A smorgasbord….

Being quite busy lately, I accumulated a lot of links to stuff I wanted to comment on but never found time. Well, it does not appear I will find time any time soon, so here are the links for you to comment on anyway (just because I link to them does not mean I agree with them – in some cases quite the opposite):
In Defense of Secrecy :

Given the pervasive secrecy of the Bush-Cheney administration, and the sorry consequences of that disposition, President Barack Obama’s early emphasis on openness in government seems almost inevitable. One of the first official communications issued by the new administration, on Jan. 21, ordered government agencies to adopt a presumption in favor of disclosure when responding to Freedom of Information Act (FOIA) requests and called for new FOIA guidelines to replace those promulgated under Bush. A later directive instructed the heads of all government agencies to strive for “transparency and open government.” Ornamenting the first order was a quotation from the great progressive reformer Justice Louis Brandeis: “Sunlight is said to be the best of disinfectants.”

The Future of the News:

After years in trouble, American newspapers are finally up against the wall.
Advertising, vanished. Profits, gone. Losses, mounting very rapidly. Around the country, newsrooms are being hollowed out, papers are shrinking, some are letting go of daily publication. Some are going away.
So, what if? What if your local newspaper just disappeared? In a world of red ink, bankruptcies, layoffs and cutbacks, it’s possible. So, what then?

Farewell to All That: An Oral History of the Bush White House :

The threat of 9/11 ignored. The threat of Iraq hyped and manipulated. Guantanamo and Abu Ghraib. Hurricane Katrina. The shredding of civil liberties. The rise of Iran. Global warming. Economic disaster. How did one two-term presidency go so wrong? A sweeping draft of history–distilled from scores of interviews–offers fresh insight into the roles of George W. Bush, Dick Cheney, and other key players.

At Voice of San Diego, a newsroom flourishes:

With several big-city dailies facing closure and the cover of Time last week pondering the fate of the American newspaper, I listened to young Voice of San Diego journalists talk about their work with words like “exhilarating,” “fulfilling” and “fun.” My tiny, ink-sotted heart soared.
The lessons out of the sunny offices on Point Loma appear to be these: A local news site can flourish on charitable donations. It helps to have one big benefactor to get things started. It makes more sense to cover a few topics well, rather than a lot poorly.

Political Science:

Behind him hangs a copy of Jacques-Louis David’s celebrated portrait of Antoine-Laurent Lavoisier, the French chemist. Varmus is one of our leading scientific figures, a Nobel Prize-winning cancer researcher who advises President Obama, but I’m not sure this is an auspicious image. Lavoi­sier’s own entanglement in politics led to his beheading during the French Revolution. Thankfully, Varmus seems quite adroit in public matters. He has also written a perceptive book about science and its civic value, arriving as the White House renews its acquaintance with empiricism.

Do we need Science Journalists? :

For one, as far as I am concerned most scientists are not particularly good writers (I include myself in that) and since I appreciate a piece of good writing I sincerely hope professional journalism will prevail. Having acquired the necessary skills and appropriate education certainly helps to this matters. I don’t know what Bora’s standards are, but I find the vast majority of science blogs not particularly well written (YOU obviously belong to the minority of brilliant writers).

More discussion here and here.
Survival of the Viral:

Studying genetic “mistakes,” like endogenous retroviruses, would have led us to a theory of evolution, even if Charles Darwin had not.

Why Facebook Is for Old Fogies:

Facebook is five. Maybe you didn’t get it in your news feed, but it was in February 2004 that Harvard student Mark Zuckerberg, along with some classmates, launched the social network that ate the world. Did he realize back then in his dorm that he was witnessing merely the larval stage of his creation? For what began with college students has found its fullest, richest expression with us, the middle-aged. Here are 10 reasons Facebook is for old fogies:

What’s the Matter With Teen Sexting?:

It’s unclear from this exchange what Gladstone believes kids need to be protected from or what issue Balkam is solving. But neither of them came to the logical conclusion of the Harvard study: that we should back off, moderate our fears, and stop thinking of youthful sexual expression as a criminal matter. Still, Balkam wants to call in the cops.
Maybe all that bullying is a mirror of the way adults treat young people minding their own sexual business. Maybe the “issue” is not sex but adults’ response to it: the harm we do trying to protect teenagers from themselves.

Republican Taliban declare jihad on Obama:

The Democrats and the liberal base have responded to all this with a mixture of cynicism and their own partisanship. They rolled their eyes at Obama’s outreach to Republicans; they hated the inclusion of the other party in the cabinet and had to swallow hard not to complain about the postpartisan rhetoric. Their cynicism is well earned. But my bet is that Obama also understands that this is, in the end, the sweet spot for him. He has successfully branded himself by a series of conciliatory gestures as the man eager to reach out. If this is spurned, he can repeat the gesture until the public finds his opponents seriously off-key.

A Balancing Act on the Web :

LAST week, I wrote that a hastily published article on The Times’s Web site highlighted a fear in newsrooms that the Internet, with its emphasis on minute-to-minute competition, is undermining the values of print journalism, which put a premium on accuracy, tone and context.

The ethics of science journalism:

This unique theme section brings together the views of all parties involved in science journalism and bringing science to the public today: writers (freelance and staff), editors, publishers, and scientists themselves. The theme section will be built online.

An Eternal Optimist — But Not A Sap:

Obama is a long way from matching the achievements of Lincoln and Roosevelt, of course. (If Obama, and the country, is lucky, he won’t have to.) But his common inclination to “steer from point to point” may serve him and the country well, especially since Obama has inherited problems of a magnitude faced by few of his predecessors other than those two titans. Obama recognizes the obvious challenge those problems present, but also sees in them opportunity. “I think that there are certain moments in history when big change is possible… certain inflection points,” he said. “And I think that those changes can be for the good or they can be for the ill. And leadership at those moments can help determine which direction that wave of change goes.”

The Oligarchs:

Everyone is always saying: how can we fix the problem as long as the people we have in charge are the people who created the problem in the first place? Very true in many ways. I’ve said it a lot myself. But this point has brought it home to me in a much more concrete way. The assumptions, the vested interests, the wealth, the political power are just too much to overcome.

The No-Stats All-Star :

The virus that infected professional baseball in the 1990s, the use of statistics to find new and better ways to value players and strategies, has found its way into every major sport. Not just basketball and football, but also soccer and cricket and rugby and, for all I know, snooker and darts — each one now supports a subculture of smart people who view it not just as a game to be played but as a problem to be solved. Outcomes that seem, after the fact, all but inevitable — of course LeBron James hit that buzzer beater, of course the Pittsburgh Steelers won the Super Bowl — are instead treated as a set of probabilities, even after the fact. The games are games of odds. Like professional card counters, the modern thinkers want to play the odds as efficiently as they can; but of course to play the odds efficiently they must first know the odds. Hence the new statistics, and the quest to acquire new data, and the intense interest in measuring the impact of every little thing a player does on his team’s chances of winning. In its spirit of inquiry, this subculture inside professional basketball is no different from the subculture inside baseball or football or darts. The difference in basketball is that it happens to be the sport that is most like life.

Legal Guide for Bloggers:

Whether you’re a newly minted blogger or a relative old-timer, you’ve been seeing more and more stories pop up every day about bloggers getting in trouble for what they post.
Like all journalists and publishers, bloggers sometimes publish information that other people don’t want published. You might, for example, publish something that someone considers defamatory, republish an AP news story that’s under copyright, or write a lengthy piece detailing the alleged crimes of a candidate for public office.
The difference between you and the reporter at your local newspaper is that in many cases, you may not have the benefit of training or resources to help you determine whether what you’re doing is legal. And on top of that, sometimes knowing the law doesn’t help – in many cases it was written for traditional journalists, and the courts haven’t yet decided how it applies to bloggers.

Nouriel Roubini: Only Way To Save US Banking System Is To Nationalize It:

The U.S. banking system is close to being insolvent, and unless we want to become like Japan in the 1990s — or the United States in the 1930s — the only way to save it is to nationalize it.
As free-market economists teaching at a business school in the heart of the world’s financial capital, we feel downright blasphemous proposing an all-out government takeover of the banking system. But the U.S. financial system has reached such a dangerous tipping point that little choice remains. And while Treasury Secretary Timothy Geithner’s recent plan to save it has many of the right elements, it’s basically too late.

The Internet, New Media, Old Media and Fame:

What is fame? When you use the word the majority of people would start rhyming of names like Angeline Jolie, Rock Hudson, JFK and even now with Barak Obama. Fame is often thought of as being the thing that actors, musicians, politicians and in very rare cases regular people can achieve through their actions. Old Media thrives on famous people because of their ability to get people to fork over their money time and time again. This type of fame though is what I would refer to as global fame. It is a fame that can cross generations and oceans but it isn’t the only kind of fame there is.

WooHoo! Blogging is dead:

Of course this is all because Dan Lyons pontificated in Newsweek – which he also pointed to from his blog – that that there is no money to be made with blogging. Of course his idea of making money is something that probably has to surpass his salary from Newsweek who I am sure gave him the big high five over the post.
I won’t bother re-hashing all the different ways that Lyons probably profited quite well from his short stint as a blogger. After all how many times can you say book deal, better paying job with more name recognition or even all the speaking dates before you get the idea that Mr. Lyons is pretty well full of shit. Sure he used the lousiest ad network out there and really only clued into the fact that there were better ones months before he supposedly shut down the Fake Steve Jobs blogs out of respect of the Real Steve Jobs health.

5 Things We Learned About Teens at TOC:

They hung out with real teenagers in their homes to get a look at their creative processes. When choosing which teens to follow, they looked for those who were creative, but not necessarily planning to go into art or design after high school. They picked those who were involved in interesting self-expression activities and who were creating digital media to share with others outside their immediate circles of friends. Here are five not-so-obvious takeaways (beyond the fairly apparent “Teens want to create identities for themselves online” and “In general, teens are pretty tech-savvy”). (The panel didn’t focus much on book publishing, but it provides useful background to YA publishers who want a better look at what their target audiences are doing online.)

Andrew Wakefield, autism, vaccines and science journals:

A word about peer review. This is the process whereby journal editors send manuscripts to experts in the field for their evaluation of scientific soundness. Based on the comments, editors then make a decision as to whether to publish or not. That decision may or may not be the same as the reviewers’. There are many considerations whether to publish something or not (is it of sufficient interest to the readership or does it make enough of a contribution to the field, for example). In general, however, depend on reviewers for the science. Most journals do closed, anonymous reviews. This means that the authors don’t know who the reviewers are and the reviews are not provided to the readers. Often the names of the authors are also kept from the reviewers so as not to prejudice their judgment. Some journals (like the one I edit) practice open review, meaning that reviewers’ names are known to the authors (and vice versa) and that the reviews themselves are available to readers when the paper is published. In the case of the Wakefield paper we don’t know the names of the reviewers or what they said.

A guide to the 100 best blogs – part I:

The online world of the bloggers and how you can connect, communicate, publish your thoughts or diaries and ‘spy’ on the famous

Who-o-o are you? Who who? Who who?:

There’s been quite a lot of discussions going on lately about author identification: Raf Aerts’ correspondence piece in Nature (doi:10.1038/453979b), discussions on FriendFeed, … The issue is that it can be hard to identify who the actual author of a paper is if their name is very common. If your name is Gudmundur Thorisson (“hi, mummi”) you’re in luck. But if you are a Li Y, Zhang L or even an Aerts J it’s a bit harder. Searching PubMed for “Aerts J” returns 299 papers. I surely don’t remember writing that many. I wish… So if a future employer would search pubmed for my name they will not get a list of my papers, but a list of papers by authors that have my name. Also, some of my papers mention jan.aerts@bbsrc.ac.uk as the contact email. Well: you’re out of luck, I’m afraid. That email address doesn’t exist anymore because I changed jobs.

How I made over $2 million with this blog:

If I had any advice to offer it’s this — get in the habit of communicating directly with the people you want to influence. Don’t charge them to read it and don’t let others interfere with your communication. Talk through your blog as you would talk face to face. You’d never stop mid-sentence and say “But first a word from my sponsor!” — so don’t do that on your blog either. I can’t promise you’ll make any money from your blog, and I think the more you try the less chance you have. Make a good product and listen to your customers to make it better, and use the tools to communicate, and you may well make money from the whole thing. To expect the blog alone to pay your bills is to misunderstand what a blog can do. You’ll only be disappointed like Dan Lyons was.

Separating science and state:

Government should have no role in funding scientific research. I say this as a person who not only greatly admires scientific research and its accomplishments, but as a person who believes strongly in the scientific enterprise in general–by which I mean, someone who believes that reason is the only proper means of knowledge and who has no truck with religion and tradition and authoritarianism. Just to get my bona fides out of the way, I am seriously devoted to and interested in all forms of science, particularly biology, and have written at great length in defense of science and the material and intellectual–indeed, spiritual–progress it has brought us. Of all the kinds of corporate welfare, I am least opposed to science welfare.

Why it’s good for us to fund scientific research.:

Tim Sandefur and I don’t agree about the proper role of government when it comes to funding scientific research. He fairly strongly believes that there are many reasons why it’s wrong for the government to fund scientific research. Tim’s provided a number of reasons to support his belief, and I agreed to use my blog as a platform to make my own case for the involvement of government in science.
In the abstract, many of the reasons that the government should not be involved in funding research sound fairly compelling. Unfortunately, those arguments were made on the internet. At the end of the day, the medium undercut the message.

A rebuttal to Mike Dunford:

Mike Dunford starts out his rebuttal cleverly pointing to the Internet as an example of the way government-subsidized research can help promote the American standard of living. Of course, it’s true that some of the research projects government has funded have ended up producing some pretty cool things. But it doesn’t undercut the message: in fact, this example makes two important points that support my position.

The Tangled Bank: An Introduction to Evolution:

This week of all things Darwin seemed like a good time to share some news about a project I’ve been working on for the past few months. It’s a book called The Tangled Bank: An Introduction to Evolution.
The inspiration for the book came from a conversation I had last year with the folks at Roberts & Company, a publishing company. They had noticed a growing number of classes about evolution for non-biology-majors, and asked if I’d be interested in writing a textbook for them. I was excited by the prospect of being able to bring together the things I’ve learned and written about over the past few years, as evolutionary biologists have made a string of surprising new advances in understanding the history of life (many of which I’ve written about here at the Loom).

ISI Draws Fire from Citation Researchers, Librarians:

A new document classification is creating confusion and drawing fire from the bibliometrics community. Confusion over the new “proceedings paper” designation in ISI’s Web of Science has many questioning whether the new classification will alter journal impact factors.

The Ideology of the Media:

It’s also that establishment journalists get disoriented by any story that doesn’t fit into their pre-formed cookie cutter narratives. They spend all their adult lives inside the bubble and just can’t relate in a real way to the rest of the country – as you’ve written about… Maybe a few of them can perceive the realness of public anger that is the fuel for social movement politics, and maybe those few can perceive the actual threat to the Establishment.

198 Scientific Twitter Friends:

Follow me on twitterI’ve been on Twitter since June 2007 and have met a lot of interesting, helpful, and generally nice people on there. Many of my almost 1400 friends and followers on twitter are connected with science in some way, they’re scientific tweeps in other words, or to coin a phrase, scientwists.
Originally, I listed 100 science types, but then more friends and followers asked if they could be on this list, so now we have almost 200. If you’re a scientwist and want to join them then tweet me, comment here, follow me, or retweet
this link bit.ly scientwists be sure to let me know and I’ll add your link and bio.

Paper Chase: A Q&A with Randy Siegel (search blogs, twitter and friendfeed for this article, to see why it is very wrong):

Absolutely. It’s the infrastructure, it’s the professional training, it’s the ability to condense massive amounts of information into accessible prose for the reader and the online visitor. It’s the editing. I mean, this notion that you don’t need editors anymore is laughable. Editors make things accessible for readers and online users, and they help educate all of us about stories and issues that we otherwise might not see. I highly doubt that your favorite blogger, for example, is in a position to fly to Iraq and cover what’s going on there, or to fly to the far East and decipher our relationship with China as an economic superpower, or to go into City Hall and expose instances of municipal graft and corruption, or to get behind the scenes of a major sporting event and help people understand why a game turned out the way it did. I believe that, in journalism, you get what you pay for. And quality journalists will always have a role in our society. And as newspaper companies evolve, great journalism will now be more important than ever. Across multiple platforms.

Battle Plans for Newspapers:

Virtually every newspaper in America has gone through waves of staff layoffs and budget cuts as advertisers and subscribers have marched out the door, driven by the move to the Web and, more recently, the economic crisis.
In some cities, midsized metropolitan papers may not survive to year’s end. The owners of the Rocky Mountain News and The Seattle Post-Intelligencer have warned that those papers could shut down if they can’t find buyers soon. The Star Tribune of Minneapolis recently filed for bankruptcy. The Detroit Free Press and The Detroit News will soon stop home delivery four days of the week to cut operating costs. Gannett, which owns 85 daily newspapers in this country, recently said it would require most of its 31,000 employees to take a week of unpaid leave.
What survival strategies should these dailies adopt? If some papers don’t survive, how will readers get news about the local school board or county executive?

non-anonymous peer review:

I spent this afternoon acting as a voluntarily non-anonymous peer reviewer – its scary. I ended up advocating rejection of the article I was reading and I have to say that Vince Smith(see end of linked post) was absolutely right that the act of signing your review “keeps you in check”. Knowing from the outset that your words are going to be linked to your name can really change what you have to say – it certainly makes you think about it for a while longer. It is scary though – I hope that I managed to convey enough of my reasoning and suggestions for ways to improve the article that the authors don’t despise me and attempt to ruin my life… I also hope that the editors of the journal manage to acquire at least one additional reviewer for this manuscript – safety in numbers! Or perhaps the editors will strip my name from my comments? Time will tell I guess.

SnailMailTweet:

mail us a tweet, we’ll post it on Twitter

Why the New York Times and Harvard Should Merge (someone wrote a good rebuttal of this, but now I can’t find who and where? – Oh, found it: PhysioProf):

But both of these are really points on a continuum. Journalists have found that in addition to breaking stories, they need to do analysis. Academicians have discovered that in addition to reviewing the past, they need to pay attention to the the future.

11 Ways Print Journalism Can Reinvent Itself:

Print journalism is in a tailspin. Embracing the Web is the obvious solution, but how is that best done? Lex Alexander, who spearheaded a well-regarded new media effort at the Greensboro, NC, News & Record, offers these tips. Notice that a few start with the word “invest,” which is counter to much recent industry wisdom.

Obama Aides Rip Cable News, D.C. Media And Political Elite:

Here’s an interesting dynamic: The yawning gap between what the pundits say about who’s winning the stimulus war and what the polls say the public thinks has created an opening for the Obama team to reclaim Obama’s campaign outsider mantle, which had slipped away during the transition to governing.

If you don’t have a blog you don’t have a resume (Part 1):

The point here is to make the case that blogging is good for your career. It’s been good for me and it’s been good for a lot of other people and I think it has potential for everyone.
Now, is everyone a blogger-in-waiting? Of course not. Would absolutely everyone actually benefit from blogging? Probably not. And if absolutely everyone did take up blogging, would the massive amount of noise generated actually cancel itself out and end up hardly benefiting anyone at all? Probably.
That being said, let’s take a look at what’s been making me think about blogging lately.

If you don’t have a blog you don’t have a resume (Part 2):

I’d also like to be more explicit about chicken/egg of interplay between our passion and commitment to the profession that blogging brings out and how that directly feeds into concrete reputation-building and the benefits that may result. In general, I believe that if you blog to become famous (in other words, to explicitly build your reputation, with cynicism not passion), that will be your reputation. If you blog to share and grow and explore, it’s that passion that will hopefully influence your reputation-building efforts and that any concrete benefits that you accrue will reflect that.
Blogging isn’t for everyone. Blog because it’s what you want to do, not because you feel you have to.
That being said, I really I really like how bluntly Neville Hobson puts it: Your Blog is Your CV.

Yet more on uneasy symbiosis of mainstream and citizen journalism:

Rosen’s much stronger and emphatic point, meanwhile, is that the blogosphere v MSM argument isn’t getting us anywhere, so, follks, quit beating this question by attacking “the other.” I could not agree more. The point is not which is better or deserves to die or has great or lousy ethics or good or awful writers. It’s that they bring different strengths and weaknesses and possibilites and constraints, we’ll make the best of both realms if we try to cross-fertilize strengths while avoiding or improving upon weaknesses.

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