Friday Fun: Second Life Edition

Very funny video of real people acting like SL people.

Communications of the ACM, September 2007

Some interesting stuff, as usual, in v50i9:

• Viewpoint: Why you can't cite Wikipedia in my class by Neil L. Waters. Interesting and mostly valid points about Wikipedia. Yet somehow still clueless. Oddly, Waters is a historian not a computing person.
  
• Online first: Evolving the ACM journal distribution program by Ronald F. Boisvert, Mary Jane Irwin, Holly Rushmeier. Important article on how ACM is going to an article-based publishing model and moving away from issue-based.

The issue also includes a special section on Beyond silicon: new computing Paradigms including articles on carbon nanotubes, quantum computers, optical computers, something called Amoeba-based neurocomputing and other strange stuff.

The PRISM Coalition: Partnership for Research Integrity in Science and Medicine

Oh, this is a sad, pathetic story.

It seems that the The Executive Council of the Professional & Scholarly Publishing Division of the Association of American Publishers got together and decide that Open Access is a Very Bad Thing and set up this Prism Coalition to combat it.

What's their problem with OA?

What's at risk

Policies are being proposed that threaten to introduce undue government intervention in science and scholarly publishing, putting at risk the integrity of scientific research by:

• undermining the peer review process by compromising the viability of non-profit and commercial journals that manage and fund it;
  
  
• opening the door to scientific censorship in the form of selective additions to or omissions from the scientific record;
  
  
• subjecting the scientific record to the uncertainty that comes with changing federal budget priorities and bureaucratic meddling with definitive versions; and
  
  
• introducing duplication and inefficiencies that will divert resources that would otherwise be dedicated to research.

And they see their role:

The Partnership for Research Integrity in Science & Medicine (PRISM) was established to protect the quality of scientific research, an issue of vital concern to:

• scientific, medical and other scholarly researchers who advance the cause of knowledge;
  
  
• the institutions that encourage and support them;
  
  
• the publishers who disseminate, archive and ensure the quality control of this research; and
  
  
• the physicians, clinicians, engineers and other intellectual pioneers who put knowledge into action.

And they hope that we, the larger commuity of those interested in scolarly publishing in science, will act:

What you can do

We encourage you to use this website to:

• Learn more about PRISM and what you can do to preserve the integrity of America's scholarly research.
  
  
• Review our PRISM Principles;
  
  
• Learn more about government intervention, the threats to peer review, and other current topics of interest;
  
  
• Endorse the PRISM Principles

So, that's their case. Personally, I think it's the actions of the representatives of an industry that scared of the future, that can't come to grips with the sea changes happening is the world around us, that can't adjust to how those changes will affect their businesses. And they definitely want what they perceive to be the status quo: big revenues, huge profits and a near monopoly on scholarly publishing.

Can these points be refuted and destroyed one by one? Absolutely. Take a look at Bora Zivkovic/coturnix's terrific post summarizing all the reactions in the scientific blogosphere. Bora does a great job of detailing the reactions. I would only suggest that you take a particular look at the posts by Peter Suber in Open Access News (and here and here). I'm not going to attempt to add more smackdown to what has already been done.

However, I would like to talk a little about the makeup of The Executive Council of the Professional & Scholarly Publishing Division.

Who are the members of this Committee? Sure, the usual suspects, representatives of the major commercial publishers such as a bunch from Elsevier, John Wiley & Sons, McGraw Hill, Wolters Kluwer Health, Springer Science + Business Media, SAGE Publications, ISI Thomson Scientific. All the major commercial publishering companies in the scitech fields. Given that they are for-profit companies, however, it's not surprising that they would act to protect their profits. Really, we shouldn't think of them as any different from a company like WalMart or the various companies in Big Pharma. They exist to make money.

Thank god, you're thinking, that the list above does not include any representatives from scholarly or professional societies. Surely they must understand the importance of free and open access to information, something which can surely only benefit their members, scholarship and society as a whole. Sadly, the Exec Committee also includes members from the IEEE (2, including the chair of the journals committee), American Chemical Society (2, including the chair), American Society of Clinical Oncology, New England Journal of Medicine, Columbia University Press, MIT Press, American Academy of Pediatrics, American Institute of Physics and University of Chicago Press. Unfortunately, scholarly societies see OA as a threat to the income from their publishing programs, which is used to finance all the other membership programs that they have like conferences and continuing education. It's really unfortunate that they can't see past these concerns to what the true interest of their members is: for their research to have as high an impact as possible and, as a byproduct of that impact, to benefit scholarship in their discipline and, hopefully, society as a whole as much as possible.

So, what can we librarians do to make ourselves heard? First of all, I'm not going to waste much breath on trying to persuade the Elsevier's of the world to get on board. They'll be the last to convert. What I think is the best plan is to work on the societies.

• If you're on a library advisory group for a society, use that forum to explain the benefits of OA to society members and to explore with the society the kinds of business models that can work
  
• At conferences, talk to the society reps and explain your displeasure with PRISM and how you think they're playing the game of the commercials
  
• Advocate with your faculty, explain the controversy to them and get them to advocate for OA with their societies
  
• Money talks. If at all possible, don't subscribe to journals just because they are from societies, even if they don't make sense
  

(See here for a list of all the members organizations of the Professional and Scholarly Publishing Division. It's basically everybody.)

Bloggers for Peer-Reviewed Research Reporting

Bloggers for Peer-Reviewed Research Reporting is a movement started by Dave Munger of the Cognitive Daily blog. Here's the idea:

BPR3 came about because several academic bloggers in different fields saw the need to distinguish their “serious” writing from news, politics, family, bagpipes, and so on.

Sister Edith Bogue, Dave Munger, Mike Dunford, John Wilkins, and Zachary Tong got together with the idea of doing something about it.

But we need your help. We’d like to design an icon that academic bloggers can use to mark posts where they discuss and cite peer-reviewed research. It’s a trickier problem than you might think: just defining “peer review” itself is hard to do.

Coming up with an icon that fairly represents many different fields is also a challenge. Dave’s blog, Cognitive Daily, already uses such an icon to discuss psychology research reports, but the icon is customized to his needs and his site’s design. In the coming weeks, we’ll be working with academic bloggers from many different disciplines to build an icon that will work for everyone.

Down the road, we’d like to use bpr3.org to aggregate all the posts discussing peer-reviewed research from across the disciplines. Stay tuned!

You can check out some of Munger's posts here, here, here and here. The BPR3 site is itself a blog and there are plenty of posts there already discussing their mission, for example, with Should PLoS ONE count as peer-reviewed? or Is BPR3 the answer to Andrew Keen’s argument?.

I think this is a great idea. The web is a wild and wooly place, with little in the way of quality control or fact-checking built into the infrastructure. Now, unlike Andrew Keen, I don't think that is all bad. Rather it's a mixed blessing: with great freedom comes great potential for creativity, innovation and expression. On the other hand, with great freedom comes great potential for dishonesty and incompetence. The BPR3 movement won't remove the faults or guarantee the benefits. However, it is an interesting start, an experiment that's worth following. Will it get a critical mass of people willing to comment on peer reviewed research and tag their posts to that effect? Will a significant majority of the people tagging their posts be in any way qualified to pass judgment or adequately summarize the research their posting about (I have visions of creationists tagging their posts on articles on evolution)? Only time will tell.

Friday Fun: Unshelved Edition

So, everybody reads Unshelved, right?

There was a week's worth starting August 15, 2007 that I thought was just hilarious, the first one being:



Check out the rest of the strips in the series, either by starting here and just clicking forward or one at a time: 1, 2, 3, 4, 5, 6.

Welcome to visitors from What's New @ IEEE in Libraries

A hearty welcome to everyone who's found their way here via the latest What's New @ IEEE in Libraries! Stick around, visit, leave a comment, send me a message on Meebo.

My most famous posts so far have been the My Job in 10 Years series, some book reviews as well as my series of interviews with people in the scitech world.

• My Job in 10 Years posts, and pdf version of whole series for printing.
  
  
• Recent book reviews: The Trouble with Physics, Dreaming in Code, Everything is Miscellaneous, Balanced Libraries
  
  
• Recent interviews: Timo Hannay of Nature, Michael Morgan of Morgan & Claypool, Jane of See Jane Compute.
  
  
• Some conferences I've blogged: WILU 2007, Computers in Libraries 2007, Ontario Library Association 2007.

For those that are interested, here's the bit about me in the newsletter:

John Dupuis, a member of the IEEE Library Advisory council and the science librarian at the Steacie Science & Engineering Library of York University in Toronto, Canada, is the author of a weblog providing news and other information for academic and science librarians. Called Confessions of a Science Librarian, the blog features an assortment of posts covering anything from book reviews, recent news, software tips, general opinions, and fun facts. Updated often and written with a refreshing combination of humor and intelligence, the blog is sure to contain something for everyone.

The Coming Revolution in Scholarly Communications & Cyberinfrastructure

That's the title for the collection of essays in the most recent CTWatch Quarterly v3i3. There's an incredible array of essays on the future of scholarly publishing, all of them very interesting and worthwhile (I've not read all of the essays yet, but I will). Authors include such notables as Clifford Lynch, Paul Ginsparg, Timo Hannay, Stevan Harnad, Peter Suber and others. This is must-read stuff for everybody in science and libraries as changes to the way scholarship is published will affect virtually everything we do.

From the Introduction (which also has author bios) by Lee Dirks and Tony Hey of Microsoft:

By now, it is a well-observed fact that scholarly communication is in the midst of tremendous upheaval. That is as exciting to many as it is terrifying to others. What is less obvious is exactly what this dramatic change will mean for the academic world – specifically what influence it will have on the research community – and the advancement of science overall. In an effort to better grasp the trends and the potential impact in these areas, we’ve assembled an impressive constellation of top names in the field – as well as some new, important voices – and asked them to address the key issues for the future of scholarly communications resulting from the intersecting concepts of cyberinfrastructure, scientific research, and Open Access. All of the hallmarks of sea-change are apparent: attitudes are changing, roles are adjusting, business models are shifting – but, perhaps most significantly, individual and collective behaviors are very slow to evolve – far slower than expected.

And the complete TOC, with brief excerpts from the articles:

• The Shape of the Scientific Article in The Developing Cyberinfrastructure by Clifford Lynch, Coalition for Networked Information (CNI)
  

  For the last few centuries, the primary vehicle for communicating and documenting results in most disciplines has been the scientific journal article, which has maintained a strikingly consistent and stable form and structure over a period of more than a hundred years now; for example, despite the much-discussed shift of scientific journals to digital form, virtually any article appearing in one of these journals would be comfortably familiar (as a literary genre) to a scientist from 1900. E-science represents a significant change, or extension, to the conduct and practice of science; this article speculates about how the character of the scientific article is likely to change to support these changes in scholarly work.

  
  
• Next-Generation Implications of Open Access by Paul Ginsparg, Cornell University
  

  The technological transformation of scholarly communication infrastructure began in earnest by the mid-1990s. Its effects are ubiquitous in the daily activities of typical researchers, instructors and students, permitting discovery, access to, and reuse of material with an ease and rapidity difficult to anticipate as little as a decade ago.

  
  
• Web 2.0 in Science by Timo Hannay, Nature Publishing
  

  Over the last 10 years or so, much of the discussion about the impact of the web on science – particularly among publishers – has been about the way in which it will change scientific journals. Sure enough, these have migrated online with huge commensurate improvements in accessibility and utility. For all but a very small number of widely read titles, the day of the print journal seems to be almost over. Yet to see this development as the major impact of the web on science would be extremely narrow-minded – equivalent to viewing the web primarily as an efficient PDF distribution network. Though it will take longer to have its full effect, the web’s major impact will be on the way that science itself is practiced.
  
  The barriers to full-scale adoption are not only (or even mainly) technical, but rather social and psychological. This makes the timings almost impossible to predict, but the long-term trends are already unmistakable: greater specialization in research, more immediate and open information-sharing, a reduction in the size of the ‘minimum publishable unit,’ productivity measures that look beyond journal publication records, a blurring of the boundaries between journals and databases, reinventions of the roles of publishers and editors, greater use of audio and video, more virtual meetings. And most important of all, arising from this gradual but inevitable embracement of technology, an increase in rate at which new discoveries are made and exploited for our benefit and that of the world we inhabit.

  
  
• Reinventing Scholarly Communication for the Electronic Age by J. Lynn Fink and
  Philip E. Bourne, University of California, San Diego
  

  Cyberinfrastructure is integral to all aspects of conducting experimental research and distributing those results. However, it has yet to make a similar impact on the way we communicate that information. Peer-reviewed publications have long been the currency of scientific research as they are the fundamental unit through which scientists communicate with and evaluate each other. However, in striking contrast to the data, publications have yet to benefit from the opportunities offered by cyberinfrastructure. While the means of distributing publications have vastly improved, publishers have done little else to capitalize on the electronic medium. In particular, semantic information describing the content of these publications is sorely lacking, as is the integration of this information with data in public repositories. This is confounding considering that many basic tools for marking-up and integrating publication content in this manner already exist, such as a centralized literature database, relevant ontologies, and machine-readable document standards.

  
  
• Interoperability for the Discovery, Use, and Re-Use of Units of Scholarly Communication by Herbert Van de Sompel, Los Alamos National Laboratory and Carl Lagoze, Cornell University
  

  One major challenge to the existing system is the change in the nature of the unit of scholarly communication. In the established scholarly communication system, the dominant communication units are journals and their contained articles. This established system generally fails to deal with other types of research results in the sciences and humanities, including datasets, simulations, software, dynamic knowledge representations, annotations, and aggregates thereof, all of which should be considered units of scholarly communication.

  
  
• Incentivizing the Open Access Research Web: Publication-Archiving, Data-Archiving and Scientometrics by Tim Brody, University of Southampton, UK, et al.
  

  The research production cycle has three components: the conduct of the research itself (R), the data (D), and the peer-reviewed publication (P) of the findings. Open Access (OA) means free online access to the publications (P-OA), but OA can also be extended to the data (D-OA): the two hurdles for D-OA are that not all researchers want to make their data OA and that the online infrastructure for D-OA still needs additional functionality. In contrast, all researchers, without exception, do want to make their publications P-OA, and the online infrastructure for publication-archiving (a worldwide interoperable network of OAI -compliant Institutional Repositories [IRs]) already has all the requisite functionality for this.

  
  
• The Law as Cyberinfrastructure by Brian Fitzgerald, and Kylie Pappalardo, Queensland University of Technology, Australia
  

  In the realm of collaborative endeavour through networked cyberinfrastructure we know the law is not too far away. But we also know that a paranoid obsession with it will cause inefficiency and stifle the true spirit of research. The key for the lawyers is to understand and implement a legal framework that can work with the power of the technology to disseminate knowledge in such a way that it does not seem a barrier. This is difficult in any universal sense but not totally impossible. In this article, we will show how the law is responding as a positive agent to facilitate the sharing of knowledge in the cyberinfrastructure world.

  
  
• Cyberinfrastructure For Knowledge Sharing by John Wilbanks, Scientific Commons
  

  Despite new technology after new technology, the cost of discovering a drug keeps increasing, and the return on investment in life sciences (as measured by new drugs hitting the market for new diseases) keeps dropping. While the Web and email pervade pharmaceutical companies, the elusive goal remains “knowledge management:” finding some way to bring sanity to the sprawling mass of figures, emails, data sets, databases, slide shows, spreadsheets, and sequences that underpin advanced life sciences research. Bioinformatics, combinatorial drug discovery, systems biology, and an innumerable number of words ending with “-omics” have yet to relieve the skyrocketing costs and increase the percentage of success in clinical trials for new drug compounds.

  
  
• Trends Favoring Open Access by Peter Suber, Earlham College
  

  While it’s clear that OA is here to stay, it’s just as clear that long-term success is a long-term project. The campaign consists of innumerable individual proposals, policies, projects, and people. If you’re reading this, you’re probably caught up in it, just as I am. If you’re caught up in it, you’re probably anxious about how individual initiatives or institutional deliberations will turn out. That’s good; anxiety fuels effort. But for a moment, stop making and answering arguments and look at the trends that will help or hurt us, and would continue to help or hurt us even if everyone stopped arguing. For a moment, step back from the foreground skirmishes and look at the larger background trends that are likely to continue and likely to change the landscape of scholarly communication.

(via STS-L and others)

Interview with Joel Spolsky

The current issue of the ACM magazine Queue (v5i5 July/August 2007) has an interesting interview with software development guru Joel Spolsky, author of the Joel on Software blog.

Some excerpts:

BF You’ve written a few books in the past few years, and I see many books piled up in your office. What are you reading now? Anything to recommend?

JS There aren’t many books on the state of the art in software development and software management right now, which are the kinds of things that I like to write and read about. Unfortunately, we haven’t moved beyond the anecdote phase, and attempts to move beyond the anecdote phase are usually just anecdotes with statistics.

Part of the problem is there really isn’t a science going on here, which is very frustrating. The same applies to an awful lot of business writing. It’s very easy to write a book called, for example, The Starbucks Principle or The Dell Way, and just bring up a whole bunch of random anecdotes and somehow tie them together thematically and pretend that this is a real thing that you can do and be successful at.

And, lo and behold, another moron then is going to try to attempt the same thing in his or her own company. It doesn’t work because it doesn’t apply or because it didn’t work in the original company, either—it’s just an anecdote that somebody pulled out of thin air. That’s one of the problems that this particular field has been suffering from.

What we do have are anecdotes from the elderly, people like me, or even the truly elderly, the Gerald Weinbergs of the world, writing brilliant things. Timothy Lister, Tom DeMarco, Ed Yourdon—these are people writing, “I’ve been here for a long time. I know I’m a curmudgeon, but let me tell you young folk what it’s like, da da da da da da da. Here are some examples. What this showed was da da da.” If you read a bunch of those anecdotes, you actually may learn something. That’s sort of the oral knowledge of our field.

*snip*

BF Since you’re passionate about how people interact with computers, I’d like to get your thoughts on the current buzz about Web 2.0 user interface technologies. Has this stuff made our lives better or worse?

JS It has made life a lot harder for programmers, but it has probably benefited users when the programmers do it well. When the user interface works in the way that it’s expected to, and the user model corresponds to the program model, then it’s great for users.

On the other hand, it’s much harder for programmers for several reasons. First, the number of languages you program in has increased. You’re always writing some JavaScript for the browser. And then you’re writing in whatever server-side application language you use—Java, PHP, etc. And then you’re writing in HTML and CSS. You’ve got a bunch of languages to learn, to know, and to keep track of.

Code lives in lots of different places. Just because you wrote a little function that calculates the time of day in the current time zone in one place—let’s say server-side PHP—does that mean it’s going to work for you in JavaScript? That requires all kinds of coordination. The number of things that can go wrong is absurd. You have to test on three or four different popular browsers, at the very least.

Once again, we have hit the world where you have to write really small amounts of code and make them very tight and very fast. For a while we had the luxury of being able to write really sloppy code and never bother optimizing anything, because computers worked “fast enough” and the amount of code didn’t really matter. When you’re writing client-side JavaScript, however, there’s download time, and then the code has to compile. There is a practical limit to the amount of code that you can write on the client side.

Friday Fun, Part Deux: First CD Edition

Keeping with the musical theme for today...

Over at Whatever, John Scalzi asks

Over at By The Way, I note today is the 25th anniversary of the commercial availability of the CD, and asked folks there, who are of an age to remember remember buying a first CD as something special, to recall what their first CD purchases were. I thought I'd ask it here, too.

So: What was the first CD you ever bought?

As I note over at Whatever, it was Tango: Zero Hour by Astor Piazzolla. I haven't listened to it in a while, so I'll have to give it a spin when I get home today. If you've never listened to Piazzolla before, you really owe it to yourself to give it a try. It's the most amazingly compelling music you can imagine.

Friday fun: Crossroads Edition

Eric Clapton has long been on of my favourite performers. Recently, he and a bunch of his blues rock buddies had a benefit concert (Wiki) for his Crossroads (Wiki) rehab facility in Antigua. A good chunk of the July 28, 2007 concert is available on the MSN site. DVD on the way, of course.

Check out the list of performers: Jeff Beck, Doyle Bramhall II, Eric Clapton, Sheryl Crow, Robert Cray, Vince Gill, Buddy Guy, BB King, Alison Krauss and Union Station featuring Jerry Douglas, Sonny Landreth, Albert Lee, Los Lobos, John Mayer, John McLaughlin, Willie Nelson, Robert Randolph and the Family Band, Robbie Robertson, Hubert Sumlin, The Derek Trucks Band, Jimmie Vaughan, Johnny Winter, Steve Winwood and Bill Murray.

Recently in the IEEE

Yesterday was the first day back at work in the library. The sabbatical is now over.

So, what am I reading this week? Some cool stuff from IT Professional, IEEE Annals in the History of Computing and IEEE Transaction on Education.

• Are Computing Students Different? An Analysis of Coping Strategies and Emotional Intelligence by Belanger, F.; Lewis, T.; Kasper, G. M.; Smith, W. J.; Harrington, K. V.
  
• Best Practices Involving Teamwork in the Classroom: Results From a Survey of 6435 Engineering Student Respondents by Oakley, B. A.; Hanna, D. M.; Kuzmyn, Z.; Felder, R. M.
  
• Alan Kay: Transforming the Computer into a Communication Medium by Barnes, Susan B.
  
• Computer Science Curriculum Developments in the 1960s by Gupta, Gopal K.
  
• Open Source Software: Is It Worth Converting? by Laplante, Phillip; Gold, Anthony; Costello, Thomas
  
• Understanding Web 2.0 by Murugesan, San

Smolin, Lee. The trouble with physics: The rise of string theory, the of a science, and what comes next. New York: Houghton Mifflin, 2006. 392

This one of those very rare books, books that make you truly smarter and more knowledgeable that when you started. What does Lee Smolin, physicist at Waterloo's Perimeter Institute, make us smarter and more knowledgeable about, you ask? First of all, the history of theoretical particle physics and the search for a theory that unifies classical physics and quantum theory. Second, the progress of String Theory as a unifying theory and it's alternatives. Third, the culture of the physics community and how it influences the first two.

It's also one of those books that just stops you in your tracks every once in a while. An insight or a story provoking intense reflection and concentration. I'd be sitting there, reading, and suddenly, staring off into space. It makes for a slow but worthwhile reading experience. Since the book treats a lot of fairly advanced topics in theoretical physics, it's also a pretty mind expanding experience, requiring a fair bit of comprehension to soak it all in. Any previous knowledge of string theory of other physics concepts will only enhance the enjoyment (and comprehension) of this book. My general physics knowledge is probably above average and there were a couple of parts where I struggled a bit. There were times when things seemed to make perfect sense while I was reading; then, after putting the book down for a bit, all comprehension simply vanished. On the other hand, as will become apparent later in the review, the hard-core physics stuff isn't really the main payoff of the book so if you find yourself skimming some of the particularly hairy parts in order to keep up your momentum, that's OK.

The main topic of the book has to do with the lack of really productive research in physics since the mid-1970s, when the Standard Model was set out. Since that time, the main focus of theoretical physics has been String Theory. However, as advanced as the theory is, there has been no experimental proof that it is valid. In this sense, compared to the insane pace of advances in the previous century (from atomic theory, to relativity to Quantum Theory to the Standard Model), physics is in a crisis. Smolin attempts to understand that crisis, both from a scientific viewpoint and from a more sociological/philosophical viewpoint as well. Now, there's no more hoary a cliche than the brilliant scientist that turns to philosophy of science in his dotage, mostly to his embarrassment, but Smolin is no geezer and he definitely doesn't embarrass himself is his attempt to understand why the incredibly bright community of physicists has failed to make significant progress in such a long time. Smolin is certainly not afraid to criticize the String Theory community for being too single-minded, for refusing to entertain alternative ideas about theoretical physics, or the physicists themselves for being a bit arrogant or dismissive of their colleagues.

This is a brave and worthwhile book. Read it to learn a lot of physics. Read it to learn a lot about the culture of physics. But definitely read it.

Two blogs to check out in relation to this book, one pro-String Theory and one more skeptical are the group blog Cosmic Variance (example here) and Not Even Wrong (here).

Here & there

A bit of catching up from around the blogosphere:

• Video games: The invisible middleman of the industry by Ted Kritsonis. It seems that Canada is not only a world leader in video game production, but in software shops that build the tools the developers use to build their games.
  
  
• Get a First Life! Reminds me of about a million science fiction stories about virtual worlds where people become so addicted that their physical selves wither away and die. There should be bibliography out there somewhere...
  
  
• Biologists helping bookstores. It seems that people are moving ID, etc, books out of science sections in bookstores and into other sections. Hmmm. Sounds like a good idea. I should make sure we don't have any ID books classified as science in our collection.
  
  
• The Seven Signs of Bogus Science. A bit of an older item, but still well worth reading. Pin it up on the notice board in your library, even.
  
  
• Issues in Scholarly Communication blog. It's new to me, but it seems like a very worthwhile blog to watch.
  
  
• Rebecca at Adventures in Applied Math has a great ongoing series which makes up a kind of Course on Supercomputing. It includes sections on parallel programming, Unix, batch scripts, makefiles and other topics. It's obviously not done yet, but I certainly look forward to more installments. Some of its a bit hairy, but well worth the effort to get the gist.

How to innovate like Google

Saying you're going to be innovative is an awful lot easier than actually creating an environment that truly encourages new ideas and is able to bring them to fruition. Probably by several orders of magnitude. One organization that seems pretty good at that process is Google. But how do they do it? What are the Google "rules of innovative organizations" that other organizations can at least hope to pattern themselves on?

Well, jump on over the Curious Cat Science & Engineering Blog and watch the YouTube video of Google's Marissa Mayer talking about the 9 ideas that encourage innovation.

A summary from Curious Cat:

1. Ideas come from anywhere (engineers, customers, managers, executives, external companies - that Google acquires)
   
2. Share everything you can (very open culture)
   
3. You're Brilliant We’re Hiring
   
4. A license to pursue dreams (Google 20% time)
   
5. Innovation not instant perfection (iteration - experiment quickly and often)
   
6. Data is apolitical (Data Based Decision Making)
   
7. Creativity loves Constraints
   
8. Users not money (Google focuses on providing users what they want and believe it will work out)
   
9. Don’t kill projects morph them

Friday Fun: Body Art Edition

Take a jump over to The Loom and check out his carefully assembled collection of people who've had their love of science tattooed on their bodies.

Rosenberg, Scott. Dreaming in code: Two dozen programmers, three years, 4,732 bugs and one quest for transcendent software.

Full bibliographic info (title field not big enough):

Rosenberg, Scott. Dreaming in code: Two dozen programmers, three years, 4,732 bugs and one quest for transcendent software. New York: Crown, 2007. 400pp.

Every organization relies on software these days. Big custom systems, shrink wrapped commercial software, all the various protocols and programs keeping the Net running. Big organizations, small organizations, tech companies of course, libraries in particular are relying on the fruits of software developers mental labours more and more. And with the rise of Web 2.0 in libraries and educational institutions, our reliance on our programmers will only get more pronounced. But how much do we really understand about the art of software development and the strange and wonderful habits of programmers, systems analysts and all the rest of the software bestiary?

Not much, it seems. And that's where this fascinating insider account a a high-profile open source software project comes in. Salon.com co-founder and author Scott Rosenberg spent three years as a fly on the way on Mitch Kapor's project to create the ultimate Personal Information Manager (PIM), Chandler. Kapor's project was highly idealistic from the very beginning; the idea was that he would use some of his software-boom fortune to finance a project to make every one's lives easier: a PIM that is flexible, sharable and open, able to handle calendaring, email, note taking and events. Unfortunately, the project was also cursed with design difficulties and numerous delays, with a schedule that stretched out from one year to two and three years and beyond (and not even implemented today). The book includes a colourful cast of both obscure and well-known software luminaries (like Andy Hertzfeld), and goes beyond merely recounting the ups and downs of Chandler but also offers a kind of history of attempts to organize and systematize software development. Name-checking such great software engineering writers as Frederick Brooks, Rosenberg talks about the whys and wherefores of structured programming, object orientation and others. Many chapters mix details of the vagaries of the Chandler project with relevant discussions of theoretical topics in software engineering (such as trying to create truly reusable software modules) with more philosophical musings on the art of software development. Most of all, Rosenberg places us firmly inside the workings of a programming project from hell, complete with gory details, tales from the historical trenches and a bit of that fantastic theoretical discussion on why software is so hard. (So, what's it really like being stuck in the programming project from hell? Trust me, I've been there and this is a pretty good example of the real thing.)

There are a couple of really good bits that really stood out for me in this book, bits that resonated with my own experiences managing and developing software. On page 54 he has a discussion of death march projects and the optimism/pessimism dichotomy that all programmers live with and obsess with every day. Having done a couple of death marches characterized by such extremes, it really resonated with me. On page 75, he begins a discussion various programming languages and the almost religious zeal most programmers have for their favourite ones – I was a big fan of Fortran as a young programmer. On page 274, Rosenberg has a telling comment about programmers' historical blindness, their inability to learn from their mistakes, to use the literature to learn from other's mistakes. I like the way he puts it: "It's tempting to recommend these [pioneering software engineering] NATO reports be required reading for all programmers and their managers. But, as Joel Spolsky says, most programmers don't read much about their own discipline. That leaves them trapped in infinite loops of self-ignorance." I like to think that as a librarian collecting the literature of software engineering, I can help in a small way to make programmers more aware of their past.

On a lighter note, I also like the joke that Rosenberg puts on page 275-276:

A Software Engineer, a Hardware Engineer, and a Departmental Manager were on their way to a meeting in Switzerland. They were driving down a steep mountain road when suddenly the brakes on their car failed. The car careened almost out of control down the road, bouncing off the crash barriers until it miraculously ground to a halt scraping along the mountainside. The car's occupants, shaken but unhurt, now had a problem: They were stuck halfway down a mountain in a car with no brakes. What were they to do?

"I know," said the Departmental Manager. "Let's have a meeting, propose a Vision, formulate a Mission Statement, define some Goals, and by a process of Continuous Improvement find a solution to the Critical Problems, and we can be on our way."

"No, no," said the Hardware Engineer. "that will take far too long, and, besides, that method has never worked before. I've got my Swiss Army knife with me, and in no time at all I can strip down the car's braking system, isolate the fault, fix it, and we can be on our way."

"Well," said the Software Engineer, "before we do anything, I think we should push the car back up the road and see if it happens again."

I'm going to use this joke when I do IL sessions for CS and Engineering grad and undergrad students, and maybe even to break the ice at a departmental meeting.

A great book, an insider view of software development, a real insight into how programmers think and work and how software projects grow and evolve, sometimes how they careen out of control. So, who would I recommend this book for? A number of different constituencies would find this book useful and entertaining.

• IT Managers would find this book very useful for its insights into the personalities of programmers as well as for its history of failed attempts to make a purely predictable engineering discipline out of programming.
  
• Programmers would find this book terrific, seeing a lot of their own eccentricities in the many stories. As well, programmers would get a lot of insights into their pointy-haired bosses attempts to turn them into engineers rather than the free-spirited hacker-artists they see themselves as.
  
• Families of the either of the two above groups will get valuable insight into the slightly deranged members of their families, their joys, obsessions and frustrations.
  
• People that support or employ software developers or managers, such as scitech librarians, HR people in tech firms, venture capitalists in software firms. They will hopefully come to understand how and why software projects are created and sometimes crash and burn. Not to mention how to mentor and encourage developers to take advantage of what is known to improve productivity. The other books and articles listed in the notes are also a treasure trove of further exploration and information. I hate it when books like this don't have a proper bibliography – it makes it a lot more trouble to sift through the notes later on for further reading.
  
• And really, anybody that uses software of any kind. And since basically everyone uses some sort of software these days, just about anyone would really appreciate this book. Understanding how the knowledge economy and the Internet boom is built from the ground up is certainly enlightening and important. You'll never see a bank machine, interact with a big company's insane internal systems procedures or even use a simple web application the same way. Understanding the challenges involved in getting these systems even close to right and the inevitability of their imperfections is an important revelation in the modern world.

Chapman, Matthew. Trials of the monkey: An accidental memoir. New York: Picador, 2001. 367pp.

Sometimes, you just get lucky with books. What with the Dover, Pennsylvania trial only a couple of years a ago and the opening of various creationist museums, the evolution vs. creationism controversy is never far out of the news. Of course, I've seen publicity for a lot of books about the issue and Matthew Chapman's 40 Days and 40 Nights: Darwin, Intelligent Design, God, OxyContin, and Other Oddities on Trial in Pennsylvania is one that I've been looking forward to reading. While waiting for the paperback of that one to come out, I was browsing at the discount table at the local bookstore when what should I encounter, but the hardcover Chapman's first book, Trials of the Monkey, about the original creationist trial spectacle, the Scopes Trial. For $7. My lucky day. So, I bought it. It hung around the house for a few months, as usual, and then one day I just picked it up and started reading the first few pages, on a whim. I had no plans to start reading it seriously as I was about 100 pages into another very interesting book. Best laid plans and all, I was hooked and raced through Chapman's fascinatingly complex and interrelated account of the twistings and turnings of his own life and the story of the Scopes trial.

The book really has three narrative threads going. First of all, Chapman's biography, the evolution of his life, a troubled and mixed up childhood through to odd jobs and finally as a successful Hollywood screenwriter and director. The first parallel thread is his plan to visit the site of the Scopes Trial (Dayton, TN) and attend the annual dramatic reenactment of the trial; this takes two parts, the first being a trip to Tennessee to research the trial and scout out the area and the second to attend the reenactment. The final thread that Chapman weaves into a couple of the middle chapters is the story of the Scopes Trial itself.

A few words about the sections dealing with Chapman's biography. Chapman has a gloriously checkered past. The great, great grandson of Charles Darwin, he first chronicles the devolution of his family line from the lofty heights of the great man to his own mediocrity (ie. What's more mediocre than Hollywood) via the alcoholism of his own mother. His childhood, adolescence and young adulthood were certainly ones of very little accomplishment and many brushes with authority as well as a few bizarre sexual obsessions and entanglements. His climb to a happy family life, albeit struggling with the pressures of Hollywood and his own hard drinking, is a happy way to end this particular thread.

His trips to Tennessee to take in the annual dramatic reenactment of the original trial takes up probably half the book. He visits with many creationists, interviewing them and following them around to gather information and get a feel for the ambiance of the place; the same with some of the local bigwigs. It's very interesting that he really makes no attempt to demonize any of them, almost going out of his way to present their best side as well as their lack of scientific rigour and their eccentricities. He often comes off as liking them personally, almost admiring their convictions. This thread ends rather strangely and I won't spoil the surprise. Needless to say, given his own biography, Chapman isn't able to end the book anywhere near the way he'd like.

The chapters where he describes the history of the Scopes trial begin with the story of George Rappleyea, the local businessman who dreamed up the whole mess as a way of promoting tourism and business for Dayton. It follows with a fairly straightforward description of the trial itself and it's aftermath. Well worth reading for a lot of the colourful interactions between the two camps, William Jennings Bryan and his merry band of creationists against Clarence Darrow and the evolutionists. While it was a bit more bare bones than I hoped, this section will lead me to the bibliography to find other works to fill in the blanks.

Which of the threads is the most interesting and compelling? Easily, Chapman's life story is the best part of the book, followed by the story of his visits to Dayton. I often found myself skipping ahead to the next relevant chapter to see what happens next in his various adventures. The story of the Scopes Trial itself is somewhat played down, not given the attention of the other two threads. But that seems appropriate in the context of the story Chapman wants to tell. He covers the details well enough, but just not with the elan of his more personal adventures.

Over all, this is a worthwhile and compelling story, filled with intimate and telling biographical detail and local Southern colour. Not strictly a science book, more of a cultural history mixed with biography. It didn't end up being what I expected at all from the book; I expected more straight reportage and less personal anecdote and cultural commentary. But on the whole, the unexpected combination worked well, being both entertaining and enlightening. If I ended up understanding a little less about the Scopes Trial than I'd hoped, I think I ended up understanding a little more about what makes Southern Christian fundamentalists tick.

I would recommend this book for any public library and any academic library that collects popular science. Of course, any library that has an interest in the evolution vs. creationism controversy can't do without this book. I look forward to reading his second book, the one about the Dover, PA trial, Forty days and Forty Nights.

And now we resume our regularly scheduled blogging

The family and I returned from our vacation yesterday, and a brilliant vacation it was. We spent nearly four weeks at a cottage near Ste-Agathe, Quebec, about 1.5 hours north of Montreal. The lake we were on is very small with pristine, clear water and doesn't allow power boats and only has about 25 or so cottages total. Activities included swimming, canoing, paddle boating, bonfires, reading, relaxing, watching old movies on VHS in the cottage, go karting, mini putting, bowling, only checking email once per week in the village, BBQing almost every night. We saw the most recent Harry Potter movie one day on a trip into Montreal and The Simpsons movie in Kingston on the way home. And speaking of Harry, we bought the new book in the village the day it came out; my wife and boys raced through it but I haven't gotten to it yet.

We spent a couple of nights in Kingston at the wonderful Casablanca B&B, which we would heartily recommend. We also went on the Kingston Haunted Walk, which was good cheesy fun.

My reading included:

• Stolen by Kelley Armstrong
  
• Clear and Present Danger by Tom Clancy
  
• Days of Infamy by Harry Turtledove
  
• Chinatown Death Cloud Peril by Paul Malmont
  
• Dreaming in Code by Scott Rosenberg
  
• Ghost Brigades by John Scalzi
  
• Ghost Road Blues by Jonathan Maberry

Reviews of all the above are forthcoming both here and on the other blog; I wrote two and a half science book reviews while on vacation. I'm finding Smolin's Trouble with Physics a tough book to write about, for some reason. Both The Yiddish Policeman's Union by Michael Chabon and The Map That Changed the World: William Smith and the Birth of Modern Geology by Simon Winchester were started and are still in progress.