Tag Archives: David Zax

iLuminate, uLuminate, we all Luminate for dance

My head(line) is a bit weak, the original line I’m paraphrasing being ‘I scream, You scream, We all scream for ice cream’ but I’m pressed for time today and I want to get this piece about dance, software, and iLuminate posted.

David Zax features an interview with iLuminate founder, Miral Kotb, in his June 15, 2012 article on the Fast Company website,

Miral Kotb is the entrepreneur behind iLuminate, a wearable lighting system that enables novel dance acts. The iLuminate dance team placed third in last season’s America’s Got Talent, and has opened two new shows in Six Flags theme parks this month. We spoke with Kotb to talk about Tron, the Royal Dutch Air Force, and whether Mark Zuckerberg secretly break-dances.

FAST COMPANY: For those who didn’t see it yet on America’s Got Talent, what’s iLuminate?

MIRAL KOTB: It’s a new technology in which dancers have these illuminated costumes on their body that I can control wirelessly. The lights turn on and off with the music, and there’s choreography to match what they’re doing. We can bring a lot of illusions to life that you couldn’t do otherwise.

Here’s a bit about her dance influences,

What are your other influences? Tron comes to mind.

Apple definitely influenced me. William Forsythe, the choreographer [venerable and long gone, British choreographer]. Other dance companies, like Momix and Pilobolus. And definitely my work at Bloomberg [she was a senior software engineer for the company]. A lot of the software involved is very similar to trading. It’s very time-controlled, with a lot of networking involved.

I have found videos for both Pilobolus and Momix. Having seen Pilobolus perform I can say the video does not fully convey the visceral pleasure of watching one of their performances and I imagine the same is true of Momix performance. Still, it’s what we’ve got for now,

Pilobolus:

Momix:

I gather the big breakthrough (although they have worked for a number of major pop stars)  for iLuminate was on the television programme, America’s Got Talent. Here’s the video from their first performance on the show,

I think I’ll have to see a live performance. While this looks interesting, I don’t experience this video as a dance performance so much as I experience it as a spectacle o f lights.

There are more iLuminate videos and information in Zax’s article. You can also find the iLuminate company website here.

Erotica, censorship, and PayPal

There’s been some talk here in Canada about censorship, journalism, and science in regards to the government requiring (since fall 2011) that journalists direct their interview requests to the communications offices of the Ministry of Natural Resources. This practice has been described as a muzzle. It is the 2nd ministry in the last few years to be given this treatment, the first was the Ministry of the Environment. In my March 7, 2012 posting I touched on this issue (scroll about 40% of the way down) in the context of an encounter with someone at the University of British Columbia (UBC). You may want to continue onto the comments for the March 7, 2012 posting where David Bruggeman of the Pasco Phronesis blog eloquently argues that neither my experience with UBC nor the government muzzles amounted to censorship. (As of today, April 30, 2012, I’m still working on my response.)

Given that in addition to censorship I am quite interested in e-publishing, the April 20, 2012 story (PayPal, You’ve Met Your Match: Erotica Writers) by David Zax for Fast Company caught my attention,

Mark Coker is the CEO of Smashwords, an e-book publishing and distribution platform. Coker recently won a highly publicized battle against PayPal, which briefly refused to work with Smashwords unless Coker removed certain naughty titles from the site. Fast Company caught up with Coker and learned, among other things, that writers of incest erotica can be very articulate.

FAST COMPANY: What is Smashwords?

MARK COKER: We’re probably the world’s largest distributor of self-published e-books and e-books from small independent presses. We were founded in 2008. A writer comes to Smashwords, uploads a Word document, which we instantly convert into multiple formats to be read on a Kindle or other device. Those are then available for sale at Smashwords.com at a price set by the author. 85% of all proceeds go to the author, so we flipped the compensation model upside-down. In traditional publishing, in the best case, an author earns 17.5% off an e-book’s list price. In 2008, we had 140 titles; in 2009, we had 6,000 titles; today we have just over 115,000.

You recently came to prominence by picking a fight with PayPal, which threatened to stop working with you if you failed to remove some smutty titles from your store.

On a Saturday, I received an email from PayPal notifying me I had about five days to remove all books containing themes of rape, bestiality, and incest. That was upsetting; we’d been working with PayPal for almost four years. I offered to meet with them, but they responded that they didn’t take meetings, and this was their policy. [emphasis mine] By luck, I called in to the general customer support line, and person who picked up happened to be an author, a member of the Romance Writers of America. She knew who Smashwords was, and knew it was a legitimate platform for indie authors, and that kind soul volunteered to walk us through the process and connect us with people who could actually listen to us.

Did you find purveyors of underage incest erotica to be surprisingly articulate?

We’ve never allowed underage erotica–we’ve always had a strict policy about that. But for the other folks, yes, I found them incredibly articulate and well spoken. Writers are great at communicating, and they were pissed off.

What happened next?

On Monday I received a phone call from a higher-level manager within the PayPal enforcement division. In that call we agreed to continue discussions in good faith, and that PayPal would not turn off its services while we gave it time to work this out. At that point I put into place a new strategy. PayPal had said that they were doing this only because of the credit card companies and banks they worked with. I thought if we could put enough pressure on the credit card companies, that would open the whole thing up. We got the press to start contacting credit card companies to ask if they were behind this or not, and we also escalated the email campaign to all our authors and then all our customers. The public anger rose, and ultimately PayPal wanted out, and the credit card companies relented and gave permission to relax the policies. I think with this incident, a lot of authors realized Smashwords was standing behind them. I think if anyone tries to push the indie author community down again, we’ll be there to help stand behind these authors. In the end I think it was a great victory for free speech, and shows the rising power of self-publishing authors in the publishing community.

There is more to Zax’s article including a discussion of a recent US Dept. of Justice lawsuit over e-book pricing and some criticism of Coker’s other responses to the PayPal anti-erotica initiative.

Zachary Knight in a March 5, 2012 posting on Techdirt covered the story as it was happening. There’s some additional insight into PayPal and its policies as well as a description of how Smashwords and Coker responded to the pressure.

Getting back to the issue of censorship, I find this striking because it seems to have been done at arm’s length. It’s not PayPal, it’s the credit card companies who have decided that these books must be removed. I’m wondering how the credit card companies, as a group, concluded that they didn’t want to have customers paying for e-book erotica. Did they meet somewhere in their secret headquarters and make a group decision? For that matter, why e-book erotica? Don’t people use credit cards to pay for other forms of erotica (movies/downloads?) and/or pornography?

Something else I found quite striking was that PayPal refused to meet because ‘that’s the policy’. I am not much enamoured of agencies (corporate, government, etc.) that make these unilateral decisions and then hide behind policies designed to eliminate any discussion.

By the way, for anyone who’s interested in Smashwords, it looks like a very interesting site with a wide range of materials. From the home page,

Angel’s Whisper    by Muhammad Nasim
You set the price! 20040 words. Language: English. Published on April 24, 2012. Nonfiction » Inspiration » Personal inspiration.
A collection of short and literary blogs of Naseem Mahnavi arranged latest first. They contain wisdom with humor and compelling opinion. Anecdotes range from ants discussing gravity to interpretation of Nistradamus’s quartains and history of America. Perhaps the most interesting part is the candid definitions of common terms compiled over a five year period of blogging. For readers of all ages.

Midnight Arpeggios: An Illustrated Philosophy of Practicing & Music    by M.J. Murphy
Price: $4.99 USD. 22650 words. Language: English. Published on April 24, 2012. Essay » Literature.
If you are looking for a discussion of musicianship at a basic philosophical level then this is for you. You will find a collection of 23 short, original essays on music that are inspired, informal, and brilliantly illustrated with classic artwork.

Blood of the Revenant    by N.R. Allen
Price: $0.99 USD. 72490 words. Language: English. Published on April 24, 2012. Fiction » Young adult or teen » Fantasy.
As Gabriel begins to unravel the dangerous mystery that surrounds the strange and dark place called Returning City, he is drawn into a very deadly secret, one that threatens to destroy not only him but everyone he has ever cared about.

Helping with Homework: A Guide for Teachers and Parents  by Irene Taylor
Price: $4.99 USD. 10250 words. Language: English. Published on April 24, 2012. Nonfiction » Education and Study Guides » Elementary.
Homework…does that word make you cringe? Homework is probably the most talked about idea in education today. Is it an unnecessary waste of energy for student and parents, or a useful tool for teachers?

10 Minute Tidy: 108 Ways to Organize Your Office Quickly, 2nd edition    by Shannon McGinnis
Price: $2.99 USD. 28020 words. Language: English. Published on April 24, 2012. Nonfiction » Business & Economics » Office management.
The 108 Tips in this book offer you fast, easy solutions for increasing your efficiency and productivity at the office. By focusing your attention on one task at a time and devoting just 10 minutes at a time to each tip, you can organize your business for success

M-CORP 2020    by Sajjad  Tameez
Price: Free! 3470 words. Language: English. Published on April 24, 2012. Fiction» Adventure » Action.
In the year 2020, M-Corp, a huge cooperation has bailed out the UK; but for the price of M-Corp having complete control. As society gets chewed up by the rich, and the government takes a back-seat, a modern day Robin Hood emerges, taking things into his own hands. But can one act change the course of the future? Or will the wicked wheels of corruption crush anything that comes in its way.

Using Astrology to Find Your Luck: What Works?   by K.C. Powers
Price: $24.99 USD. 37750 words. Language: English. Published on April 24, 2012. Nonfiction » New Age » Astrology.
Ever wondered what a Lottery Winners Chart looks like? Ever wondered if maybe YOU could win something big? What planets cause the biggest wins and what are the best Triggers of a Lucky Event? These questions have been the subject of my passionate research for over a decade. This book concentrates on Luck and Good Fortune and what really works in astrological prediction.

Reporting Live: Articles and Letters from the 1904 St. Louis World’s Fair   by Lyndon Irwin
Price: $10.99 USD. 67620 words. Language: English. Published by Gregath Publishing Company, Inc. on April 24, 2012. Nonfiction » Biography » Historical biography.
Articles and Letters from the 1904 St. Louis World’s Fair

Make Your Own Beer   by Dee Phillips
Price: $2.99 USD. 6160 words. Language: English. Published on April 24, 2012. Nonfiction » Cooking, Food, Wine, Spirits » Beer.
Here is all the information you need to start making your own great tasting beer at home. From informing you about how the beer making process works to telling you about the different types of beers, you will be able to start making your own beer. 10 great tasting beer recipes included!

The Open Bible – The Gospel of Matthew: Chapter 17    by Open Bible Matthew
Price: Free! 1090 words. Language: English. Published by The Open Bible on April 24, 2012. Nonfiction » Religion and Spirituality » Bibles.
Chapter 17 of Matthew from the Open Bible, a simple easy to understand translation, produced to enable anyone to create their own Bible video and audio recordings etc without any legal restrictions. Chapter 17 includes the account of the Transfiguration on the Mount, and also the miracle of the money in the fish’s mouth

Any budding authors out there? As for censorship and science, I will be getting back to that soon.

NanoRacks and Science Exchange

I had written about Science Exchange (a marketplace for scientists and research facilities) in my Sept. 2, 2011 piece posted about one month after the service was publicly launched. I generally wouldn’t write about them again for a while but a Dec. 14, 2011 article by David Zax for Fast Company (Need A Lab In Outer Space? Try ScienceExchange, The Airbnb Of Weird Science) caught my eye,

Let’s say you’re a scientist, and you’re running an experiment, but there’s just one pesky thing getting in your way: gravity. A few years ago, you’d pretty much have been out of luck. But now, with a startup called ScienceExchange, a marketplace for research assistance, you can send your samples up to the International Space Station in about nine months. ScienceExchange, which opened to the public in August, was originally intended to help forge much more sublunary connections within the research community. But in the few months it’s been operational, says cofounder Dan Knox, ScienceExchange has also become a marketplace for extreme and weird science, too.

“It’s been one of the most fun aspects, hearing about these amazing resources,” Knox tells Fast Company, “and realizing that at the moment there isn’t a good way for them to gain exposure outside of creating their own web presence…I love the fact that NanoRacks listed their facility.”

NanoRacks is where you turn if you want to remove gravity from your experiment. NanoRacks works together with astronauts at the International Space Station, where it maintains laboratory equipment. In 2005, Congress designated a portion of the ISS a national laboratory and directed NASA to “increase the utilization of the ISS by other Federal entities and the private sector.” NanoRacks, which has been open for business a little over a year, is a part of that.

Given my particular interest in all things nano, I felt compelled to investigate. I still don’t understand why this business calls itself NanoRacks (what makes it nano?) but I was able to find out a little more about the services that are offered (excerpted from the About us page,

NanoRacks provides the ultimate ‘Plug and Play’ microgravity research facilities allowing small standardized payloads to be plugged into any of our platforms, providing interface with the International Space Station power and data capabilities.

Our philosophy is to bring together three concepts as our driving force: low-cost, standardization of hardware, and understanding the customer. We like to believe that in space, small is the new big. …

Our company brings together entrepreneurs, scientists and engineers who have real-life experience and share a passion for space including humanity’s utilization of low-earth orbit.

I believe this organization is in Kentucky as they are affiliated with a number of agencies based in that US state. From their Vision page,

Our philosophy is to bring together three concepts as our driving force: low-cost, standardization of hardware, and understanding the customer. Our corporate structure includes a Houston team steeped in the experience of working payload development for every launch vehicle and space stations from Mir to ISS. We are seamlessly interfaced with our non-profit partner Kentucky Space –which includes University of Kentucky and Morehead University, which handle payload operations as well as having their own interest in space-based educational programs.

Here’s a video that demonstrates some of what NanoRacks is about,

Getting back to Zax’s article, there is some discussion of other projects such as imaging an entire mouse’s brain at the ‘sub-micron’ scale or needing to simulate a Category 5 hurricane. As for the reference to Airbnb, that is a business that also connects people (from the Wikipedia essay),

Airbnb is an online service that matches people seeking vacation rentals and other short-term accommodations with those with rooms to rent, generally private parties that are not professional hoteliers. The site was founded in August 2008 by Brian Chesky and Joe Gebbia. In July 2011, the company had over 100,000 listings in 16,000 cities and 186 countries. Listings include private rooms, entire apartments, castles, boats, manors, tree houses, tipis, igloos, private islands and other properties.

I gather Airbnb suffered some sort of a scandal earlier this year when someone who used the service didn’t behave well in the other person’s home. Zax asks Knox about the potential for similar problems on Science Exchange,

Yes, it’s something I worry about,” says Knox. ScienceExchange is tightly controlled, though, where Airbnb is open: “We check who a provider is, verify who they are, and that they have the ability to provide.” These concerns are independent to ScienceExchange, he adds, and exist any time a researcher entrusts another facility with her samples.

So if you’re in the market for a research facility or you’re in a research facility that wants to sell its services, you have the option of forging out on your own or going through Science Exchange.

Vanished; a mystery game

Vanished sounds like a game where you won’t even notice that you’re being educated. (Having looked at a few ‘education’ games, that’s a major kudo from me.)

April 4, 2011 is the date that the Smithsonian Institute and MIT (Massachusetts Institute of Technology) launched an eight-week online game for middle school children that was two years in the making. From the Feb. 22, 2011 MIT news release,

The Smithsonian Institution and MIT announced the April 4 launch of VANISHED, an 8-week online/offline environmental disaster mystery game for middle-school children, meant to inspire engagement and problem solving through science.

Developed and curated by MIT’s Education Arcade (a research group of Comparative Media Studies) and the Smithsonian Institution, VANISHED is a first-of-its-kind experience where participants become investigators racing to solve puzzles and other online challenges, visit museums and collect samples from their neighborhoods to help unlock the secrets of the game. Players can only discover the truth about the environmental disaster by using real scientific methods and knowledge to unravel the game’s secrets.

To navigate through the mystery game’s challenges, participants will gain access to Smithsonian scientists from such diverse disciplines as paleobiology, volcanology, forensic anthropology and entomology.

This project is a consequence of a conclusion reached by researchers at the US National Science Foundation that people learn most of their science informally, i.e., outside the classroom. David Zax’s April 19, 2011 article on the Fast Company website notes,

Over many years, after conducting many surveys, the NSF made an intriguing conclusion: A good deal of the public’s understanding of science derives from outside of the classroom. NSF developed a program in “Informal Science Education,” and Osterweil’s team–jointly housed by MIT’s Comparative Media Studies program and its Scheller Teacher Education Program–nabbed an NSF grant to work on a game, back in 2009. Two years later, more than 5,000 students are playing the game, Vanished, and leaving about 4,000 posts a day on the sites forums.

There’s more about Vanished here (including Frequently Asked Questions) and you can register here. The game ends on or about May 31, 2011. It is still possible to sign up. Players must be 10 1/2 to 14 years old. People of other ages may sign up as observers.

Canadians and ‘smart’ Christmas trees

This isn’t my usual kind of thing but since it does involve Christmas trees, some science, and Canadians, why not? David Zax in his article, Scientists Build “Smart” Christmas Tree With Long-Lasting Needles and Fragrance (on the Fast Company website) writes,

We live in the era of smart grids, smart phones, smart entrepreneurs, and all other manners of smartness. It may be no surprise to learn, then, that we’re on our way towards having a “smart” Christmas tree–one capable of retaining its needles for twice the normal length of time.

That’s according to Dr. Raj Lada [Dr. Rajasekaran Lada], a plant physiologist at the Christmas Tree Research Centre at Nova Scotia Agricultural College in Truro. “The cutting edge is that we should have to have a tree,” Dr. Lada said on NPR, “which I call a smart tree.”

The idea came a few years ago when a devastated small-business owner called on Lada. The man was ruined: his entire crop of Christmas trees had already lost their needles. As Lada began to investigate, he learned that it wasn’t a blight or a disease that was likely to have caused this crop’s loss. Rather, it was a disorder common to many Christmas tree producers: trees often shed their needles quickly, and there was no consensus over how to fix the problem.

You can find the original interview (audio and transcript) on US National Public Radio here. From the transcript of the interview,

FLATOW [Ira Flatow, Science Friday, radio program host]: Raj, you have a new study that’s out now in the journal Trees, where you were able to make trees keep their needles twice as long as usual. How did you do that?

Dr. LADA: That’s true. We started with – I think the problem itself is widespread, basically. Some people talk about it, some people don’t. And it started with the producer, who sent a shipment of trees to Vancouver, B.C., and turned out to be all the needless dropped, and he has not even paid the check. So that is a severe problem.

And we looked at it as a scientific approach. And any of these physiological things now, any of these abscission or flowering, everything is regulated by hormonal changes in plants or trees, basically. And this is one of it, basically. But nobody knows about it. We didn’t even know that there is such a regulatory process.

FLATOW: Right.

Dr. LADA: We from our other herbaceous plants, like cotton and cut flowers and banana ripening, we know that there is a hormone that triggers and – that ages the cell and triggers the hormone level. And once the hormone level reaches to a certain point, that induces the organ shed, basically, the leaves or the fruits or flower petals or whatever it is that can abscise from their tree or plant.

FLATOW: So this is a natural hormone in the tree that sort of signals the tree to shed its needles.

Dr. LADA: Exactly. This is a natural hormone. We just call it the gaseous hormone. It’s (unintelligible) natural gaseous hormone that is produced by the plant cells, basically, in response to various factors. It could be environment. It could be physical, mechanical manipulations, or any abuse, basically.

FLATOW: What’s the name of the hormone?

Dr. LADA: It’s called ethylene.

The interview is quite interesting but the work has yet to move from the laboratory into the field, i.e., you can’t get a ‘smart’ Christmas tree this year. Still, Dr. Lada does have a tip for this year’s Christmas trees,

FLATOW: I see. And you have studied the effect of Christmas lights on trees?

Dr. LADA: Exactly. And that’s another very interesting story to tell about, especially in the Christmas time. The lights, what we used, you know, people think – sometimes, we turn off the lights, and we put on all kinds of lights, sometimes incandescent lights and sometimes fluorescent lights just on top, sometimes halogen lights beaming on the trees. It looks great, but they – each one of those light spectrum is so different physiologically, and they could alter these metabolic functions critically.

So what we identified was we tried to use the recent technology, which is the LED technology, which people use it on Christmas trees all the time. We tested different spectrums – white, blue, red spectrums. And also, we had a control, which were sitting in dark, and also one other control, which were sitting in the gentle, fluorescent light and incandescent light situations.

FLATOW: Mm-hmm.

Dr. LADA: And we found that the white light has got nearly 30, 35 days better needle retention capacity compared to the dark-retained ones, or the controls with the normal lighting.

FLATOW: Wow. So did you get a whole extra month?

Dr. LADA: Oh, we have a whole extra month, basically. Significant…

FLATOW: With the white – with white – would that be like a full-spectrum light?

Dr. LADA: It is a full-spectrum LED, I would say

FLATOW: Wow. And that’s the is that part of the lights you would string on the trees?

Dr. LADA: That’s important to spring, keep that white light in there, basically, especially from the LEDs. You should put more of the white lights in there, basically, rather than the other spectrum.

FLATOW: And so…

Dr. LADA: In fact, the worst performer in our experiment was the blue.

FLATOW: Wow. And so that would seem to say to me that you don’t want to turn your lights off at night. You want to keep them…

Dr. LADA: Absolutely. You should not turn your lights off at night, basically. Because the reason why I’m suggesting is, as you keep them in dark, it started respiring more. And then it’ll use all its carbohydrates that are in the trees, basically. And then it’s – it can be starved to death, (unintelligible).

There you have it.

Goats, spider silk, and silkworms

A few years ago (2008), I attended the Cascadia Nanotech Symposium organized by the now defunct, Nanotech BC (British Columbia, Canada) and heard Dr. Frank Ko speak. He is a Canada Research Chair at the University of British Columbia (UBC) who leads the Advanced Fibrous Materials Laboratory and, in his talk, he mentioned that he had added spider genes to goats with the intention of easing the process of spinning goat’s milk thereby exploiting spider silk’s properties.

I’m never especially comfortable about mixing genes between species that, as far as I know, would never have occasion to mingle their genetic material together. It’s a little too close to ‘The Isle of Dr. Moreau’ (Victor Hugo’s novel which I have never read but have heard about). But there were people who had some similar concerns about electricity, which I take for granted, violating the natural order of things as per Carolyn Marvin’s book, When old technologies were new. Consequently, I’m willing to think about it but not terribly happy to do it.

Getting back to spider silk and Dr. Ko’s work, he and others are very interested in exploiting the strength inherent in spider silk. Here’s a description of that strength from an article by David Zax on Fast Company,

Oftentimes, nature is better at building stuff than we are. Spider silk is an example. The tiny threads spun by our eight-legged friends has a tensile strength comparable to high-grade steel. If humans could harness the spider and turn it into a manufacturing agent, the industrial and commercial potentials could be immense. One problem, though: Spidey hasn’t been cooperating. Spiders just don’t spin the stuff in great quantities, and there is no commercially viable way of mass-producing spider silk.

In looking at Dr. Ko’s webpage I see that adding a spider gene to goats may have been his solution to the problem of producing more spider silk (and perhaps other issues as well),

An internationally recognized expert in 3-D complex fiber architecture for structural toughening of composites Professor Ko’s pioneering work on the development of continuous nanocomposite fibrils by co-electrospinning has provided a new pathway to connect nanomaterials to macrostructural design. With an objective to understand the structural basis for the outstanding combination of strength and toughness in spider silk Professor Ko has played a leading role in the study of nanocomposite fibrils from recombinant spider silk. It was demonstrated that 10X increase in strength and 5X increase in modulus were attainable with the addition of 1-3 weight % of carbon nanotube to the recombinant spider silk. Research has been extended to various filler geometry that include graphite nanoplatelet (GNP); nanoparticles such as nanodiamonds and various functional particles.

Zax’s article highlights a different approach to producing greater quantities of spider silk,

There is, however, already a silkworm industry, which yields most of the silk–less strong than the spider’s–that we’re familiar with. A few scientists got a bright idea: what if you could make the silkworm, which is already equipped for industry, spin spider silk?

Notre Dame, the University of Wyoming, and Kraig Biocraft Laboratories, Inc. joined heads, and recently announced that they had succeeded in genetically engineering silkworms so that they produce artificial spider silks. Several biologists teamed up to splice certain DNA from spiders into the genomes of silkworms. The altered silkworms now spin cocoons that are a mixture of silkworm silk and spider silk. Though the tensile strength of the altered silk still falls well short of that of pure spider silk, it’s a step in the right direction.

I can certainly see benefits to this but I sometimes wonder if humans have enough humility and foresight as we embark on ever more subtle manipulations of life.

ETA October 29, 2010: If you are interested in the goat/spider issue, take a look at Andrew Manard’s October 27, 2010 posting on his 2020 Science blog. He’s running a poll on the question,

… why not take the gene responsible for making spider silk, and splice it into a goat [to produce more spider silk]?

Be sure to take a look at the comments, if you’re interested in the history of the technique, which apparently stretches back to the 1950s!

Is peer review a good idea?

I’ve been meaning to write a piece about science publishing and peer review in the light of a number of recent articles and postings on the subject. As there hasn’t been anything new for at least three or four days now this might be an opportune moment.

I did touch on a related topic in an April 22, 2010 posting where I focused amongst other issues on a paper about publication bias.  From my posting (quoting a news item on physorg.com)

Dr [Daniele] Fanelli [University of Edinburgh] analysed over 1300 papers that declared to have tested a hypothesis in all disciplines, from physics to sociology, the principal author of which was based in a U.S. state. Using data from the National Science Foundation, he then verified whether the papers’ conclusions were linked to the states’ productivity, measured by the number of papers published on average by each academic.

Findings show that papers whose authors were based in more “productive” states were more likely to support the tested hypothesis, independent of discipline and funding availability. This suggests that scientists working in more competitive and productive environments are more likely to make their results look “positive”. It remains to be established whether they do this by simply writing the papers differently or by tweaking and selecting their data.

These papers with their publication bias would have, for the most part if not all, been peer-reviewed which time-honoured system is currently being tested in a number of ways.

There’s the LiquidPublication project in Europe which offers scientists a faster and more dynamic way to publish. From the news item on Nanowerk,

Scientists spend too much of their time publishing papers and ploughing through the mountains of papers produced by their colleagues, and not enough time doing science.

That’s the observation – and frustration – that spurred Fabio Casati and his collaborators to launch LiquidPublication, an EU-financed [European Union] research project that seeks to revolutionise how scientists share their work and evaluate the contributions of their peers.

“The more papers you produce, the more brownie points you get,” says Casati. “So most of your time is spent writing papers instead of thinking or doing science.”

Besides wasting untold hours, Casati says, the current scientific publication paradigm produces other toxic fallout including an unduly heavy load for peer reviewers and too many papers that recycle already published research or dribble out results a bit at a time.

“The current system generates a tremendous amount of noise,” he says. “It’s hard to find interesting new knowledge because there’s so much to see.”

Casati and his colleagues are developing and promoting a radically new way to share scientific knowledge, which they call “liquid publication”. They want to tap the power of the Web – including its ability to speed communication, facilitate data storage, search and retrieval, and foster communities of interest – to replace traditional peer reviews and paper publications with a faster, fairer and more flexible process. [emphasis mine]

David Bruggeman at Pasco Phronesis commented on this project,

The project acknowledges the influence of arXiv.org, but would have some important differences. The plan includes having scientists and so-called ‘invisible colleges’ of researchers develop their own journals which would be created via the platform. There is also the thought that readers of these papers and journals could add value by linking related papers.

David goes on to give support for it while noting that LiquidScience should not be used in the place of peer review and that the more means of publishing research and critiquing it, the better.

The August 2010 issue of The Scientist features three articles on peer review. From the Breakthroughs from the Second Tier article by the staff,

Often the exalted scientific and medical journals sitting atop the impact factor pyramid are considered the only publications that offer legitimate breakthroughs in basic and clinical research. But some of the most important findings have been published in considerably less prestigious titles.

Take the paper describing BLAST—the software that revolutionized bioinformatics by making it easier to search for homologous sequences. This manuscript has, not surprisingly, accumulated nearly 30,000 citations since it was published in 1990. What may be surprising, however, was the fact that this paper was published in a journal with a current impact factor of 3.9 (J Mol Biol, 215:403–10, 1990). In contrast, Nature enjoys an impact factor more than 8 times higher (34.5), and Science (29.7) is not far behind.

One of the most commonly voiced criticisms of traditional peer review is that it discourages truly innovative ideas, rejecting field-changing papers while publishing ideas that fall into a status quo and the “hot” fields of the day—think RNAi, etc. [emphasis mine] Another is that it is nearly impossible to immediately spot the importance of a paper—to truly evaluate a paper, one needs months, if not years, to see the impact it has on its field.

Jef Akst offers a specific example in his article, I Hate Your Paper,

Twenty years ago, David Kaplan of the Case Western Reserve University had a manuscript rejected, and with it came what he calls a “ridiculous” comment. “The comment was essentially that I should do an x-ray crystallography of the molecule before my study could be published,” he recalls, but the study was not about structure. The x-ray crystallography results, therefore, “had nothing to do with that,” he says. To him, the reviewer was making a completely unreasonable request to find an excuse to reject the paper.

Kaplan says these sorts of manuscript criticisms are a major problem with the current peer review system, particularly as it’s employed by higher-impact journals. Theoretically, peer review should “help [authors] make their manuscript better,” he says, but in reality, the cutthroat attitude that pervades the system results in ludicrous rejections for personal reasons—if the reviewer feels that the paper threatens his or her own research or contradicts his or her beliefs, for example—or simply for convenience, since top journals get too many submissions and it’s easier to just reject a paper than spend the time to improve it. [emphasis mine] Regardless of the motivation, the result is the same, and it’s a “problem,” Kaplan says, “that can very quickly become censorship.”

In the third article, this one by Sarah Greene, there’s mention of a variation on the traditional peer review, post-publication peer review (PPPR),

In the basic formulation of PPPR, qualified specialists (peers) evaluate papers after they are published. Instead of hiding reviewers’ identities and comments, they become part of the published record and open to community review and response. Renowned educator Paolo Freire once said, “To impede communication is to reduce men to the status of things.” PPPR at its best facilitates ongoing dialogue among authors, peer reviewers, and readers.

Presumably, PPPR will be part of the LiquidPublication experience. Interestingly, in a recent article on Techdirt (a site focused on intellectual property issues), there was this mention of PPPR,

Apparently, people are realizing that a much more open post-publication peer review process, where anyone can take part, is a lot more effective:

We are starting to see examples of post-publication peer review and see it radically out-perform traditional pre-publication peer review. The rapid demolition [...] of the JACS hydride oxidation paper last year (not least pointing out that the result wasn’t even novel) demonstrated the chemical blogosphere was more effective than peer review of one of the premiere chemistry journals. More recently 23andMe issued a detailed, and at least from an outside perspective devastating, peer review (with an attempt at replication!) of a widely reported Science paper describing the identification of genes associated with longevity. This followed detailed critiques from a number of online writers.

I’m not sure I’m ready to get quite as excited about PPPR as some of its supporters do. Traditional peer review is not the only process that can be manipulated as the recent events with Virology Journal point out. I first came across the incident in a Fast Company (which mostly focuses on business, marketing, design, and technology) in an article by Davdi Zax,

It must get tedious sometimes, running a scientific journal–all that dull data, all those pesky p-values. Wouldn’t it be cool if science journals had accounts of Biblical miracles, and speculation on events thousands of years in the past? That seems to be what the editors of Virology Journal were thinking, when they decided to publish a speculative analysis of a Biblical miracle by Ellis Hon et al., of Hong Kong.

Even from the very first sentence of the abstract, which mentions a woman with a fever cured “by our Lord Jesus Christ,” it ought to have been clear to the article’s reviewers that it was not written to the highest objective scientific standards. The authors go on to present evidence that the woman likely had the flu: “The brief duration, high fever, and abrupt cessation of fever makes influenza disease probable.”

The paper was swiftly eviscerated online, particularly on the blog Aetiology.

An apology was issued both the editor and the author fairly soon after, as per this news item on physorg.com,

Editor-in-Chief of the journal, Robert F. Garry, publicly apologized for publishing the article, saying it “clearly does not provide the type of robust supporting data required for a case report and does not meet the high standards expected of a peer-reviewed scientific journal.” He also apologized for any “confusion or concern” the article may have created among readers.

One of the blogs that brought the paper to notice was This Scientific Life, by Bob O’Hara. O’Hara said the lead author of the paper, Kam L.E. Hon from the Department of Paediatrics at the Chinese University of Hong Kong, had replied by email to his queries and confirmed he had agreed to the retraction and was “astonished” the article had produced such a negative response since it was only intended for thought provocation. He went on to apologize for the inconvenience caused to the Journal and anxiety caused to himself. He said he would never to write this kind of article again. [emphasis mine]

You might think it was a bad piece of science that was caught by the vigilant online community but according to an August 17, 2010 posting by Kent Anderson at the Scholarly Kitchen,

Recently, BioMed Central’s Virology Journal published a case report speculating that the woman in the Biblical story in which Jesus cures her of fever was suffering from the flu. The case report was obviously quite tongue-in-cheek, akin to many others in the literature, but also applied clinical reasoning to the scant evidence offered by the Bible.

In most case reports that seek to plumb historical facts, investigators review documentation, try to translate what they can into modern meaning, then attempt a diagnosis, usually for the sport of it.

I’ll wager that the authors and editors expected this little bit of fluff to pass quietly into oblivion, a harmless lark in an obscure journal. It’s not an unreasonable expectation. In the traditional journal world, reports like this were shielded from widespread evaluation due to relatively small circulations in tight-knit communities. Even in the last decade, the lack of robust commenting on journal articles has helped insulate scholars.

Today, things are different. Now, a science blogosphere bent on sensationalism and hungry for topics is perfectly willing to pick up on a silly article and beat the bejeezus out of it.

Sometimes people behave badly. No system is a perfect bulwark against this tendency. So while the Virology Journal article had been peer-reviewed (which has its own problems),  it was the set of post-publication reviews which resulted in an apology both from the editor and the author who has promised he’ll never write this type of article again. In essence, a kind of mob mentality seems to have ruled and I expect that mob mentality will be seen in the PPPR process as well. My conclusion is that the more ways we have of disseminating and publishing information the better.