets of X-ray diffraction data at atomic resolution (0.92–0.99 [Angstroms]) over a broad pH range (4.5, 5.2, 5.8, 7.3 and 9.0).” And Figures 1, 2, and 4 are beautiful… (If you don’t currently subscribe to that journal, the paper’s graphical abstract has a taste of what you’re missing…)

This isn’t the first atomic resolution X-ray crystal structure of a protein – there’s also a 1.0 Angstrom structure of cutinase from Longhi et al., a 0.78 Angstrom structure of subtilisin from Kuhn et al., a 0.95 Angstrom structure of a pancreatic elastase/N-acetyl-Asn-Pro-Ile-CO2H complex from Katona et al., a a series of atomic resolution structures of RNase A from Berisio et al., and a 0.95 Angstrom structure of cholesterol oxidase from Lario et al.

Lyubimov et al. remind us that "[i]n 1936, Mirsky and Pauling wrote, ‘The importance of the hydrogen bond in protein structure can hardly be overemphasized’" – I’m sure that Mirsky and Pauling would be really interested to read the aforementioned papers, as we are now able to examine the role of hydrogen atoms in enzymatic catalysis for fairly large proteins (cholesterol oxidase is 56 kDa, for example).

Hopefully this field will continue to grow and we’ll see more atomic resolution structures in the RCSB Protein DataBank – I don’t know about you, but I’d love to see a 0.9 Angstrom structure of the ribozyme in action…

Joshua

Joshua Finkelstein (Associate Editor, Nature)

They’re worth a cool $57 billion to the United States each year, that’s what.

Next time you dismiss insects as mere creepy-crawlies, ponder for a while on what life would be like without them. Our six-legged friends might be more valuable than you think — research estimates that they’re worth at least a staggering $57 billion to the US economy every year.

Read the story here.