Two recent OA articles

Two articles, with Open Access (OA) to the full text (PDF):

Putative cancer stem cells in malignant pleural mesothelioma show resistance to cisplatin and pemetrexed, Int J Oncol 2010(Aug); 37(2): 437-44. [PubMed citation].

Possible involvement of stem-like populations with elevated ALDH1 in sarcomas for chemotherapeutic drug resistance, Oncol Rep 2010(Aug); 24(2): 501-5. [PubMed citation].

Comment about these journals:

Spandidos Publications publishes six journals. Of these six, two are: International Journal of Oncology (2009 Impact Factor: 2.4) and Oncology Reports (2009 Impact Factor: 1.6). This publisher provides a hybrid open access option. The Information for Authors for all six journals includes, at the bottom of the page, this information: "Should authors prefer or require their article to be freely available as soon as it has been published, they may request open access immediately upon publication for a fee of EUR 450."

Secrecy in Astronomy and the Open Science Ratchet

Probably because of the visibility of the GalaxyZoo project, I think several of my colleagues and I have been under the impression that astronomy is a somewhat more open field than chemistry or molecular biology. It was easy to rationalize such a position because patents are not an issue, as they clearly are in fields which rely more on invention than discovery. However, after reading "The Case for Pluto" by Alan Boyle, I am left with a much different impression.

This book does an excellent job of covering the recent debate over Pluto's designation as a true planet. A key trigger for this debate has been the discovery of dwarf planets with sizes very close to that of Pluto. However, these discoveries did not occur without controversy.

The story of the controversy regarding the discovery of Haumea is a particularly good example (starts on p. 108 of the book - a good summary also on Wikipedia). Starting in December 2004 Michael Brown at Caltech discovered a series of new dwarf planets. Instead of immediately reporting his team's discoveries, he worked in secrecy until July 20, 2005 when he posted an online abstract indicating the discoveries would be announced at a conference that September. However, on July 27, 2005 a Spanish team led by José Luis Ortiz Moreno filed a claim with the Minor Planet Center for priority in discovering one of these dwarf planets. This forced Brown's hand in disclosing his team's other discoveries within days - much sooner than he had anticipated.

Apparently this stirred up a great controversy in the community and officially no name was associated with the discovery, although the Spanish team's telescope at Sierra Nevada Observatory was recognized as the location of the discovery. However, Brown was allowed to select the name Haumea for the dwarf planet.

Even though the Minor Planet Center accepted Moreno's submission, most reports seem to side with Brown. The main argument is no less than academic fraud on Moreno's part because he accessed public telescope logs and found some of Brown's data. It was as simple as Googling the identifier that Brown inserted in his public abstract.
If Moreno had hacked into a private computer from Brown's team I can understand fraud. But is it fraud to access public databases? We chemists do that all the time - reading abstracts from upcoming conferences to try to glean what our competitors are up to. That hasn't stopped anyone from submitting a paper or patent.
Secrecy only works if everyone competing follows the same rules. If there is a rule that planet discoveries must be made at conferences or by formal publication then this could not have happened. Moreno's submission to the Minor Planet Center should have been rejected if such a rule existed. If there is a rule that telescope logs should not be accessed then why make them public and indexed on Google?
Now there may exist field specific conventions. I don't know what they are in the case of discoveries such as these but here is an interesting quote from Michael Brown's Wikipedia page:

When asked about this online activity, Ortiz responded with an email to Brown that suggested Brown was at fault for "hiding objects," and said that "the only reason why we are now exchanging e-mail is because you did not report your object."[3] Brown says that this statement by Ortiz contradicts the accepted scientific practice of analyzing one's research until one is satisfied that it is accurate, then submitting it to peer review prior to any public announcement. However, the MPC only needs precise enough orbit determination on the object in order to provide discovery credit, and Ortiz et al. not only provided the orbit, but "precovery" images of the body in 1957 plates.

It seems to me that there is a clash of what are the conventions in the field. Certainly the Minor Planet Center did not recognize the convention of peer review before public disclosure. They only required sufficient proof for the discovery.

One way to look at this story is that Moreno acted more openly than Brown by disclosing information before peer review. This action forced Brown to disclose scientific results much more quickly than he had anticipated.

In a sense this is a type of Open Science Ratchet. The actions of scientists that are most open set the pace for everyone else working on that particular project, regardless of their views on how secretive science should be.

Imagine how the scenario would have played out if one of the groups had used an Open Notebook. On December 28, 2004 everyone with a stake in the search for planets would have had the opportunity to know that a very significant find had been made. There were still details to work out - and the Brown group might not be the first to do all the calculations to completely characterize the discovery. Certainly it would affect what other researchers did - even if they were completely opposed to the concept of Open Science.

Essentially secrecy in this context is an all-or-nothing gamble. Everyone is free to not disclose their work until after peer reviewed publication. In some cases the discoverer will get full credit for the discovery and the complete analysis. But in other cases another group working in parallel will publish first and leave nothing to claim.
As scientists become more open, it is likely that their ability to claim sole priority for all aspects of a discovery will be reduced. However, they will retain priority for the observations and calculations that they made first.
The more open the science, the faster it happens. And because of the Open Science Ratchet, a few Open Scientists scattered across various fields could have a larger hand than expected in speeding up science.

Mediterranean Diet Helps Protect Aging Brain

(HealthDay News) -- Eating a Mediterranean diet may help keep your brain healthy as you age, findings from an ongoing study show.

"This diet emphasizes vegetables, fruits, fish, olive oil, lower meat consumption, and moderate wine and non-refined grain intake," study author Dr. Christy Tangney, of Rush University Medical Center in Chicago, said in a news release from the American Society for Nutrition.

Rather than asking people to avoid certain foods, the study found data that "adults over age 65 should look to include more olive oil, legumes, nuts, and seeds in their diet in order to improve their recall times and other cognitive skills, such as identifying symbols and numbers," Tangney said.

The study included 4,000 adults aged 65 and older who were given a series of tests to examine their cognitive (or thinking) skills every three years over a 15-year period. Those who scored highest in following a Mediterranean diet were least likely to suffer cognitive decline, the study authors found. Read more...

Mental health

Guess This!

UPDATE:  SOLVED at 12:11 CDT by Dwight

Cheers, all.  Hope you’ve had a good week since I last puzzled you.  I’ll try to do it again.  I know; I have an evil streak.

Today’s object (yes, you’ll be looking for an object) is so familiar to everyone, you can guess it even if you haven’t been a blog reader and this is your first riddle attempt.  That’s the trip-up for the people who are used to the riddles; so don’t over-look the obvious.  Ready?  Okay…

NASA/ESA Hubble image of IRAS 05437+2502... No, it's not the answer, it's a clue.

This object is thought of as one thing… and it is one thing… mostly.

It used to be much smaller than it is now.

It’s not finished.

There are two little surprises at the center of this wonder.

One of the surprises is responsible.

This absolutely horrified our ancestors…

… and then it was forgotten.

When it was rediscovered, it was something different.

Now it carries the designation of “number one”.

It makes an appearance in modern literature and games.

This used to be visible to the unaided eye, but no longer.

In the northern hemisphere, you must search the winter sky to find this.

That should do it.  I’ve given you a lot of clues today, but watch out.  Sometimes a lot of information isn’t quite as helpful as it looks.  Still, this is a fun little brain-buster, and should only be up a few minutes, so get your guess in!

(when two phobias collide)

Dispute over longevity research getting more coverage | Gene Expression

Earlier this week I pointed to the controversy which has erupted around the widely reported new paper, Genetic Signatures of Exceptional Longevity in Humans. Newsweek did the most thorough early reporting, but now The New York Times has published a follow up story covering the scientific criticisms to the original paper’s methodology. There’s nothing new in The Times‘ piece as such, but it shows that concerted scientific objection to the reception or interpretation of a particular finding which is widely disseminated in the media can yield results. Too often the mainstream media ends up serving as a glorified press release service, but in this case scientists are making their voices heard, and the media narrative is adjusting to the underlying discussion in the scientific community.

I’ve been told there may be more coming out which may shed light on this controversy next week. Stay tuned…

“Keep a Distance From the Media” | The Intersection

Andy Revkin has the scoop on a letter from the IPCC (very misguided, to my mind) advising its scientists against having media contacts. An IPCC scientist, Edward R. Carr, also thinks this is a very bad idea. More specifically, IPCC chair Rajendra Pachauri wrote this to researchers:
I would also like to emphasize that enhanced media interest in the work of the IPCC would probably subject you to queries about your work and the IPCC. My sincere advice would be that you keep a distance from the media and should any questions be asked about the Working Group with which you are associated, please direct such media questions to the Co-chairs of your Working Group and for any questions regarding the IPCC to the secretariat of the IPCC. What Pachauri's letter should have said is the following:
I would also like to emphasize that enhanced media interest in the work of the IPCC would probably subject you to queries about your work and the IPCC. For this reason, the IPCC has developed a number of tip sheets, trainings, and other content to help scientists who may receive queries from the media. We also have several trained media consultants available at any time to answer your questions about the ...


Video Illusions | Bad Astronomy

I love optical illusions, and I’m fascinated by the mechanics of vision, so I have to share with you this video. This technique of animation has been known for a long time, but it’s still pretty cool.

Another video discusses how this is done. I had a card I carried in my wallet for years that did a similar type of illusion using a lenticular overlay which, when you moved the card back and forth, made it look like little colored spirals were rotating in different directions. I bought it when I was in college, but sadly I lost it last year (I’m pretty sure I dropped it at Comic Con). I have no idea how to replace it. If any of you has seen something like it, please let me know!

Tip o’ the Fresnel lens to BABLoggee Cristiana Senni.


When Does 3D Become Necessary?

This summer's blockbusters are available (for a premium ticket price) in 3D in select theaters. Hollywood has decided that 3D is a good bet, perhaps even a necessity for a big movie. Television makers are telling us that 3D will be the next big thing in our homes. But will it? Most of us are conserv

A Dose of Precaution

Should medical equipment designers respond to "public dose hysteria" and build safeguards against overexposure into their machines? Some government agencies contend that such actions are needed to restore public trust in medical imaging. There's evidence that patients are avoiding needed CT scans ou

World in Your Hand?

Proliferating technical applications for Web-enabled devices can be an office in your pocket. Has the advent of such technology enhanced your productivity, or does it add to the "clutter" in your professional and private life?

The preceding article is a "sneak peek" from Hydraulics, a newsletter fr

Intersexed athlete Caster Semenya given green light to compete

South African sprinter Caster Semenya has been given approval by the International Association of Athletics Federations (IAAF) to race as a female. The 19 year old runner is an intersexed individual with internal males testes that are producing testosterone at rates considerably above average for women. After a gender test in September 2009, the IAAF decided to ban her from racing, citing a biological advantage that was not of Semenya's doing. Now, after conducting an investigation, the Federation has passed a ruling allowing Semenya to race again.

This is a very interesting, if not perplexing, decision, and I wonder how it's going to play against the International Olympic Committee's (IOC) recent decision calling for intersexed athletes to have a medical procedure in order to qualify for the Olympics. By all accounts, Semenya has not had the procedure, or if she has, is not disclosing that information to the public. Moreover, the results of her most recent gender test are not being disclosed.

Very fishy.

So why did the IAAF suddenly change its mind, and why are they not giving any reasons? Did they feel pressured by the public? Is this a case of political correctness on the track? Or did Semenya have the medical procedure? And if so, why not disclose it? Or would that open a huge can of worms -- and a possible charge of a human rights violation?

Let's assume Semenya did not have the procedure. Has the IAAF therefore decided that intersexed persons are good to compete against unambiguously gendered individuals? And what about her competitors? I can't imagine that they're very happy right now. This would seem to be a dangerous and ill conceived precedent. Semenya is not the only intersexed athlete currently competing in Olympic sports. What about them?

I have a feeling this story is far from over.

Video games as art?

The interwebs are angry because Roger Ebert, a film critic who knows virtually nothing about video games, is arguing that video games will never be considered an artform. Grant Tavinor of Kotaku takes a more nuanced approach to the question and uses the popular BioShock video game to make his case:

Finally, and this is my judgment, BioShock is the result of the intention to make an artwork. Intentions can be slippery things, but it seems evident enough in the game that it is intended to be something more than just a game: BioShock is intended to have the features listed above (they are not accidental) and it is intended to have these features as a matter of its being art.

Hence, BioShock seems an entirely natural candidate for art status. It has, in some form, all but one of the criteria. The one it lacks-belonging to an established artistic form-it lacks because of the very newness of video games. BioShock is not necessarily a masterpiece (the last act is problematic) but this is beside the point; the vast majority of art works are not masterpieces. Surely it would be unfair to deny BioShock art status when it has so many of the qualities that in other uncontested art works accounts for their art status?

I agree that part of the problem is the nascent status of video-games-as-art. Pacman never attempted to be artist; Bioshock clearly does. It's still early days.

Moreover, even if you dismiss current games as having any artistic merit, Ebert's claim that they will never be legitimate artforms is suspicious. Never? Really? Not even when augmented reality enters the picture? Or completely immersive virtual reality?

Even more profoundly, a number of years ago I speculated about the potential for directly altering subjective and emotional experience and how mental manipulation could become an art form. In the article, Working the Conscious Canvas, I wrote:

It's conceivable that predetermined sets of emotional experiences could be a future art form. Artists might, for example, manipulate emotions alongside established art forms, a la A Clockwork Orange-but certainly not for the same questionable ends.

For example, imagine listening to Beethoven's "Ode to Joy" or "Moonlight Sonata" while having your emotional centers manipulated in synch with the music's mood and tone. You'd be compelled to feel joy when the music is joyful, sadness when the music is sad.

The same could be done with film. In fact, last century, director Orson Welles, who was greatly influenced by German expressionistic filmmaking, directed movies in which the subjective expression of inner experiences was emphasized (Touch of Evil, for example). In the 1960s, Alfred Hitchcock, also a student of expressionism, went a step further by creating and editing sequences in a way that was synchronized with subjective perception, such as the quick-cut shower sequence in Psycho.

In the future, audiences could share emotional experiences with a film's protagonist. Imagine watching Saving Private Ryan, Titanic or Gone with the Wind in such a manner. The experience would be unbelievably visceral, nothing like today's experience of sitting back and watching.

The beauty of such experiences is that sophisticated virtual reality technology isn't required, just the control mechanisms to alter emotional experience in real-time.

Of course, some will argue that when artists can directly manipulate emotions, they will have lost a dialogue with their audience, as audience members will simply be feeling exactly what's intended. But this won't necessarily be the case. Rather, audience members will respond to emotional tapestries in unique ways based on their personal experiences, the same way they do now to other art forms.

Imagine this same technology, but in the context of video games. Now there's some scary potential.

Art, whether it be traditional or novel, has always been about transcending the individual and sharing the subjective experience of others. As I've written before, "The greatest artists thrill us with their stories, endow us with emotional and interpersonal insight, and fill us with joy through beautiful melodies, paintings and dance. By doing so they give us a piece of their selves and allow us to venture inside their very minds—even if just for a little bit."

And yes, this includes video games.

Economist: War in the Fifth Domain

The latest cover article of The Economist poses the question: are the mouse and keyboard the new weapons of conflict?

Important thinking about the tactical and legal concepts of cyber-warfare is taking place in a former Soviet barracks in Estonia, now home to NATO’s “centre of excellence” for cyber-defence. It was established in response to what has become known as “Web War 1”, a concerted denial-of-service attack on Estonian government, media and bank web servers that was precipitated by the decision to move a Soviet-era war memorial in central Tallinn in 2007. This was more a cyber-riot than a war, but it forced Estonia more or less to cut itself off from the internet.

Similar attacks during Russia’s war with Georgia the next year looked more ominous, because they seemed to be co-ordinated with the advance of Russian military columns. Government and media websites went down and telephone lines were jammed, crippling Georgia’s ability to present its case abroad. President Mikheil Saakashvili’s website had to be moved to an American server better able to fight off the attack. Estonian experts were dispatched to Georgia to help out.

Many assume that both these attacks were instigated by the Kremlin. But investigations traced them only to Russian “hacktivists” and criminal botnets; many of the attacking computers were in Western countries. There are wider issues: did the cyber-attack on Estonia, a member of NATO, count as an armed attack, and should the alliance have defended it? And did Estonia’s assistance to Georgia, which is not in NATO, risk drawing Estonia into the war, and NATO along with it?

Such questions permeate discussions of NATO’s new “strategic concept”, to be adopted later this year. A panel of experts headed by Madeleine Albright, a former American secretary of state, reported in May that cyber-attacks are among the three most likely threats to the alliance. The next significant attack, it said, “may well come down a fibre-optic cable” and may be serious enough to merit a response under the mutual-defence provisions of Article 5.

Link.

NYT: Until Cryonics Do Us Part

The New York Times has published a piece about cryonicists and how not all family members buy into it. The article focuses on Robin Hanson, a name that should be familiar to most readers of this blog:

Among cryonicists, Peggy’s reaction might be referred to as an instance of the “hostile-wife phenomenon,” as discussed in a 2008 paper by Aschwin de Wolf, Chana de Wolf and Mike Federowicz.“From its inception in 1964,” they write, “cryonics has been known to frequently produce intense hostility from spouses who are not cryonicists.” The opposition of romantic partners, Aschwin told me last year, is something that “everyone” involved in cryonics knows about but that he and Chana, his wife, find difficult to understand. To someone who believes that low-temperature preservation offers a legitimate chance at extending life, obstructionism can seem as willfully cruel as withholding medical treatment. Even if you don’t want to join your husband in storage, ask believers, what is to be lost by respecting a man’s wishes with regard to the treatment of his own remains? Would-be cryonicists forced to give it all up, the de Wolfs and Federowicz write, “face certain death.”

Link.