Norms are changing

by TankGirlJones

[Crossposted at SpreadingScience]

Column on NIH and Harvard policies:
[Via Open Access News]
Karla Hahn, Two new policies widen the path to balanced copyright management: Developments on author rights, C&RL News, July/August 2008.

A light bulb is going off that is casting the issue of author rights management into new relief. On January 11, 2008, the National Institutes of Health (NIH) announced a revision of its Public Access Policy. Effective April 7, 2008, the agency requires investigators to deposit their articles stemming from NIH funding in the NIH online archive, PubMed Central. Librarians have been looking forward to such an announcement, especially since studies found that the voluntary version of the policy was achieving deposit rates of affected articles on the order of a few percentage points.

Since we as taxpayers pay for this research, it should not be bound up behind access control. Now, because of the NIH’s revision, it won’t.

With the article deposit requirement, researchers can no longer simply sign publication agreements without careful review and, in some cases, modification of the publisher’s proposed terms. While this may be perceived as a minor annoyance, it calls attention to the value of scholarly publications and the necessity to consider carefully whether an appropriate balance between author and publisher rights and needs is on offer.

The norm in science has been to always quickly sign over copyright so that the paper could be published. This sometimes resulted in the absurd prospect that the author of a paper could not use his own data in slides, since he no more owned the copyright of it than any other random scientist. Now there is a little leverage for the author to retain some aspects of copyright.

As institutions, as grantees, become responsible for ensuring that funded authors retain the rights they need to meet the NIH public Access Policy requirements, there is a new incentive for campus leaders to reconsider institutional policies and local practices relating to faculty copyrights as assets. …
The February 2008 vote by the Harvard Faculty of Arts and Sciences to grant Harvard a limited license to make certain uses of their journal articles is another important indicator of an accelerating shift in attitudes about author rights management, and also reveals the value of taking an institutional approach to the issue. …

Academic pressure is coming to bear on these policies and it will be interesting to see how it all plays out. In most instances, providing open access will be the better route but now the individual institutions will be responsible for providing the necessary infrastructure.

Perhaps something like Highwire Press will appear. Here , instead of each scientific association having to develop their own infrastructure, Highwire does it for many of them, greatly simplifying publishing for all. Highwire now has almost 2 million article published with free access. Perhaps something similar for institutional storage would be helpful.

Norms are always more difficult to change than technologies. We are now witnessing a key shift in norms for sharing scholarly work that promises a giant step forward in leveraging the potential of network technologies and digital scholarship to advance research, teaching, policy development, professional practice, and technology transfer. …

What scientists expect when they publish a paper is changing rapidly. What once took 6-9 months from submission to publication can now happen in weeks. Where once all rights had to be assigned to the publisher, now the authors can retain some for their own use.

What will the norms be like in five years?

Technorati Tags: Government, Science, Web 2.0

I’ve been saving my money

by aussiegall
Apple introduces the new iPhone 3G:
[Via Apple Hot News]

The new iPhone 3G combines all the revolutionary features of iPhone with 3G networking, built-in GPS, and iPhone 2.0 software that supports Microsoft Exchange ActiveSync and runs hundreds of third party applications built with the iPhone SDK. Available in 22 countries on July 11, iPhone 3G comes in two models: an 8GB model priced at $199 (US) and a 16GB model priced at $299 (US).

Now I just have to see what ATT will charge. Wish they had it as a pay as you go phone.

Technorati Tags: Entertainment, General

No wonder

by blakespot
Why is the FEC Using TRS-80’s?:
[Via Balloon Juice]

Am I not understanding this:

The record-shattering fundraising by Democratic presidential candidates Barack Obama and Hillary Clinton has reshaped the financing of presidential elections and generated breathless coverage and analysis of the otherwise arcane area of campaign finance.

Yet it’s had another consequence that has gone all but unnoticed. The campaign finance reports filed by Obama and Clinton have grown so massive that they’ve strained the capacity of the Federal Election Commission, good government groups, the media and even software applications to process and make sense of the data.

A milestone of sorts was reached earlier this year, when Obama, the Illinois senator whose revolutionary online fundraising has overwhelmed Clinton, filed an electronic fundraising report so large it could not be processed by popular basic spreadsheet applications like Microsoft Excel 2003 and Lotus 1-2-3.

Those programs can’t download data files with more than 65,536 rows or 256 columns.

***

If you want to comb through Obama or Clinton’s cash, you either need to divide and import their reports section-by-section (a time-consuming and mind-numbing process) or purchase a more powerful database application, such as Microsoft Access or Microsoft Excel 2007, both of which retail for $229.

The FEC can’t afford a copy of Excel 2007? I can lend them my laptop if they need, but they better not talk while I am watching BSG, and they should be warned that Tunch loves company and will probably pester them when they come over.

It is not clear that from the article that the SEC has any problem with the data. It is simple stating that the files from Clinton and Obama are so big that you could not use Excel 2003 for them. It does not state that the SEC does not have Excel 2007.

So it is pretty much a filler article trying to look more important than it is. The main bit of real information - the campaigns now have so many donors that they overwhelm old software. Whoopi.

Technorati Tags: Education, Government, Politics

Openness helps everyone

[crossposted at SpreadingScience]
Bursty science depends on openness:
[Via Science in the open]
Image via Wikipedia

There have been a number of interesting discussions going on in the blogosphere recently about radically different ways of practising science. Pawel Szczesny has blogged about his plans for freelancing science as a way of moving out of the rigid career structure that drives conventional academic science. Deepak Singh has blogged a number of times about ‘bursty science‘, the idea that projects can be rapidly executed by distributing them amongst a number of people, each with the capacity to undertake a small part of the project.
[More]

There will be many of these little experiments - using online conversations for scientific endeavors. Even inside an organization, having an online area to ask for help can be useful. Trying to use email for this purpose has little effect.

There are several ways to use Web 2.0 approaches to ask/answer questions. An online forum works well if it is substantially populated and active. A forum with a 3 month old unanswered question will not be very useful.

One approach that works is to have one person, or a small group, act as troubleshooters. They probably already exist in many organizations. They are the ones every one goes to when they have a problem in the lab.

They usually have a wide range of knowledge and often work to help people find a solutions to a research problem.

Have these people move online. A troubleshooting page on a wiki would allow questions to be asked. The troubleshooters have the opportunity to find answers. FAQs could be written to respond to the endless questions many troubleshooters receive.

Then when someone asks for some help, there is already a team with responsibility to find answers. And, because all this is open and transparent, the troubleshooters can finally get the well deserved credit they should.

Helping in the lab is generally invisible to others, particularly when evaluation time comes around. It is hard to document just what the help accomplished.

A troubleshooting wiki, on the other hand, would provide ample documentation on just what help was provided and the effect that help had on the organization. The ability to actually document who helps the organization move forward will be very valuable.

Technorati Tags: Education, Science, Web 2.0

Higher Tides

Warning on rising Med Sea levels. Levels in the Mediterranean Sea are rising rapidly, with potentially serious effects in coastal areas, a study finds. [BBC News | News Front Page | World Edition] 

That is 10 cm a decade or half a meter in 50 years. That is a huge amount if you are close to the water.

Immunology stuff

Cognate CD4+ T cell-dendritic cell interactions induce migration of immature dendritic cell through dissolution of their podosomes.Dendritic cells (DC) control T cell-based immunity. To do so they need to mature and migrate to sites of T cell priming. We have previously shown that cognate interactions of human CD4⁺ T cells with DC induce DC maturation. We show here that CC chemokines produced during antigen-specific T-DC interactions also induce strong morphological modifications and migration of immature DC. These modifications are required for efficient T cell activation. Moreover, we show that CC chemokines produced during antigen-specific DC-T cell interactions induce the dissolution of structures involved in cell motility and present on immature DC, i.e. podosomes. We thus propose a model in which chemokines secreted during Ag-specific contact between T cells and DC induce disassembly of interacting and neighboring immature DC podosomes, leading to recruitment of more immature DC towards sites of antigenic stimulation and to amplification of T cell responses.[BLOOD First Edition Papers] 

Have to check this out.

Evolution on Colbert

Guest post by Neil Shubin: preparing for TV [Pharyngula]. 

I thought it might be useful for the readers of Pharyngula to get my sense of the Colbert show experience.

Being a scientist on the show carries with it some challenges. We need to convey facts of science correctly and do so in a way reveals how fun our science is to do and to think about. We need to educate, enlighten, and excite. The challenge is we need to do this in 5 minutes with Stephen Colbert sitting across the table. To make matters worse, the show does not tell you the tack Colbert is going to take in advance, largely because so much of what he does is ad lib.Because of this, I was terrified when I received the invitation last Fri. I took a few hours to accept, largely because I needed a family conference on the strike. Once I came to terms with my decision (the readers do a good in the commentary on the various issues that swirled for us), I began to prepare for the interview.How did I prepare for the Colbert interview? In watching successful science interviews (of which there are a number of real good examples to emulate) I saw some general patterns to a successful visit. It also definitely appears that Colbert likes scientists and he want them to be able to tell their story.The best answers I saw responded to Colbert’s questions with a sentence that captured the essence of the science in an entertaining way. So, the day of my interview I came up with a number such answers for the questions I thought I’d get. For the most part, I prepared with answers defending evolution vs. other non-scientific approaches.I was pretty nervous before the interview, so much so that I didn’t sleep much the night before. And, as it turned out, my predictions about Colbert’s questions were largely wrong– Colbert didn’t even touch creationism and did a number of riffs on things that weren’t even in the book (like the final questions). I was aided, though, by the experience of preparing my answers. It exercised my brain in a way that allowed me to respond to the questions he really asked.In thinking about the experience a few days later I have one thought on language. As scientists we are very used to using language with a great deal of precision (note the string in the commentary on common ancestry, group inclusion, etc.). The challenge is adapting our highly precise vocabulary to the demands of a five minute performance on a show which is fundamentally not about science. It is a tough tightrope to walk to balance between language that is both engaging and precise. I had mixed success, but that has to be our aspiration for these kinds of experiences.You can ask the question, a valid one, why bother with these kinds shows? If it is so difficult, and the conceptual and linguistic apparatus of science doesn’t easily conform to this venue, why do it? For me the answer is that we need to make science part of the public conversation. We live in a society where Britany Spears latest foible gets more ink than Mello and Fire’s 2006 Nobel discovery of RNAi– a breakthrough on a little worm that will likely lead to treatments of many diseases. Something is wrong here.Thanks for your comments and criticisms and I hope my personal experience gives some perspective.

Neil Shubin

Read the comments on this post… By PZ Myers none@example.com. [ScienceBlogs : Combined Feed]

He has some very useful insights into preparing for such a show. I watched it and he did a great job, even though there were a couple of times Colbert had to cut him short, knowing that a scientist will talk for hours about what interests him, even if he does an amusing job of talking.

Darwin and Faith

Darwin: Defender of the Persecuted [Afarensis]. Kristine - of the Amused Muse comes up with a gem over at Antievolution.org. You can find the entire story here. Suffice to say it concerns Darwin, Wallace, and a conflict over spiritualism and shows Darwin at his ethical best and is a must read!Speaking of Kristine, be sure and check out this post and note that afarensis gets a Shimmy!Read the comments on this post… By afarensis, FCD none@example.com. [ScienceBlogs : Combined Feed]

Darwin was a better man than almost all of us.

Bird flu vaccine

Bird flu vaccine production boost. Researchers discover how to stretch out bird vaccine stocks so more people can be immunised in a pandemic. [BBC News | Health | World Edition] 

A simple reformulation could increase the number of doses 4-fold. Not bad.

Bad Business

Banning Anyone Who Reviews Your Shop Online Isn’t Likely To Generate Much Business. We all know that sometimes customer reviews online can be a bit harsh, but it’s something that companies need to learn to deal with. Some take proactive approaches by responding to the complaints with their own side of the story or by apologizing and promising that changes will be made to avoid similar problems in the future. However, one cafe owner has taken things to a different level, apparently putting a sign in the window of the cafe, saying that users of popular online review site Yelp are not allowed as customers. This is effectively saying that the shop owner has no interest in what its customers think of it, has no interest in improving the quality of service and doesn’t seem to realize that this will only encourage anyone who has a bad experience to go to Yelp and post about it. In fact, putting this sign in the window seems likely to damage the reputation of the cafe a lot more than any bad review on Yelp. [Techdirt] 

Not a good business move, I think. How is this business planning on enforcing this?

Google Grief

SF Chronicle’s Stages Of Google Grief Lead To Suggestion For Google To Just Buy Newspapers. First off, before someone brings it up in the comments, I’ll point out that the following post refers to the views of various columnists at the SF Chronicle, rather than any sort of discussion among those who have any real impact on the SF Chronicle’s strategy. However, it is quite amusing to see the “stages of Google grief” showing up on the editorial pages of the struggling San Francisco newspaper who has had to rid itself of hundreds of reporters lately. Back in March, columnist David Lazarus (who apparently is no longer at the paper) vented his frustration about the internet by suggesting that newspapers get rid of free content entirely, with the goal of blocking off so-called moochers like Google News (despite the fact that, yes, Google News actually sends the Chronicle more readers). Then, in May came the bizarre suggestion on the SF Chron editorial pages that Google had a social or moral obligation to simply hand money over to newspapers. That got lots of people laughing, so now, yet another columnist at the Chron has adjusted the thinking to suggest that rather than just hand over money, Google should buy some newspapers, but then just leave them alone, noting that Google would probably make for a better newspaper boss than Rupert Murdoch. This seems to be sort of the full circle Google of thinking here. First, denial that Google is an opportunity to actually drive more business to newspapers. Then, anger at Google and a plan to block it off. Then there’s the bargaining/begging phase where they suggest Google simply owes them money. Next comes depression (represented by all the layoffs) and finally acceptance that Google as a buyer could be the savior for newspapers. [Techdirt] 

More papers will be going through the 7 stages of Google grief. I would imagine most would rather Google buy them than Murdoch.

Better Science

I guess it’s not just Andrew Wakefield who doesn’t do controls when running PCR. Remember a couple of months ago, when I discussed testimony at the Autism Omnibus trial that showed how Andrew Wakefield had failed to do the controls when running PCR that would have revealed that the results that he interpreted as the presence of the measles virus from a vaccine strain in the guts of autistic children was nothing more than a bunch of false positives due to widespread contamination of the laboratory with plasmid containing measles sequences?It turns out that it’s not just autism pseudoscientists who forget to do the right controls when running PCR. Mike the Mad Biologist describes an example of a very similar sloppiness of experimental technique in the microbiology world that also lead to what is almost certainly a false positive result.I just can’t understand how such obvious, first year graduate student mistakes manage to get published in the peer-reviewed literature. It doesn’t happen that often, but it does happen at a rate that is high enough to be distressing. In the case of Andrew Wakefield, the results of his sloppy science were catastrophic, namely an antivaccination scare about the MMR that nine years later still hasn’t fully run its course.Read the comments on this post… [Respectful Insolence]

Usually it is good to do the control BEFORE you submit the paper for publication. And usually the reviewers will notice such a mistake.

Memory Gone

Erasing memory in rats gives dementia patients hope. LONDON (Reuters) - Researchers have found a way to erase long-term memory in rats without damaging their brains in a study that could lead to targeted drugs for people suffering from dementia. [Reuters: Science] 

Sounds like the beginning of a Jim Carrey movie.

Mon, 13 Aug 2007 23:40:35 GMT

Common Plastic Ingredient May Be Cause for Concern. Federal panel says bisphenol A may be harmful to babies [ScienceNOW]

As they say, invoke the precautionary principle.

Mon, 13 Aug 2007 21:27:00 GMT

Konstantin Popadin, Leonard V. Polishchuk, Leila Mamirova, Dmitry Knorre, and Konstantin Gunbin Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals

PNAS
published
August 6, 2007,
10.1073/pnas.0701256104
(
Evolution
)[Abstract]

[PDF]
[Supporting Information] [PNAS Early Edition]

Very nice approach, using large body size as a measure of small populations vs. small body size and large populations. I’ll have oto check this out in more detail