Archive for January 10, 2012

Storer Lectures – Jane Lubchenco – Jan 11-12

January 10, 2012 Leave a comment

Categories: Seminar Announcements

Student Seminar Series – Weston Powell – Jan 11 @ 13h10 in LSA1022

January 10, 2012 Leave a comment

It is time for the first talk of this BMCDB Student Seminar Series this Winter Quarter and Weston Powell will be the speaker this Wednesday. If you want to eat free pizza every other week, please come and don’t forget to sign in. You can also help the speaker with comments and suggestions

Wednesday 2012 Jan 11

Weston Powell

LaSalle Lab
The Prader-Willi syndrome lncRNA 116HG remains tehtered to its site of transcription by SAF-A
LSA 1022
Free pizza
This is not only a great opportunity to meet and keep in contact with your fellow students from different years and learn about what student speakers are doing, in specific for 1st years.
Note, there are two spots available. If you want to speak, email me or Ralph ASAP.
Your participation is the only way this seminar series will succeed!
See you all on Wednesday.
Daniël and Ralph

The schedule for this quarter is:

Fall 2011
Oct 05 – Nadia Ono
Oct 19 – Kasia Koscielska
Nov 02 – Anna Erickson
Nov 16 – Gordon Walker
Nov 30 – Katrina Garvey

There is still space to talk in the Winter and Spring, so please contact me before all the spaces are gone!!!!! Especially those who want to practice for their upcoming QE.
Winter 2012
Jan 11 – Weston Powell
Jan 25 – Alan Raetz
Feb 08
Feb 22 – Haifeng Wang
Mar 07 – Ariadne Vlahakis

Spring 2012
Mar 28
Apr 11 – Brian Avanzino
Apr 25 – Angela Monterrubio
May 09 – Kristen Beck
May 23 – Damian Guerra

Categories: Seminar Announcements

“Research Works Act” to legally solidify the share of federal funding for the ‘scientific’ contribution of publishing companies

January 10, 2012 2 comments

by Daniël P. Melters

Previously we brought to your attention the intricacies of how the academic publishing industry makes money. In short, the publishing companies have copyright of all the work published in their journals, even though the research was funded by the public. For the public to read the work they funded, they have to pay the publishers. If you buy an individual article you pay between $20 and $50 per article, which would be $1,67-$4,17 per page for a 12-page article, which includes the 1-2 pages of references at the end of an article.

Things are getting even more crazy if US Congress passes the ‘Research Works Act (HR 3699)‘. This bill will guarantee that the publishing industry has absolute rights of its published content, even though they have done no experiments or manuscript writing to fill up the journals empty pages. How far will this go? Currently, research funded by the National Institutes of Health has to be made publicly available within 12 months after publication, although journals are encouraged to do so at the time of publication. Under the proposed ‘Research Works Act’, this would be illegal. The only way the public can read the research they funded, is if researchers publish their work in Open Access journals, such as the various PLoS journals.

In response to this act, Micheal Eisen, a professor at UC Berkeley, brother of UC Davis’ professor Jonathan Eisen, and co-founder of the Public Library of Science (PLoS), wrote an op-ed in the New York Times. This follows after Micheal and Jonathan Eisen complained about this proposed bill on their own blogs (here, here, herehere, here, and here). Jonathan Eisen is even considering an embargo of the AAAS meeting in Vancouver later this year.

If journals add value to a product, this bill might make sense, but this is not the case. So, what do journals add during the publishing step? Fundamentally, they add two things (besides self promotion). They try to assert if the manuscript has the WOW! factor they think their journal represents on the market and they coordinate the peer review process. The results from the latter step also has a big role in determining the former step. Surprisingly enough, the peers who review a manuscript do this for free. They volunteer their time to help these journals. Is this peer review process well managed by the journals? Everyone has heard of numerous cases of scientific misconduct and retracted papers. So the short answer is: mistakes are frequently made. This has been pointed by out in various blogs, including by Michael Nielsen, another advocate for Open Access, who wrote a piece debunking three myths about peer review. These myths are: 1) scientists have always used peer review. 2) peer review is reliable. and 3) peer review is how we determine what’s right and wrong in science. Also, Michael Eisen recently commented on the problems of peer review. The good thing about science is that over time the mistakes are recognized and corrected. Though, this can take many years depending on the mistakes made (or what really is an assumption believed to be fact).

Earlier I already mentioned that buying an individual article is expensive, but what about journal subscriptions? A student subscription to Science is $75/yr or $149/yr for non-students. A Nature subscription is $199/yr and Cell costs $223/yr. These are just three of the top-tier journals. For a scientist to stay up to date, you have to read more than just Nature, Science and Cell, even though these three together will cost you $497/yr as a student in the US, $571/yr as a non-student in the US. Of course you can buy individual articles as well, but these cost you between $20-$50 per article. Rather expensive if you want to read up on the latest findings of say brca1 and brca2, two genes associated with familiar breast cancer. It would be difficult to limit yourself to reading only 5 articles, which would cost you between $100 and $250.

Now these publisher companies want to make it a law that they behold absolute rights about the research published in their journals. Research for which they have done little to nothing to justify such claims. They have not designed any of the experiments. They have not held any of the pipets. They have not analyzed any of the data. They have not written a single letter of the manuscript submitted. They have out-sourced the review of the manuscript for best price possible: free. They have demanded money for the manuscript to be published, extra if you want colour figures. They demand full copyright of your published manuscript. They demand money for you to read your own published work. Now they also want to prevent you from depositing your NIH funded and published research to made available to the public who funded your research.

Can I think of a comparable situation to further highlight the ridiculousness of this bill? Say you are an obstetrician and you helped a baby be delivered. As an obstetrician you have not done much in the process of fertilization (unless of course you are the father), in carrying the baby for ~40 weeks, neither for the development of the fertilized egg to a foetus. Would it make sense to demand ownership of this newborn, as you sort of guided the mother in the delivery process? If you are a publishing company, you would say: “yes, of course!”

What can you do to stop this bill? Call and write your congress representative to urge them to oppose the ‘Research Works Act’ and tell your friends all around the country to do the same thing. Comment on the White House Office of Science and Technology Policy’s request for information (RFI) on public access. The latter option has to be done by Thursday January 12th.

Results from publicly funded research should remain in the public domain, not in the hands of a few publishing companies.


This is the actual text of the proposed bill:


    This Act may be cited as the `Research Works Act’.


    No Federal agency may adopt, implement, maintain, continue, or otherwise engage in any policy, program, or other activity that–
    (1) causes, permits, or authorizes network dissemination of any private-sector research work without the prior consent of the publisher of such work; or
    (2) requires that any actual or prospective author, or the employer of such an actual or prospective author, assent to network dissemination of a private-sector research work.


    In this Act:
    (1) AUTHOR- The term `author’ means a person who writes a private-sector research work. Such term does not include an officer or employee of the United States Government acting in the regular course of his or her duties.
    (2) NETWORK DISSEMINATION- The term `network dissemination’ means distributing, making available, or otherwise offering or disseminating a private-sector research work through the Internet or by a closed, limited, or other digital or electronic network or arrangement.
    (3) PRIVATE-SECTOR RESEARCH WORK- The term `private-sector research work’ means an article intended to be published in a scholarly or scientific publication, or any version of such an article, that is not a work of the United States Government (as defined in section 101 of title 17, United States Code), describing or interpreting research funded in whole or in part by a Federal agency and to which a commercial or nonprofit publisher has made or has entered into an arrangement to make a value-added contribution, including peer review or editing. Such term does not include progress reports or raw data outputs routinely required to be created for and submitted directly to a funding agency in the course of research.
Categories: Recent News

Chancellor’s Colloquium Distinguished Speakers – Ralph Cicerone

January 10, 2012 Leave a comment

Today (Tuesday, Jan 10th), Ralph Cicerone, the president of the National Academy of Sciences and chair of the National Research Council will give a talk in the Chancellor’s Colloquium of Distinguished Speakers. To RSVP click here. He will be talking about climate change, his area of experitice. This talk also falls in line with the Career Options Seminar we had earlier today by Sharon Bergquist, who talked about her graduate fellowship at the National Academy of Sciences in Washington DC.

Ralph Cicerone, NAS president and NRC chair

Climate change: Human causes and responses

Tuesday, Jan. 10, 2012

4 p.m.

Jackson Hall – Mondavi Center

Categories: Seminar Announcements

New DNA Reader

January 10, 2012 Leave a comment

From Reuters by Sharon Begley:

A new DNA reader could bring genetics to medical clinics.

After years of predictions that the “$1,000 genome” – a read-out of a person’s complete genetic information for about the cost of a dental crown – was just around the corner, a U.S. company is announcing Tuesday that it has achieved that milestone and taken the technology several steps ahead.

The new genome-sequencing machine from Ion Torrent, a division of Life Technologies Corp. (LIFE.O), in Guilford, Connecticut, is 1,000 times more powerful than existing technology, says CEO and chairman Jonathan Rothberg.

Taking up about as much space as an office printer, it can sequence an entire genome in a single day rather than six to eight weeks required only a few years ago. The new sequencer, says cardiologist Eric Topol, chief academic officer of private California hospital and doctor network Scripps Health, “represents an exceptional advance and can change medicine.”

Ion Torrent will sell the tabletop machine, called the Ion Proton Sequencer, for $99,000 to $149,000, making it affordable for large medical practices or clinics; existing sequencers cost up to $750,000. The computer chip and biochemicals to sequence a genome will cost $1,000, compared to, for example, $3,000 to test for mutations just in the BRCA genes that raise the risk of breast and ovarian cancer and $5,000 for a complete genome sequencing by Ion Torrent competitor Illumina Inc (ILMN.O).

For a graphic on the shrinking cost of genome sequencing, see:

For now, Rothberg expects research labs to be his main customers, using Proton to obtain the complete genome sequence of people with cancer or autism, for instance, and thereby elucidate a disease’s underlying genetic causes as well as possible ways to treat it. The company has signed on Baylor College of Medicine, Yale School of Medicine and the Broad Institute as its first customers.

Other scientists and physicians, however, say the long-awaited arrival of the $1,000 genome opens the door to widespread whole-genome sequencing even of people who are not ill. And that raises ethical, legal, and medical issues that experts are only beginning to grapple with.

“I’m a big proponent of bringing genetics into the clinic,” says Thomas Quertermous, chief of the division of cardiovascular medicine at Stanford University and an expert in the genetics of heart disease. “But it has to be done in a timely way, and not before its time.”

Babies might be first in line for whole-genome sequencing. Every state requires newborns to be screened for at least 29 genetic diseases.

“If the cost of whole-genome sequencing gets sufficiently low, you could sequence all the genes in a newborn” for less than the individual tests and follow-ups required when one comes back positive, says Richard Lifton, chairman of the genetics department at Yale University. “I’m increasingly confident that’s going to happen. But we need to be careful how we utilize this information. Do you tell a newborn’s parents his apoE status” — that is, whether he has the form of a gene that raises the risk of Alzheimer’s disease?

The cost of whole-genome sequencing will continue to plummet. Lifton foresees a “zero-dollar genome,” making it likely that “we will just do it as part of routine clinical care” for children and adults. A Yale team led by Murat Gunel has already used partial genome sequencing of the 1.5 percent of the genome, called the exome, that codes for proteins to determine the cause of a mysterious and still unnamed genetic disease that results in severe brain malformations.

Because no genes had been identified as causing the malformation, it was not possible to do a standard genetic test, which reveals whether a particular gene is normal or mutated. But exome sequencing showed that a previously unknown gene on chromosome 19 is responsible, he and colleagues reported in 2010. “The new Proton instrument is a big step up,” says Lifton. “It promises to markedly increase the speed and reduce the cost of genome-level sequencing.”

Read the entire article here.

Categories: Interesting link

Gut Bacteria Different in Autistic, Non-Autistic Children

January 10, 2012 Leave a comment

From the Huffington Post UK:

Scientists have found that the bacteria in the gut of autistic children is different from that of non-autistic children.

Researchers from the Mailman School of Public Health at Columbia University found that microorganisms residing in the gut of autistic children are different from other children but they are yet to determine whether these gut differences are a cause or an effect of autism, reports the American Society For Microbiology (ASMUSA).

The results, published in the mBio journal, found that a bacteria belonging to the Sutterella group in the gut was found in 12 of 23 tissue samples from autistic children. The same bacteria were not present in the samples of non-autistic children.

According to Jorge Benach, Chairman of the Department of Microbiology at Stony Brook University: “The Sutterella bacteria has been associated with gastrointestinal diseases below the diaphragm, and whether it’s a pathogen or not is still not clear. It is not a very well-known bacterium.”

Scientists are now hoping to find out why this organism is only present in autistic children.

“The relationship between different microorganisms and the host and the outcomes for disease and development is an exciting issue,” says Christine A. Biron, Professor of Medical Science at Brown University.

“This paper is important because it starts to advance the question of how the resident microbes interact with a disorder that is poorly understood,” adds professor Biron.

Read the entire article here or read the original manuscript here.

Categories: Interesting link