Schwartz et al.
Genome-wide analysis of Polycomb targets in Drosophila melanogaster
Balasubramanian et al.
Consonni et al.
Conserved requirement for a plant host cell protein in powdery mildew pathogenesis
Comments welcome.
My neighbor Noriko Cuevas found this intergeneric rosemary-lavender hybrid in her garden and it is now growing in mine. I think it might be a chimera since each stem produces two kinds of leaf, short rosemary-scented ones and long, lavender-scented ones. If it is a hybrid and not a chimera I would be interested to know whether combining the metabolisms of these two classic fragrant Lamiaceae produces any new terpenes. Is anyone with a GC-MS from Givaudan or IFF lurking?
Paradigm, the Whitehead Institute’s quarterly magazine, has a short piece in the Spring 2006 issue (scroll down to page 20) about the paper from the Weinberg lab that was published in the journal in September 2005. The paper described a new mouse model of metastatic melanoma, showing that Slug, a regulator of neural crest cell migration, is required for metastasis in this model. The Paradigm article by Eric Bender briefly outlines the origins of this work in the Weinberg lab, and traces its ultimate success to timely help from collaborators:
In the summer of 2002, graduate student Piyush Gupta came up with an idea about the mechanisms that might drive the growth of melanomas, an often deadly form of skin cancer. In September 2005, he and his colleagues published a paper in Nature Genetics that validated the idea. His three-year journey demonstrated how biological research thrives on informal collaborations inside and outside a home laboratory…
Some US science policy and politics news courtesy of Mike Stebbins. Mike notes that Senator John McCain has introduced an amendment to the ‘American Innovation and Competitiveness Act of 2006’ (S.2802). McCain’s amendment would essentially force the President’s science adviser, John Marburger, to come up with written policies that will allow government scientists to tell the truth in public as they see it. An early draft can be found here, which has clearly been offered in response to recent embarrassing attempts by officials to interfere with free and open communication by government scientists. Mike also points out that Senator Bill Frist is under increasing pressure to bring up for a vote a bill to end the ban on federal funding for embryonic stem cell research. This bill has already passed the House of Representative. Rick Weiss, writing in the WaPo (as the bloggers like to say), has more on the politics behind the senator’s dilemma.
A User guide to Nature Genetics editorials 2004-6
One journal, two coordinating visions of the *Wiring Diagram and the *Risk Engine.
Professional Research Strategy
Postdocs and career training
Involvement of children in research
How to discuss ancestry and ethnicity
Credit for unpublished association studies
Public resources from a research corporation
The need to take risks and forge interdisciplinary collaborations
Synthesizing knowledge by reconciling opposing hypotheses
Social and Political
The need for a US genetic nondiscrimination act
A ban on reproductive cloning to enable therapeutic cloning
The ineffective US discussion on therapeutic cloning
Therapy versus enhancements
Advances in fields of genetics
We like plant genetics
*Mendelian genetics
Modeling complex traits in mice
The power of mouse genetics
The importance of structural human genome variation
Systematically documenting structural variants
Genomics
Genomic sequencing technology
Does all research benefit from replication? Even genome annotations?
Epigenome projects are good value for money
Integration
A grand quest to access all human genomic variants via HUGOBase
Fanconi anemia and high-input biology
* Currently open access
Senée et al.
Bar-Even et al.
Noise in protein expression scales with natural protein abundance
Barrett & Cardon
Evaluating coverage of genome-wide association studies
Pe’er et al.
Evaluating and improving power in whole-genome association studies using fixed marker sets
Comments welcome.
Telltale X reveals traces of prolonged sex with the ex.
David Reich and colleagues have delivered the latest of a long series of breathtaking blows to our amour propre with their new Article in Nature. This work should elicit pant-hoots of delight from those of us who relish science as the antidote to the prevalent and entirely misplaced view that the position of the human species in the natural world is in any sense “special”.
The period during which humans speciated from chimpanzees was apparently a long and ignominious sexual morass, a messy four million years or so of breaking up, getting back together, producing fertile and infertile offspring and finally getting the knack of making do without one another.
What David and his colleagues at the Broad did was to look at 800 times more primate genomic DNA sequence than previously examined, aligning 87Mb of newly assembled gorilla sequence with the exisiting human and chimpanzee genomes, 18.3Mb from five primates, including 1.2Mb from chromosomes 7 and X. This allowed them to compare the sex chromosome with autosomal sequence. Overall they concluded that the divergence time since human-chimp speciation showed enormous variation across the genome and even included chunks of the genome that were more similar between human and gorilla than between human and chimpanzee.
The human X was the youngest of all, a situation that could only have arisen in a scenario where chimpanzee-human hybrids occurred after the initial speciation event, and directional selection for hybrid fertility imposed some systematic restriction on our pattern of reproduction (the authors suggest backcrossing to chimpanzee males for the purpose of discussion).
All this is reminisiscent of the scene in Nagisa Oshima’s film “Max, mon amour”, where the British diplomat in Paris adapted with admirably civilized sang froid to the passionate sexual relationship between the eponymous chimpanzee and his wife – the immor(t)ally irresistible Charlotte Rampling. Of course he did, we’ve seen it all before.
Hear my thoughts on the chimpanzee genome on ABC’s Science Show.
The blog Epigenetic News has a helpful post on the new five-year strategic plan for the NIEHS. The full plan can be found here.
Smyth et al.
Henderson et al.
Witt et al.
A degradation-sensitive anionic trypsinogen (PRSS2) variant protects against chronic pancreatitis
Comments welcome.
Eloquence and good sense from Art Caplan in the Philadelphia Inquirer:
The scientists I know are full of reverence for life, for people, and for our future possibilities together. They are in awe of nature. They are humble in the presence of the simplest cell, bacteria, virus or bit of mold in a lab dish. There is a spirituality about pursuing science as deep and as sincere as any to be found in religion. There are indeed important moral and ethical questions to be debated about the “humanness” of the genetic research being carried out in labs, behind closed corporate doors, and in distant lands whose cultures and traditions make us edgy.
That said, I do not know a single genetic scientist, not one, who thinks that moral, ethical and even public reflection about the morality of genetic engineering is silly, pointless or unnecessary. In the halls I am lucky enough to travel in universities, companies and research institutes, these subjects are debated and discussed as hotly and as with as much passion as they are at the Vatican; in your church, synagogue or mosque; or at your dinner table. Scientists do care, and they care deeply what their peers think and what you and I think.
What we need is what C.P. Snow once called for: a bridge between the two cultures. For him, the bridge was between the sciences and the humanities. Today we need a bridge between those who do science and those who do values. Scientists do “do values” – it is just that few outsiders get to see them do so. And many of us are fascinated by genetic science but quickly give up trying to follow it because there are so very few to teach us. What we need today is a dialogue, a conversation, some old-fashioned jawing. We do not need demagoguery, fear-mongering or stereotyping. We certainly do not need bans and fiats and Do Not Pass Go restrictions.
What scientists need to do – and quickly – is come out of their laboratory lairs and be seen in public. You need to know about their aspirations, dreams, hopes, and values. You need to know they stand shoulder to shoulder with all of us in wanting a better world. They see a better future and a way to get there.
Genetic research in the hands of those who practice is not aimed at power, fame, ambition, or transforming oneself into a god. If it is about anything, it is about love: the love of life, the love of people, the drive to make a better life for the sick and those at risk of becoming so.
To ensure the future of this century, we must ensure sufficient education, dialogue, oversight, accountability and control over the industrialization, commercialization and financing of genetic science. In the hands of its practitioners, that science is very, very unlikely to take us anywhere we do not want to go. But ignorance, inattention or indifference to what governments, business and the military do with genetics could land us in places no one wanted to reach.
Caplan’s complete editorial can be read here.