Today, I asked Stephanie Willen Brown to answer a few questions.

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your (scientific) background?

I’m Stephanie Willen Brown, aka CogSciLibrarian living in the Triangle area in North Carolina. I’ve been a librarian since 1996, and I started calling myself the CogSciLibrarian in 2004, when I was the librarian for the School of Cognitive Science at Hampshire College in Amherst, MA. I started the blog as a way of sharing cool cognitive science stories and books that I thought my colleagues would enjoy.

My scientific background is limited to that of a librarian, supporting faculty and students working in cognitive science, communications, and psychology over the years. I’d grown up intimidated by math and science, but cognitive / brain / neuroscience is so interesting AND there is so much good, accessible writing about it that I have become a fan.

My current reading interests include the effect of mindfulness on the brain, the development and use of language, and concussions in NFL and other athletes.

Tell us a little more about your career trajectory so far: interesting projects past and present?

I’m thrilled to be working at my dream job, as director of the Park Library at the School of Journalism and Mass Communication at the University of North Carolina, Chapel Hill. It incorporates many of my interests, such as library science, journalism, marketing, and advertising. I am a consumer of mass media, and I love to be around academics who are studying various aspects mass communication.

My first love is helping students and colleagues find resources that will enhance their research, and the work is double-plus good when it involves subject matter I find interesting as well as amazing library colleagues at the UNC Libraries.

I do miss supporting cognitive and communication science, as I don’t have much interaction with my all-time favorite database PsycINFO. It’s got great content and robust metadata (did you know you could limit your search to age group of subjects studied? Or that you can limit results to just empirical studies or literature reviews?), though it’s not the go-to database of choice for mass communication.

What aspect of science communication and/or particular use of the Web in science interests you the most?

Science needs good public relations right now, and I agree with @ErinBiba’s essay in the May issue of Wired “Why Science Needs to Step Up Its PR Game.” I’d like to play a small part in the merger of science and PR by training public relations professionals to do good research and generally supporting their academic endeavors. Libraries and news* (newspapers, news outlets, etc.) need good public relations too, but that’s for another post.

How does (if it does) blogging figure in your work? How about social networks, e.g., Twitter, FriendFeed and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

One of the great things about my job is that I feel empowered – even obligated! – to read about social networking and participate in various social networks professionally and personally. I promote the Park Library via Twitter (@JoMCParkLib and Facebook and have dabbled in FriendFeed.

I believe we in the School of Journalism and Mass Communication should be teaching our students to use social networks in their professional work, so I think of myself as modeling good professional use of social networks.

I tweet as @CogSciLibrarian as well, which is where I keep up with my science buddies and science news.

When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?

I discovered science blogs years ago as I began my own blog, though I read science librarian blogs such as John Dupuis’ Confessions of a Science Librarian more than practicing scientist blogs. I met science documentarian Kerstin Hoppenhaus at ScienceOnline2010 and really enjoy her More Than Honey blog.

I’ve since migrated to Twitter for most of my online / science interactions, and I follow some great science folks there, including @SteveSilberman , @tdelene (DeLene Beeland), @VaughanBell (contributor to Mind Hacks), and my favorite psychology radio show @allinthemind (Australia’s Natasha Mitchell).

What was the best aspect of ScienceOnline2010 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

Gosh, I loved #scio10! It was great to be exposed to so much science in a casual, friendly environment, and I enjoyed spending time with like-minded librarians like Christina Pikas, John Dupuis, and Bonnie Swoger . I was also happy to meet Irtiqa’s Salman Hameed and Tom Linden’s Master’s students in UNC’s Program in Medical & Science Journalism. There were many more as well, but the most amazing aspect of ScienceOnline is the interaction with interesting and interested science, journalism, and library professionals. I have just put #scio11 on my calendar and look forward to meeting more interesting folks!

Thank you so much for the interview. I hope to see you soon, and of course at the next conference in January.

In 2003 the US Department of Agriculture created the Rural Energy for America Program (REAP, then known as “Section 9006”) to provide grants to farmers and rural small businesses to cover up to 25% of the total costs associated with purchasing and installing renewable energy systems and making energy efficiency improvements.

As with any government program however, there’s a tedious process to go through and paperwork to fill out before receiving the funds. One of the first steps in the process is having an independent professional engineer conduct an audit estimating the potential energy savings on the specific project that they’re applying for to receive grant money. Kurt Creamer, Ph.D., says that the “actual percentage energy savings, in some cases are quite phenomenal.”

That’s where Senergy Inc., the Apex-based company hired to conduct these energy audits, comes in. Kurt Creamer, PhD, president of Senergy, founded the company in 2003 in response to REAP while he was still enrolled in the Biological and Agricultural Engineering PhD program at North Carolina State University and working full-time at the school. Even though there was a new need for energy auditors, business remained relatively slow for a few years.

“In the early days farmers had to pay up front for the energy audits which were often times quite difficult for the farmers,” Creamer said. Business for Senergy spread solely through word-of-mouth and only those farmers that could afford to front the initial costs of an audit got on board for the first 5-6 years of the program.

But then, in 2008, the North Carolina Farm Bureau got involved. The Farm Bureau covers the costs of the audits up front so that the farmers are much more willing to go through the process of applying for the REAP grants. The program (and business for Senergy) skyrocketed. It’s “been a real boom to my business to have the Farm Bureau involved in the project,” Creamer said.

Senergy’s work

Senergy typically works with farmers in Eastern North Carolina specializing in grain farms, but has had the opportunity over the years to work with a variety of types of farms including tobacco farms, some on swine & poultry farms, and a handful of dairy farms, often times on some very nontraditional projects.

One particular project on a hog farm required comparing the energy efficiency of burning the dead hogs to composting them—composting is more energy efficient, in case you were wondering. Creamer has also worked on energy efficient organic dairy farm feed grinding systems, poultry barns, irrigation systems, and grain dryers. But he’s not just limited to working on energy efficiency projects. Kurt also works on some renewable energy projects, including one this fall where he’ll be working on a “project to look at the use of sweet potatoes in an anaerobic digester,” Creamer explained, that “could generate enough biogas from the sweet potatoes to meet the requirements of the farm.”

What’s next?

Creamer says that he would love to expand in several ways:

• Geographically: There is still plenty of opportunity to pursue this program in other parts of North Carolina and beyond
• Explore the energy needs of rural small businesses (outside of the farm base)
• Take on more renewable energy projects
• Improve his engineering methodologies

At the end of the day Creamer says he really enjoys the work he does and “it’s a really good program for the farmers, and a good program for the environment.”

Dan Vorhaus

Dan Vorhaus is a lawyer with Robinson Bradshaw and Hinson in Charlotte, N.C. where a portion of his practice comprises the growing field of personal genomics law. Given the interest in personal genomics in the Triangle, I thought I’d create an expanded version of the short question-and-answer interview I did with him for an up-coming issue of the Sci-Tech section in the Charlotte Observer and the Raleigh News and Observer (be on the lookout for that next Monday in print and online), and post it here. Vorhaus also authors the Genomics Law Report, a blog about the legal side of personal genomics, and he will be giving testimony to the Food and Drug Administration in the near future as the agency attempts to sort out particulars of how it plans to regulate genomic diagnostic testing.

How did you become interested in concentrating on personal genomics as an area of the law?
I have a master’s in bioethics; I did that degree before I went to law school. So as I started thinking about the areas of law and policy that were most interesting to me, that was clearly one of them. And it seemed like there was a tremendous opportunity for a field that is developing and emerging and creating all sorts of new and exciting legal issues. And it’s something that I’ve always had an interest in the underlying science and technology, and I was fortunate enough in law school to start working with some real pioneers in the field, specifically George Church in the personal genome field. Everything sort of built from there. Now, it’s how I make my living, it’s my career. And I love it. It’s something new and fascinating every single day and I can’t get enough of it.

It sounds like the bioethics degree had a big influence on you.
It did, although I already had this interest before, that was what caused me to pursue the bioethics degree. And I knew I was going to law school. I kind of applied those two things simultaneously. So, they have kind of worked together simultaneously. And I decided kind of early on that I was more interested in pursuing the law than some of the pure policy or philosophy or ethical issues behind a lot of these technologies. I think there is a real need… One thing you find with the law is that new areas tend to lag in new areas of technology and new areas of social development. And that is certainly true in the areas of personal genomics, personalized medicine, there is a long way for the law to go to catch up to where science and technology already are. And they continue to press on ahead. And the law continues to play catch up. So it seems that there is a real opportunity to be involved in helping to lay the legal framework for what I think will be important and meaningful technologies and services in people lives for years and decades to come.

That formalizes what I had suspected, with some of the things I’ve read about the Myriad ruling and the FDA announcing its intent to regulate direct-to-consumer genomic testing, it does seem that these formal regulations and policies are lagging behind the business practices.
That’s right. Both the examples you gave, the Myriad litigation — and really, the state of biotechnology patents more broadly – and the FDA and Congress’s involvement in genetic testing, especially consumer genetic testing, both of those are areas where there is a lot of uncertainty right now whether the law today is doing as good a job as it could be as far as protecting individuals and enabling commerce, and really striking the right balance between allowing the science and the technology to press forward while making sure that we have the right protections in place for people using these technologies. That is always going to be a tension in this area, I don’t ever foresee that dissipating; but that does not mean that we should work any less hard to get that balance as close as we can as quickly as we can.

You’ve posted about the Myriad gene patent litigation, in which a federal judge invalidated patents that Myriad held for human genes, BRCA-1 and BRCA-2, which are used to test for the likelihood of developing breast cancer. What was the most unusual thing about this ruling, because it seems to have caused quite a splash?
You’re right, it does cause a splash, but I would say the splash that it caused is probably greater than its legal significance, at least for right now. It’s important to keep in mind that this was a district court ruling, so without getting to much into the weeds, there is a long way to go with this litigation before it gets to the point where it will really impact the commercial landscape, before it really impacts what people feel comfortable doing in laboratories – whether it is research laboratories or commercial laboratories – it needs to .. It’s already been appealed to the federal circuit, which is the federal appeals court that hears patent cases. And it’s quite possible that from there it will go to the Supreme Court, and we’re talking at least another year. Perhaps two. Maybe even three more years before we get a final resolution in this case. The reason I think it garnered so much attention is because it really struck a nerve – and going back to this idea of law not always keeping up with where science is – it really struck a nerve when people heard that there were companies out there that held patents on human genes. And we are talking about isolated human genes, genes outside the body, no one owns you, but it is the case that some companies have patents on genes, and they have the ability if they want – and Myriad has done this because of the way patents work – they grant the patent holders monopoly rights, they have the ability to keep other people from doing tests to analyze those genes, to sequence those genes, to ask what does this mean, in the case of BRCA, for the susceptibility of a woman’s or a man’s, risk of getting breast cancer. And I think that struck a nerve with a lot of people.

It’s not the only sort of development with this area… [Other reports] have gone to the Secretary of Health and Human Services that looked at these issues and looked at the gene patent landscape and said this is a problem, this is impeding our ability to do the type of diagnostic or clinical work that we need to do, to advance the state of science and technology. There is another supreme court case that will likely come out on Monday, that also may be significant as far as the extent of biotech patents, in terms of how far they can reach. And it all goes back to this question of trying to strike the right balance. In the case of patents, we’re trying to strike the right balance of information disclosure and getting these technologies out there and allowing people to benefit from them, and preserving the commercial incentive to investments. That is how our legal system works, we build up this body of law over years and decades – in this case, patenting of human genes which reaches back to a 1980s Supreme Court case, probably even further, and it built up incrementally. And science does not work that way, it moves much faster. It was only 10 years ago that we published the first draft of the human genome sequence, and now, 10 years later, we are routinely sequencing whole genomes, let alone individual genes. And so, again, it’s that pace of technological innovation and scientific advancement that is much faster than we have the ability to move in the legal realm. So that causes a conflict in cases like Myriad where now everyone has to sit down and ask, do we have the right balance here? Should genes be patentable? Is this where we want to be? I think there is plenty of debate about that. It may be something that litigation solves, or maybe Congress steps in, or maybe there are people out there working on industry private solutions to work things out without having to wait on the courts to solve it.

One thing that confused me about this, is the idea of patenting human genes. In the case of Myriad, one of the things I was wondering was why do they have to patent a human gene? Why can’t they just patent their test? That seems like a more level playing field.
You’re right, that would be a more level playing field, and I think the simple answer is that if you are going to invest a lot of money into developing a test and researching an association between a gene a certain disease, and then figuring out the corresponding test, you may not want a level playing field. You may want to do all the testing, and that is what Myriad does. I should mention, there are other companies out there that have patents on human genes, and they have a patent that allows them to have exclusive rights to practice that patent. So, to conduct a test, or even to examine the gene, if the patent is one the gene itself; but they license out that patent or set of patents. Myriad, for example, I think has several dozen patents with almost two hundred claims, so we’re not talking about one or two patents, they have a whole suite of patents, that protects this business they’ve built around diagnostic testing for breast cancer, but there are other companies out there that have similar patents that do license them out to other people, and they say, here you can use this technology, you can use this gene that we’ve patented, there is going to be some sort of commercial terms with that, you’ll pay us some sort of royalty, or some kind of fee based on tests that you do, but you can get in the game too and essentially provide the same sort of service that we are providing.

Or, Myriad is a good example. They did not actually patent this themselves, they licensed this from the University of Utah. And so it is interesting because one of the reasons why Myriad was swept up in this litigation is because there are thousands of genes that are patented, Myriad only has patents on a handful, but the reason they became a target in this litigation is partly due t otheir practice of not licensing out their IP, their intellectual property, and not giving people a chance to conduct or to develop competing gene tests. But that is the prerogative of a patent-holder. You have the right to exclude everybody else from practicing your patented invention. You can wave that right, in the form of a license, out to other people, if you want, but you don’t have to. So that is why there is this big question over what should be patentable. The technical discussion centers around section 101 of the Patent Act which defines what is patentable subject matter. And the question is, are genes patentable subject matter, or are they what is considered to be a product of nature?

Is it that things in the natural world can’t be patented?
Well, it doesn’t specifically say that in the Patent Act, but that is the way it has developed in the case law over time. The 1980 case that I referred to earlier … said that what is patentable is anything under the sun made by man. And there is this products of nature doctrine, and it says, well the Supreme Court says, that something that is a product of nature can’t be patented. And then the question is, what is a product of nature? And Myriad argues, in this case, that this is not a product of nature because you are taking genes, which occur naturally in the body, and you are separating them out, you are isolating them, you are doing things to them technically that make them no longer products of nature. And in the technical sense, that is correct because genes do not naturally occur in laboratories. But what Judge Sweet ruled is that what is fundamentally important in these genes, what really makes them significant, is the information that they carry. And that is the same whether you are talking about a BRCA gene in your body, in my body, or in Myriad’s laboratory. The information content is the same, and that is what is significant, so they are products of nature and they can not be patented. Whether that ruling stands up, remains to be seen. There is quite a good chance that it won’t.

That’s an interesting interpretation.
And it’s one that people share. I think it resonates quite strongly with people at a gut level. But again, there are limits to how that can be implemented by law in courts. Congress of course has the ability to change the law. As has happened in many, many cases, if Congress does not like a law they have the ability to go out and change the law.

The Food and Drug Administration is constricting regulations for direct-to-consumer genetic testing services offered by companies that scan a person’s genome and offer analysis for health risks or ancestry. What are the FDA’s specific concerns?
It’s interesting… since the whole Walgreens-Pathways thing blew up about five or six weeks ago now, they went after five or six companies. They’ve taken a step back and said, you know, we think we need to regulate all genetic testing. It’s important to remember that most genetic testing is not what is known as DTC [direct to consumer] or commercial or consumer genetic testing. Most of it occurs in a clinical context, done in clinical laboratories, and that is the vast majority of genetic testing on the market right now. Now, the concerns they raise about taking a risk-based approach to regulation, and specifically they are concerned about the safety and efficacy of these tests. So, making sure that the tests are accurate, making sure that – accurate in the sense that when you test for X, you actually get X – that’s what’s called analytical validity.

And then also what is known as clinical validity, which is making sure that the association or the link reported by the tests so that if you do have X, that means you have an increased risk of getting breast cancer, is actually a valid one. And in an area of science that is so new and so changing, that is something that can be difficult to show. Or it may be controversial. So there is a lot of recorded genetic associations that require confirmation, maybe they need more traditional studies to confirm the results, and some studies that have disproved associations, so that is a concern too.

Then there is a third problem which is what is known as clinical utility which is that even if you measure the association correctly and it does mean what you say it does, so you have X, you’ve actually measured X accurately and it does mean that you have an increased risk of disease Y, then clinical utility asks, Can I do anything with this? Can I take this to my doctor and can he start me on a new medication, or tell me that if I lose 15 pounds, then I can prevent myself from developing condition Y. That’s the clinical utility prong, and there is a lot of disagreement there about whether that is something the FDA should really be concerned with, or if that is something that should be left up to individuals. And there are varying definitions as to what constituted clinical utility. Alzheimers is a good example. There aren’t many drugs on the market right now that can be used to reverse the effects of Alzheimers, or be used as a preventative measure for preventing Alzhiemers.

But there are a lot of lifestyle changes that have some evidence that they might help. And there are lot of people that argue that for me, clinical utility means just knowing. If I want to know, then I should be able to know because then I can engage in family planning. I might decide to take an earlier retirement. I might do other things differently. There is going to be a big public meeting July 19 and 20 in DC where I will be at the FDA to talk about some of these issue and give them feedback as they start writing regulations. And of course, in addition to the FDA, the House of Representatives, Congressman Waxman’s committee, have gotten involved with writing letters and they appear to be gearing up to hold hearings and maybe do something in this area. I heard recently that Senator Hatch has a bill out that would address genetic tests and specifically create a new division within the FDA to address those. There is another bill on the House side, I think,… that would also wade into this area. So there are a number of different pathways on the table right now for how the regulation of genetic tests may develop. It’s a bit of a scramble right now.

Even though you said that direct-to consumer genomic tests are a small slice of the genomic testing pie, what legal concerns do consumers need to be aware of when using personal genomic testing?
Well, it is a small… let me back up by saying that consumer genetic testing is a small slice of the overall genetic testing pie, but diagnostics — and that includes an increasingly large percentage of what we think about when we talk about personalized health care – and there are some people that believe that within the not-to-distant future, it’s going to be diagnostics riving therapeutics, so drugs and pharmaceuticals, and not the other way around. Right now, you’ve got these big diagnostic companies, and you’ve got big pharmaceutical companies, but that may flip. We are really looking at, I think, a shift coming down the road. There are some questions associated with consumer tests. A lot of the issues are similar to just the issues associated with learning about genetic information in any context. You want to know that you understand… what information you will find out, if it will be useful to you.

There have always been concerns about somebody else getting ahold of that information and somebody else using that against you. That’s one reason we passed the information non-discrimination act in 2008, to prevent employers and health insurers from using that information. But, that doesn’t mean that other people can not potentially get access to that information and use it against you. That could be your friends, or your co-workers or your family workers.

One thing you hear happening is non-paternity as a result of genetic testing, so you go get tested and your father gets tested and you find out, wait a second, our DNA doesn’t match. I think it’s something like a 10 percent non-paternity rate in this country, which is pretty high compared to what the known rate of non-paternity is. So there is a lot of those cases out there that I think are probably unknown to the family. So you can find out information that might be upsetting to you, or that might be surprising to you. You can also find out information that might be very useful, or interesting to you. That is a balance that everybody needs to sort of strike for themselves and think carefully about. So there are privacy concerns, discrimination concerns. The accuracy of the information… you have to be prepared that it’s not always accurate. There is clinical genetic testing and consumer genetic testing.

Have you tested your genome?
I have. I’ve had myself genotyped by 23AndMe, which is one of the companies that is in the middle of all this. Probably one of the most prominent companies. I paid for it myself. I did not want a conflict of interest because they have gien away a number of reduced cost or low-cost kits and I did not want to have any conflict there. And I think that is all I’ll say about that, because I’m going to be talking publicly about that in the not-too-distant future.

What I wrote last month,

“I think of myself as a reasonably curious and informed person, and I have visited at least a couple of infrastructure plants, but almost every anecdote and every little tidbit of information were new to me. Scott’s point – that we don’t know almost anything about infrastructure – was thus proven to me.”

…was reinforced when I read the book itself: I don’t know anything about infrastructure. But after reading the book I can say I know a little bit, understand how much I don’t know, and realize how much more I’d like to know. I bet it was fun watching me as I was reading it, exclaiming on average five times per page “This is so cool”, and “Hey, this is neat” and “Wow, I had no idea!” and (rarely) “w00t! Here’s a tidbit I actually heard of before” and “Hey, I know where this is!” (as I lived in Raleigh for eleven years, I know the area well).

A few years ago, Scott was just as ignorant about infrastructure as most of us are. But then his curiousity got better of him and he started researching. He would start at his house in Raleigh and trace all the wires and cables and pipes going in and out of the house to see where they led. Sometimes there would be a crew on his street digging into the asphalt and fixing something and he would approach them and ask questions. At other times he would figure out where the headquarters are and who to ask to talk to:

“What Scott realized during the two years of research for the book is that people in charge of infrastructure know what they are doing. When something doesn’t work well, or the system is not as up-to-date as it could be, it is not due to incompetence or ignorance, but because there is a lack of two essential ingredients: money and political will. These two factors, in turn, become available to the engineers to build and upgrade the systems, only if people are persuaded to act. And people are persuaded to act in two ways: if it becomes too costly, or if it becomes too painful to continue with the old way of doing things. It is also easier to build brand new systems for new services than it is to replace old systems that work ‘well enough’ with more more modern ways of providing the same service.”

In a sense, this book is a memoir of curiosity as Scott describes his own adventures with a hard-hat, a modern Jean Valjean sloshing his way through the Raleigh sewers, test-driving the public transportation, and passing multiple security checks in order to enter the nearby nuclear plant.

But it is more than just a story of personal awe at modern engineering. Scott weaves in the explanations of the engineering and the underlying science, explains the history and the politics of the Raleigh infrastructure, the historical evolution of technologies underlying modern infrasturcture, and illustrates it by comparisons to other infrastructures: how does New York City does that, how did Philadelphia did it 50 years ago, how did London 500 years ago, how about Rome 2000 years ago?

“What is really astonishing is how well the systems work, even in USA which has fallen way behind the rest of the developed world. We are taking it for granted that the systems always work, that water and electricity and phone and sewers and garbage collection and public transportation always work. We get angry on those rare occasions when a system temporarily fails. We are, for the most part, unprepared and untrained to provide some of the services ourselves in times of outages, or to continue with normal life and work when a service fails. And we are certainly not teaching our kids the necessary skills – I can chop up wood and start a wood stove, I can use an oil heater, I know how to slaughter and render a pig, how to get water out of a well, dig a ditch, and many other skills I learned as a child (and working around horses) – yet I am not teaching any of that to my own kids. They see it as irrelevant to the modern world and they have a point – chance they will ever need to employ such skills is negligible.”

And this brings me to the point where I start musing about stuff that the book leaves out. As I was reading, I was constantly hungry for more. I wanted more comparisons with other cities and countries and how they solved particular problems. I wanted more history. I wanted more science. I wanted more about political angles. But then, when I finished, I realized that a book I was hungry for would be a 10-tome encyclopic monograph and a complete flop. It is good that Scott has self-control and self-discipline as a writer to know exactly what to include and what to leave out. He provides an excellent Bibliography at the end for everyone who is interested in pursuing a particular interest further. His book’s homepage is a repository for some really cool links – just click on the infrastructure you are interested in (note that “Communications” is under construction, as it is in the real world – it is undergoing a revolution as we speak so it is hard to collect a list of ‘definitive’ resources – those are yet to be written):

What many readers will likely notice as they go through the book is that there is very little about the environmental impacts of various technologies used to ensure that cities function and citizens have all their needs met. And I think this was a good strategy. If Scott included this information, many readers and critics would focus entirely on the environmental bits (already available in so many other books, articles and blogs) and completely miss what the book is all about – the ingenuity needed to keep billions of people living in some kind of semblance of normal life and the interconnectedness that infrastructure imposes on the society, even on those who would want not to be interconnected:

“There are people who advocate for moving “off the grid” and living a self-sufficient existence. But, as Scott discovered, they are fooling themselves. Both the process of moving off the grid and the subsequent life off the grid are still heavily dependent on the grid, on various infrastructure systems that make such a move and such a life possible, at least in the developed world.”

My guess is, if there’s anyone out there who could possibly not like this book, it will be die-hard libertarians who fantasize about being self-sufficient in this over-populated, inter-connected world.

At several places in the book, Scott tries to define what infrastructure is. It is a network that provides a service to everyone. It has some kind of control center, a collection center or distribution center. It has a number of peripheral stations and nodes. And there are some kinds of channels that connect the central place to the outside stations and those stations to the final users – every household in town. There is also a lot of redundancy built into the system, e.g., if a water main breaks somewhere, you will still get your water but it will come to you via other pipes in surrounding streets, with zero interruption to your service.

Scott covers surveying of land, stormwater, freshwater, wastewater, roads, power, solid waste, communications (phone, broadcast media, internet) and transportation (e.g., public transportation, trains, airplanes). These are the kinds of things that are traditionally thought of as ‘infrastructure’. But aren’t there other such systems? I’d think security has the same center-spokes model of organization as well: police stations and sub-stations (distribution centers) that can send cops out wherever needed (distribution channels), with potential criminals brought to court (processing centers) and if found guilty placed in prison (collection center). Similarly with fire-departments. Ambulances are just the most peripheral tentacles of the health-care infrastructure. The local-county-state-federal political system is also a kind of infrastructure. So is the military. So is the postal system. So is the food industry and distribution.

Thinking about all of these other potential examples of infrastructure made me realize how many services that require complex infrastructure undergo cycles of centralization and decentralization. For transportation, everyone needed to have a horse. Later, it was centralized into ship, railroad, bus and airline infrastructures. But that was counteracted by the popularity of individually owned cars. And of course taxis were there all along. And as each decade and each country has its own slight moves towards or away from centralization, in the end a balance is struck in which both modes operate.

You raised your own chickens. Then you bought them from mega-farms. Now many, but not most citizens, are raising their own chickens again. It is not feasible – not enough square miles on the planet – for everyone to raise chickens any more. But having everyone fed factory chicken is not palatable to many, either. Thus, a new, uneasy balance.

Nowhere is this seen more obviously today as in Communications infrastructure. We are in the middle of a big decentralization movement, away from broadcast (radio, TV and yes, newspaper industry infrastructure with its printing presses, distribution centers and trucks) infrastructure that marked about half of 20th century, and forward into something more resembling the media ecosystem of the most of human history – everyone is both a sender and a reciever, except that instead of writing letters or assembling at a pub every evening, we can do this online. But internet is itself an infrastructure – a series of tubes network of cables and it is essential not to allow any centralized corporation to have any power over what passes through those cables and who gets to send and receive stuff this way.

Finally, as I was reading the book I was often wishing to see photographs of places or drawings of the engineering systems he describes. As good as Scott is at putting it in words, there were times when I really wanted to actually see how something looks like. And there were times when what I really wanted was something even more interactive, perhaps an online visualization of an infrastructure system that allows me to change parameters (e.g., amount of rainfall per minute) and see how that effects some output (e.g., rate of clearing water off the streets, or speed at which it is rushing through the pipes, or how it affects the water level of the receving river). That kind of stuff would make this really come to life to me.

Perhaps “On The Grid” will have an iPad edition in the future in which the text of the book is just a begining of the journey – links to other sources (e,g., solutions around the globe, historical sources), to images, videos, interractive visualizations and, why not, real games. After all, it is right here in Raleigh that IBM is designing a game that allows one to plan and build modern infrasctructure – CityOne. These two should talk to each other and make something magnificient like that.

For most of us, our neurons remain malleable throughout our lives, giving us the opportunity for lifelong learning (though it does get harder with age). But for those afflicted with the rare genetic disease Angelman syndrome, the synapses are almost completely incapable of being remodeled. By the time children with Angelman syndrome are toddlers, their synapses have largely lost their plasticity, hardening like concrete into rigid structures that can no longer easily relay new information.

The result is quite tragic – children whose bodies grow and age normally but whose brains are locked forever in the state of a two year old. But there is also reason to hope, as tremendous progress has been made in the understanding of Angelman syndrome, say many of the researchers, clinicians, and parents in attendance at a recent conference on the disorder. The 2010 Angelman Treatment and Research Institute Scientific Symposium, held at the Carolina Inn in Chapel Hill on June 15 and 16, showcased the current research on the genetic disease, with efforts tapping into the latest technological tools from mouse models, brain imaging, stem cells, proteomics and gene therapy.

“Over the span of the conferences I have attended, I really feel like I can see the gap getting smaller between the cellular molecular finding and its clinical applications,” said Heather Adams, a neuropsychologist from Massachusetts who specializes in kids with cognitive impairment. She also has a daughter with Angelman syndrome.

Angelman syndrome is a rare intellectual disorder that affects about one out of every 15,000 people. It is often placed on the autism spectrum because of the shared language difficulties and inappropriate social behavior. The language impairment in people with Angelman syndrome is much more severe than in those with autism – in fact, most of them never speak a single word. And whereas individuals with autism might shun social interaction, those with Angelman are quite social.

“One of the very endearing things about these individuals is they have a very happy demeanor,” said one of the conference’s organizers, Ben Philpot, an Associate Professor in Cell and Molecular Physiology at the University of North Carolina. “They are often said to have inappropriate laughter, but I think that they just find more things in life funny than we do.”

Their child-like view of the world – and the detrimental ramifications of a brain that is unable to change — all stem from a defect in a single gene called UBE3A. If the gene is mutated or deleted, the result is Angelman syndrome. But if it is duplicated, it may result in one of the more classic forms of autism. And altering its function can also lead to tumors of the cervix, though in the cancer field the gene goes by the name E6AP. So studying this one gene and its effects on the plasticity of our brains could have far-reaching implications.

“The work related to synaptic plasticity in genetic syndromes is forming thrilling insights as far as how we reason and learn things,” said conference attendee William Snider, director of the UNC Neuroscience Center.

At the two-day conference, scientists from across the country presented their latest findings on the role of this infamous gene in disease. One of the invited speakers, Harvard’s Michael Greenberg, explained the findings he had recently published in the journal Cell on targets of UBE3A. The molecule’s main job is to mark other proteins to be broken down or destroyed, so if UBE3A is absent then certain proteins accumulate to inappropriately high levels, causing subtle but lasting damage to our brain cells.

“If we know what the targets are we may be able to produce therapies that can break them down when UBE3A is no longer able to do its job,” said Philpot.
Philpot’s own work has indicated that pharmacotherapeutics or behavioral modifications may be able to restore the brain’s plasticity. He is currently using funding from the NC Translational and Clinical Sciences Institute (NC TraCS) to search for new molecules to treat Angelman syndrome, an area that is understandably of intense interest for many in the field.

“As a scientist I say the progress that has been made so far is remarkable, but as a parent, I say it is not fast enough,” said Alina Szmant, a marine biologist from Wilmington who has a 31-year-old daughter, Selena, with Angelman Syndrome.

Mark Nespeca, a clinician at Children’s Hospital in San Diego who also attended the conference, says that the pace of research depends a lot on your perspective. Because he does not conduct research himself, conferences like this one help him keep up with the many advances that have occurred since he was in medical school.

“With the advances in technology today, people are talking about sequencing your entire genome for just a thousand dollars,” said Nespeca. “There may come a day when kids will be coming to us at two months of age newly diagnosed, and we can say is there something we can do to make a difference so you can walk, can talk, not have seizures. But for a parent dealing with this illness day in and day out, it must be hard to wait and hope for that day to come.”

I interviewed Vanessa after the 2008 event and blogged (scroll down to the second half of the post) about her 2009 session ‘Blogging adventure: how to post from strange locations’. At the 2010 conference, she was one of the five storytellers at the ScienceOnline Monti on Thursday night (and did another stint at The Monti in Carrboro a couple of months later). I have since then also met her husband Brian Hare and we instantly hit it off marvelously.

I have read Vanessa’s previous book, ‘It’s every monkey for themselves‘, but never reviewed it on the blog because I felt uneasy – that book is so personal! But it is an excellent and wonderfully written page-turner of a book so I knew I was in for a treat when I got a review copy of her new book, Bonobo Handshake (amazon.com). I could not wait for it to officially come out so I could go to the first public reading (where I took the picture) at the Regulator in Durham on May 27th, on the day of publication.

Vanessa recently moved her blog to a new location on Psychology Today network and had a few interviews in local papers, more sure to come soon.

Vanessa will also soon read/sign the book at Quail Ridge Books on June 9th at 7:30pm, and at Chapel Hill Borders on June 12th at 2pm (also June 22 at Barnes & Noble on Maynard in Cary, June 30 at The Country Bookshop in Southern Pines, and Aug. 10 at Broad Street Café in Durham, in-between readings in other cities on the East and West coasts) and I hope you can make it to one of these events as they are fun, especially the way she tries to talk about a species renowned for its sexual behavior by using language that is appropriate for the kids in the audience

The book weaves four parallel threads. The first is Vanessa’s own life. Bonobo Handshake starts where ‘Each monkey’ leaves off. And while the ‘Monkey’ covered the period of her life that was pretty distressing, this book begins as her life begins to normalize, describing how she met Brian, fell in love, and got married – a happy trajectory.

The second thread is the science – the experiments they did on behavior and cognition in bonobos and chimps, and how the results fit into the prior knowledge and literature on primate (including human) nature.

The third thread reports on the conservation status of great apes, especially bonobos, and all the social, cultural, financial and political factors that work for or against the efforts to prevent them from going extinct.

The fourth thread is the country of Congo, where all the bonobos in the wild live, especially its recent history of war and its effects on the local people.

The four threads are seamlessly intervowen with each other, but it takes some time into the book to realize that there is, besides the fact that Vanessa was there and did the stuff and wrote about it, another unifying thread – the question of cooperation vs. competition. Vanessa and Brian sometimes love, sometimes fight: what determined one behavior at one time and the opposite at another time?

For the most part, chimps compete and bonobos cooperate: why is that? And what accounts for occasional exceptions to that rule? When threatened, or perceiving to be threatened, animals become insecure. Chimps deal with that insecurity by lashing out – becoming violent and aggressive, or at least putting out a great show of machismo. When bonobos feel insecure (including when they are very young), they solve the problem (and release the tension) by having sex with each other. If chimps won the national elections in the USA, they would probably rule by fear and force, investing mightily into the military, the police and the prison system, going around the world bombing other countries, declaring various internal “Wars on X”, and generally trying to keep the population fearful, subdued and obedient. Bonobos in such a position would always first try to find out a diplomatic solution: how to turn a stranger, or even an enemy into a friend and ally? Share something! Whatever you have: food, shelter, sex…. Everyone is safer that way in the end.

Of course, there are reasons why chimps are one way and bonobos the other. Food is scarce where chimps live, thus there is competition for it, thus the strongest individual wins, and the winner takes all. The position in the hierarchy is the key to survival. Individualism rules. On the other hand, there is plenty of food where bonobos live, enough to share with everyone, eat enough to get bloated, and still plenty left over to just let rot. Why fight over it? Thus, communitarian spirit rules, and if a big strong male starts to feel his oats a little too much, the females will get together and gang up on him as a sisterhood and beat the crap out of him – a rare exception to their usual non-violence, but an act that restores harmony to the group as a whole.

What can we learn from it? That, being equally related to both species, as well as being smarter, we are quite capable of switching between the two modes of reaction to perceived threats: competitive or cooperative. Some people (probably due to the social environment in which they were raised) tend to respond more like chimps, others more like bonobos, but all are capable of behaving both ways. Thus, all are capable of making choices how to react. And the society as a whole can teach people about the exictence of this choice and, in some general ways regarding different kinds of issues, suggest which of the two reactions is condoned by the society and which one will lend you in jail. Studying both chimps and bonobos, comparing them to each other and to humans, can help us understand this choice better, and what it takes to make one or the other reaction to a perceived threat. And even how to study, as researchers, competitions versus cooperation, something that was historically colored by the social upbringing of individual scientists.

[An aside: this is not really relevant to the book as whole, but if I remember correctly it occurs once in the book, and Vanessa sometimes mentions it in her public speaking and on her blog. She mentions the old trope that we are about 98% identical to both chimps and bonobos. That number denotes the identity of sequences of DNA that is expressed in adult, sexually mature individuals at a particular time of year and particular time of day. It ignores all the unexpressed DNA, individual differences, seasonal/daily changes in expression, and effect of the environment. It also ignores the fact that the sequence is not what really matters - it is how the developing organism (from zygote, through embryonic and post-embryonic development, through metamorphosis, growth, maturation, puberty, adulthood and senescence) uses those sequences to effect the development of traits and the day-to-day response of the organism to the environment. It is not the sequence that matters, but which gene is expressed in which cell at what time and in conjunction with which other genes that matters. The number "98% equal" reeks of genetic determinism, which originates with Adaptation and Natural Selection, the 1966 book by George Williams which corrupted generations of biologists, and 'The Selfish Gene', the 1976 book by Richard Dawkins which ruined generations of lay readers and science journalists. It peaked in late 1990s (I wrote this in 1999) with the hype over Human Genome Project ("Holy Grail", "Blueprint of Life"!) and currently survives only in the realm of that abomination of science we all know as Evolutionary Psychology. There is a lot of literature explaining the poverty of the genocentric and deterministic view of biology, most notably the entire opuses of Stephen Jay Gould and Richard Lewontin, their numerous students and proteges and fans, and an entire generation of evo-devo researchers (the field was spawned/inspired by Gould's 1977 book 'Ontogeny and Phylogeny') and Philosophers of Science (e.g.., Bob Brandon, Bill Wimsatt) who spent some years proving it wrong and, successfully done that, have since moved on to more fertile topics. Actually, one of the easiest-to-read books on the topic for lay audience is titled - What it Means to be 95% Chimpanzee: Apes, People, and their Genes. Saying that humans and bonobos are 98 (or 95, or 99, different numbers are thrown out) percent identical to us is like saying that an airplane and a house are identical because both are built with identical sizes, shapes and colors of Lego blocks - except that one propeller-piece that the airplane has and the house does not. So, Vanessa, drop it. Bonobos and humans are similar because our development is similar, leading to similar phenotypes - not much to do with the sequences of c-DNA libraries. Aside over.]

Conservation of Great Apes depends on humans cooperating to make it happen, but also has to take into account the instrinsic proclivities of different species (chimps, bonobos, gorillas, orangutans and gibbons are all different) towards violence vs. collaboration which dictate the sizes and shapes and organizational schemes of their sanctuaries and eventual wild refuges.

Finally, civil war in Congo is an enormous example of violent competition, but what were its causes? Who chose to compete in this way and why? What was the competition about? Did the end of the Cold War sufficiently weaken the Non-Aligned Movement in a way that reduced the national pride of the people of its member-nations (allowing tribal instincts to take over), reduced the economic cooperation between the member countries (thus sending some of their economies into a downward spiral leading to hopelessness which often leads to lashing out at perceived enemies), or reduced the military cooperation between the members that would scare any potential leader of a tribal movement, or reduced the authority and thus ability of the Movement’s leadership to intervene and prevent wars between the members?

Why did some people come out of war utterly changed – the “living dead” – while others emerged hopeful, energetic and optimistic, full of life and love? How did collaboration of some people help save some of them from murder, and save their psyches from lifelong scars?

Vanessa weaves these four threads expertly and, at the end of the book, you cannot help but care about all four! It is a fast and easy read, you never feel bored or inundated by information, yet you end the book with vastly more knowledge than when you began. And once you know about something enough, you start caring.

I remember as a kid, before the Internet, trying to find something to read after I have finished all 20 library books I took out and still having a couple of weeks of boring vacation ahead of me. Stuck somewhere outside of civilization, with nothing else to do, there was nothing else but to explore the enormous leather-bound classics, each thousands of pages long, each unabridged – stuff that every home has. So I read, slowly and carefully as there was no need to rush, such books as David Copperfield, Pickwick Papers, Teutonic Knights, Moby Dick, Les Miserables, The Road to Life and Martin Eden and others. Being a kid, I did not know anything about any of those topics, and these ancient authors LOVED to write lengthy treateses on various topics over many pages, yet, by getting informed about them, I got to care about Victorian England, Medieval Religious Wars in Poland, classification of whales (and how Melville got it horribly wrong), Paris sewers, educational reforms, and the hard life of becoming a writer. Once, when I contracted something (rubella? scarlet fever?) that made me sick for a couple of days but contagious for another three weeks, with nothing to do at home, I read the unabridged five volumes of War and Peace – at the beginning I did not, but at the end I did care about Russian aristocracy and military strategy (or “how to lose a land war in a Russian winter, part I”).

I don’t know about you, but before I picked up ‘Bonobo Hanshake’ I cared about Vanessa, being a friend, and was thus interested to see what happened after the ‘Monkeys’ book was published. I was interested in bonobo behavior (as we discussed it a lot back in grad school – I did my concentration in Animal Behavior and was a part of the Keck Center for Behavioral Biology) especially as I did not follow the scientific literature on it over the past 6-7 years. I had no idea how endangered bonobos were, nor did I know anything about the civil war in the Congo (and how it is related to the civil war in Rwanda). And while Vanessa did not emulate the 19th century writers, and instead of long chapters on each topic she intertwined brief updates on each of the four threads within each short chapter, I still learned a lot – enough to start caring about the apes, about the people of Congo, about the primatologists working in dangerous places, about individual bonobos and individual Congolese people whose lives intersected Vanessa’s over the past few years. More you know, more you care. So, even if the four themes of this book do not automatically excite you, I suggest you pick up the book – a couple of hours later, you will deeply care about it, know more, want to know even more, and will feel good about it.

I first saw Phaedra Boinodiris speak as the opening speaker at TEDxRTP (my review) back in March, but this was a different kind of talk, geared more towards scientists and science communicators.

I remember playing Pong when it first came out. I remember spending many hours back in 1980 or so playing The Hobbit on Sinclair ZX Spectrum. And I played many games at arcades (still not knowing which games started out as arcade games adapted to computers and which the other way round). Then I quit playing games for a couple of decades until my kids were ready for them. I loved Zoombinis – an amazing game of logic and a brilliant preparation for taking IQ tests! I loved Richard Scarry’s Busytown – the one and only game I know about infrastructure, where players build stuff and deliver it to others for the good of the town – from baking bread to paving roads – learning along the way how those things are done.

And sure, Phaedra Boinodiris started with a slide depicting Pong (to the chuckle of the audience) but soon got into the real stuff – the serious gaming and the story of how she got involved in developing such games, as well as about studies of gaming and how different kinds of games help develop different real-work skills, from eye-hand coordination to leadership to cooperation. Her first game – INNOV8 – was developed as a prototype, a proof of concept, in only three months and instantly became a huge hit. It is used by businesses and business schools around the world to teach Business Process Management. It is essentially a first person shooter game (without guns) in which the player is brought as an outside consultant into a company where s/he has to figure out the flow, the bottlenecks, etc. (including by interviewing employees, as well as data-sheets) and experiment in making it more efficient. The 2.0 version came soon after, adding such problems as traffic, customer service and supply chains.

Click here to view the embedded video.

The next game, recently announced and coming out in October 2010, will be a Sim-City-like serious game CityOne, designed to help city planners, town councils, citizens, and engineers plan better, more efficient infrastructure for their cities. Put in your city’s specs and start building new infrastructure, see how much it will cost, see what problems will arise, see what solutions are available – probably something you could not have thought of yourself and may be surprised.

As I am currently reading ‘On The Grid’ it occured to me that the developers of CityOne should read that book, and that Scott Huler should be given a test-run of the game, perhaps for him to review for Charlotte Observer and Raleigh News&Observer and the local NPR station. And for Science In The Triangle, of course.

The store was packed. The store sold out all the books before Scott was even done talking. The C-Span Book TV crew was there filming so the event will be on TV some day soon. Scott was also, earlier yesterday, on WUNC’s The State Of Things (the podcast will soon be online here) and the day before that he was on KERA’s Think with Krys Boyd (download MP3 podcast by clicking here).

Scott’s energy and enthusiasm are infectuos. He held the audience captive and often laughing. The questions at the end were smart and his answers perfectly on target. But most importantly, we all learned a lot last night. I think of myself as a reasonably curious and informed person, and I have visited at least a couple of infrastructure plants, but almost every anecdote and every little tidbit of information were new to me. Scott’s point – that we don’t know almost anything about infrastructure – was thus proven to me.

What Scott realized during the two years of research for the book is that people in charge of infrastructure know what they are doing. When something doesn’t work well, or the system is not as up-to-date as it could be, it is not due to incompetence or ignorance, but because there is a lack of two essential ingredients: money and political will. These two factors, in turn, become available to the engineers to build and upgrade the systems, only if people are persuaded to act. And people are persuaded to act in two ways: if it becomes too costly, or if it becomes too painful to continue with the old way of doing things. It is also easier to build brand new systems for new services than it is to replace old systems that work ‘well enough’ with more more modern ways of providing the same service.

There are people who advocate for moving “off the grid” and living a self-sufficient existence. But, as Scott discovered, they are fooling themselves. Both the process of moving off the grid and the subsequent life off the grid are still heavily dependent on the grid, on various infrastructure systems that make such a move and such a life possible, at least in the developed world.

What is really astonishing is how well the systems work, even in USA which has fallen way behind the rest of the developed world. We are taking it for granted that the systems always work, that water and electricity and phone and sewers and garbage collection and public transportation always work. We get angry on those rare occasions when a system temporarily fails. We are, for the most part, unprepared and untrained to provide some of the services ourselves in times of outages, or to continue with normal life and work when a service fails. And we are certainly not teaching our kids the necessary skills – I can chop up wood and start a wood stove, I can use an oil heater, I know how to slaughter and render a pig, how to get water out of a well, dig a ditch, and many other skills I learned as a child (and working around horses) – yet I am not teaching any of that to my own kids. They see it as irrelevant to the modern world and they have a point – chance they will ever need to employ such skills is negligible.

I got the book last night and am about to start reading it – very eagerly so. Scott started with his house in Raleigh and traced all the wires and cables and pipes going in and out of the house to see where they led. He compared what he learned in Raleigh and its various infrastructure experts and officials, to the equivalent services in other geographical places, and traced them back in history. I can’t wait to read the synthesis of all that research. I hope you will read it, too.

Today, I asked Antony Williams from ChemSpider to answer a few questions:

Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Where are you coming from (both geographically and philosophically)? What is your (scientific) background? Tell us a little more about your career trajectory so far: interesting projects past and present?

Hi Bora…thanks for the invitation to connect! Where do I come from? When people meet me they’ll interpret my mongrel accent in many ways assuming that I am from Australia commonly (especially the Canadians) or from England (which is of course the common term for the United Kingdom over here). Well, I am from the UK but I am Welsh, not English. Earlier in life I was going to be a Welsh teacher but it’s been almost 30 years since I had a conversation in Welsh! I grew up in a small village in Wales of less than a hundred people. From there I went to Liverpool University to do a degree in Chemistry. I found Organic Chemistry very easy but really struggled with Physical Chemistry, especially spectroscopy. I found it very challenging but something in my personality, my friends call it a defect, has me prefer a challenge over something that it easy. I tend to take on those things that challenge me and push me rather than those things that are easy. So, naturally, I focused on physical chemistry, specifically spectroscopy, and in my final year of my degree did a summer project on NMR and got hooked. From there I went to London University to do my PhD looking at the effects of High Pressure on Lubricant Related Systems by Nuclear Magnetic Resonance, funded by Shell Oil. I engineered my own High Pressure Vessel made from non-magnetic titanium to stick into a magnet and apply pressures of up to 5kbar to liquids and look at the molecular dynamics under pressure. I was writing software to analyze the data and fit to specific models. Fun times – engineering, chemistry, computing – the type of diversity I like in a project.

From there I went to Ottawa, Canada to work at the National Research Centre (NRC) labs switching from Nuclear Magnetic Resonance to Electron Spin Resonance for about 18 months. It was a great place to work and I truly enjoyed the switch to a new type of spectroscopy. However, NMR definitely had more applications so I switched back to NMR and went to the University of Ottawa to run their NMR Facility, again for about 18 months. Lack of funding and the inability to get new equipment in to run even some of the more mundane modern NMR experiments had me look for other opportunities and move South to the United States to work at Kodak in Rochester as their NMR Technology Leader. There I had the responsibility to set the technology vision for NMR and manage a number of their NMR labs. During that period I was focused on the development of walk-up technologies to provide access to modern analytical technologies in the hands of chemists in a “walk-up” environment delivering robotic control, offline data access and processing and an “analytical LIMS” – a laboratory information management system to track samples, structure and spectra through our lab. We build the first web-based LIMS system, called WIMS (Web-based Information Management System) on Netscape Navigator (remember that?) and got a lot of attention and visits from the LIMS vendors. We developed software systems under the simple adage of “The Web is the Way”…how right we were. That work was done in 1996.

From Fortune 500 America I joined a small start-up chemistry software company called Advanced Chemistry Development. I joined as their product manager for NMR and over the next few years grew the product line into the industry leader for NMR prediction, for third party NMR processing and databasing and, one of the best undertakings of my scientific career, a platform for Computer Assisted Structure Elucidation. I had the opportunity to work with some of the best small molecule NMR jocks in the world, an incredible team of developers and scientists at ACD/Labs and then move my skill set outside of NMR. I managed the development of an entire analytical data management system (ADMS) covering Nuclear Magnetic Resonance, Mass Spectrometry, Chromatography, Infrared Spectroscopy and a myriad of other analytical techniques. I managed the structure drawing software, ChemSketch, that has had over a million downloads as it is now freeware, and the nomenclature product line for generating systematic names from structures and converting names to structures. The product lines became so successful that we had to bring in a group of other product managers who could focus on the individual product lines. I became their Chief Science Officer with a major focus on business development but always kept my hands in direct product management, marketing and sales. My passion remained the application of software to data handling, manipulation and delivery to scientists and trying to extract as much information as possible from available data.

A few years ago I floated an idea inside ACD/Labs regarding how it might be possible to index chemical compounds within an organization. Not just ones sitting inside a structure database but those represented in documents, reports, papers, publications, patents and represented by chemical names and structure images. It would require the culmination of multiple technologies including entity extraction techniques to find chemical identifiers, algorithms and look-up dictionaries to convert names to structures and software to convert structure images to structures. The intention was to index inside a central database and provide a tool to structurally index the network. We never moved the project forward because there was too much going on.

A couple of years later I was working extreme hours, focused a lot on sales, marketing and business. While it was fun there was a creative part of me not being exercised and I decided to start a hobby project to stress that particular muscle. I’d been watching what was going on with PubChem and a number of other online databases such as DrugBank. Web technologies had come a long way and I implicitly still believed in the “web is the way”. The concept of spidering an organization’s network had expanded to spidering the internet. Admittedly a major undertaking, a lot of the tools were coming together to allow it to happen. A few of my friends and I got together to create a platform for centrally indexing chemistry on the internet with the intention of linking chemical compounds to related resources on the web. And so ChemSpider was born.

Once ChemSpider went online as a structure searchable database of about 10 million chemicals we expanded the database by adding data from various other data sources, added functionality to query the data in various ways and added various services to allow organizations to tap into the resource we were building. Our target shifted over the next couple of years to one of building a structure centric community for chemists and, as we started to assemble and index the public chemistry on the internet it became clear that there was an enormous quality issue in the majority of the public compound databases we wanted to link too. There were so many errors in these databases it was quite shocking. As we assembled our database we were inheriting these errors and it was clear that we would need to curate these data in both robotic and manual ways. We built a curation platform to allow crowdsourced curation of the data so that users of ChemSpider could help us clean up the data. We added a deposition system for users to deposit their own chemistry and we added a series of tools to allow users to annotate the data and add supplementary information. The database today is almost 25 million unique entities assembled from over 300 data sources. We’ve truly built a community of chemists around ChemSpider with thousands of users coming to the site everyday and with a number of these users curating, annotating and adding data on an ongoing basis.

In June of last year the Royal Society of Chemistry acquired ChemSpider and that is where I am now as the Vice President of Strategic Development.

What is taking up the most of your time and passion these days? What are your goals?

Our focus remains consistent with the original goal of building a central portal for chemists to facilitate traversing the web to find chemistry related data, information and knowledge. At present we remain focused on linking together structure-based data and resources but will eventually expand this out to chemical compounds that cannot be explicitly defined by a chemical structure table…things such as polymers, minerals and mixtures (coal tar, mineral oil, etc.). We busy building curated disambiguation dictionaries and use them as the basis of chemical name (entity) extraction and recognition so that we can perform semantic markup and linking. We continue to expand the breadth and improve the quality of the data on the database with the intention of being able to query and link to every structure-based database that can be accessed via the internet. Chemists have different personae – there are synthetic chemists, analytical scientists, medicinal chemists, chemistry students and teachers to name just a few. While each of these would want to access different types of data for their work and research a Venn Diagram would provide a specific set of query overlaps – let them search by chemical name, chemical structure/substructure and properties. From there they would layer on different expectations about what to do with the result set. The goal is simple…make the internet structure-searchable and provide interfaces and services to allow chemists to query and use the results.

What aspect of science communication and/or particular use of the Web in science interests you the most?

One specific area of interest I have right now is to encourage crowdsourced collaboration in chemistry. My bias at present is to present an environment whereby members of the chemistry community can give/share/contribute/educate/enable/improve chemistry on the internet. In our terms this means allowing them to add their data to the ChemSpider database, annotate what’s already online, validate and curate out the junk. By applying their skills and contributing they can build their own professional profile in the community and bring benefit to other chemists. We are intending to layer on recognition and rewards systems and allow chemists to form connection networks of collaboration. We ourselves are already immersed into the network of Open Notebook Science providing access to services and data allowing others to perform their research. One of our areas of focus right now is ChemSpider SyntheticPages, an online database of synthetic procedures built for the community by the community. There is so much chemistry, so many chemical reactions that are performed in labs across the world but the synthetic details and associated analytical data never sees light of day and never gets published. It might make it into a thesis but then that will get put on the supervisors shelf or in a library somewhere. Despite the fact that these can be electronically enabled and discoverable the reality is it hardly happens. If we can get just a fraction of the chemistry community to donate one SyntheticPage a week the database will explode. As it’s a free resource chemists have much to benefit. The challenge is to how to encourage a chemist to invest some of their time in writing up their procedure and putting it online. Contributors to date have commented that if its already in electronic format it might add another 15-30 minutes to their day but the result is public exposure of the work, a permanent record of value to other chemists, a public profile for the submitted (including a digital object identifier for the resume!), and an opportunity to engage the community as they can provide feedback and comments. Everyone wins.

How does (if it does) blogging figure in your work?

I don’t blog as much as I used to simply because I don’t have as much time on my hands. When ChemSpider started I was “dragged” into blogging because of some attacks made on ChemSpider made by very vocal members of the blogosphere. I couldn’t figure out how to defuse some of the misinformation and accusations being made about our efforts with ChemSpider except to become a participant in the blogosphere. I found that blogging became a great way for me to engage the ChemSpider users and get their feedback on ideas for improving the service, to communicate new functionality in the system, to express my views of things going on in the community and to generally release creative expression again through writing.

The ChemSpider blog remains a way to communicate what we’re up to in terms of new developments on ChemSpider and other Cheminformatics projects internal to RSC. It also gives me a voice to comment on what’s going on in chemistry that interests me, what’s happening in the world of Open Science and engaging our users in dialog.

How about social networks, e.g., Twitter, FriendFeed and Facebook? Do you find all this online activity to be a net positive (or even a necessity) in what you do?

Facebook for me, at present, is more of a personal tool in terms of interacting with my friends and family in the UK and around the world. I use Twitter quite regularly (as @ChemSpiderman) and certainly while I am sitting in conferences and seminars. I have found Twitter surprisingly useful, more than I had ever imagined when it first showed up on the scene. My interactions via Friendfeed are certainly useful and I stay connected to certain groups of people on there and stay connected and informed. While each of these takes time it is definitely a net positive, though I would clarify, not a necessity for what I do. I am definitely an advocate for LinkedIn and find the networking aspects of that platform in particular very enabling.

When and how did you first discover science blogs? What are some of your favourites? Have you discovered any cool science blogs by the participants at the Conference?

I first discovered science blogs when I was dragged into the blogosphere by some particularly negative commentaries that were being made about ChemSpider. Lots of judgments, the majority of them not fact-based, were made about what we were trying to achieve with ChemSpider. As they say however, “no press is bad press” and once the fire was lit I entered the blogosphere to respond to the accusations. Without doing so I feel that our reputation would have been very negatively tarnished. It is one of the downsides of the blogosphere unfortunately…people get to say whatever they want, whatever they perceive and, in certain cases have no facts or data to back up their claims. That is when things get very interesting and engaging though!

My Google Reader follows a number of bloggers from my domain. I have a particular appreciation for the insights of Derek Lowe on his “In the Pipeline” blog. I follow Cameron Neylon, Jean-Claude Bradley, Egon Willighagen, Milkshake’s “Org Prep Daily“, Paul Docherty’s “Totally Synthetic” and many others of a similar nature. I had to slim down what was feeding the reader recently as following too many people was becoming overly distracting. I didn’t start following any particular blogs after the ScienceOnline conference but I do watch a lot more people via Twitter now and, when they tweet a post of interest, I navigate over to their blog. Twitter has become another way to link me into blogposts of interest without me overpopulating my reader.

What was the best aspect of ScienceOnline2010 for you? Any suggestions for next year? Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?

ScienceOnline was fun. I attend a lot of conferences in a year but the energy at ScienceOnline is simply contagious. The level of engagement and contribution far outweighs that I have experienced at any other conference other than the two SciFoo meetings I have attended. Participants at these types of meeting are there to do more than listen. They want to speak…they want to engage and they want to share their opinions. At many conferences there are blocks of time when I am not in sessions. At ScienceOnline there were too many sessions I wanted to sit in on and couldn’t. A much better situation! I walked out of the meeting with new connections, new collaborations and new possibilities. Definitely worth attending.

My one embarrassing moment was when I stood up to do the Lightning (Ignite) Talk at the dinner and hadn’t read the rules of engagement as it were. A pure oversight on my part regarding the flow of the Ignite Talk it actually worked for some strange and unknown reason. Keep the Ignite Talk format next year at the dinner…they were great fun.

It was so nice to see you again and thank you for the interview. I hope to see you again next January.

Monday, May 17

BizMix: A Professional Approach to After-hours Business Connections

5:00 – 7:00pm

The Matthew House, 317 West Chatham Street, Cary, NC 27511

Looking for a business after-hours that’s worth your time? Benefit from a structured setting, connect with leaders and meet our reporting staff.

$15 Triangle Business Journal subscribers; $25 others. Read more here.

Tuesday, May 18

Widening the Pipeline: Excellence in STEM Education (Luncheon)

12:00 – 1:30pm

CED’s Entrepreneurship Center, 100 Capitola Drive, Durham, 27713

How Do We Build the Pipeline of Next Generation STEM Employees? Join the Contemporary Science Center for lunch as we explore and discuss with award-winning Science, Technology, Engineering & Math educators from Charlotte and Raleigh.

Registration $20. Register here.

TARDC May Lunceon

12:00 – 1:15 pm

RTP Headquarters, 12 Davis Drive

Speaker: Dr. Maria Escolar, Director of the Program for the Study of Neurodevelopmental Function in Rare Disorders at UNC Chapel Hill. Lunch will be provided.

Free for TARDC members; $35 others; $25 CED members. RSVP to rousseau@rtp.org

Wednesday, May 19

President’s National Export Initiative Luncheon

11:30am – 1:00pm

Hotel Indigo, 151 Tatum Drive, Durham, NC 27703

TOPIC: President’s National Export Initiative; Speaker: Ro Khanna , Deputy Assistant Secretary, U.S. Department of Commerce, International Trade Administration, Office of Domestic Operations.

Free. More info here.

CED’s BioTech Forum

5:30 – 8:00 pm

North Carolina Biotechnology Center, RTP, NC

During this presentation and interactive panel discussion we will answer several key questions to provide insight into what will likely drive the pharmaceutical and biotechnology industries’ partnering efforts moving forward.

Find out more here.

Speed Networking in the Triangle

5:45 – 8:45pm

Wyndham at RTP, 4620 South Miami Boulevard, Durham, NC

Based on the format of speed dating, attendees will have five minutes to network with each new person you meet. Once the five minutes is up, you will move to the next person and continue networking.

Only 50 attendees allowed! Purchase a ticket here.

Thursday, May 20

If It Isn’t Broke, It Will Be! Reinvent your Business Model

11:30 – 1pm

CED Headquarters, 100 Capitola Drive suite 106 Durham , NC 27713

Participants will focus on evaluating, creating and re-inventing current business models.  This seminar teaches state-of-the art methods that produce transformative ideas and solutions.

$20, including lunch. Sign up here.

Quality In BioPharma Conference (through Fri, May 21)

8:00am (5/20) – 5:00pm (5/21)

NC State University, Centennial Campus, 2410 Campus Shore Drive #218, Raleigh, NC 27695

The focus of the two-day event will be Environmental Monitoring in Biomanufacturing, and will have noteworthy talks, discussions, and networking events for professionals involved in the Quality, Manufacturing, Environmental Microbiology, and Process Engineering areas of the industry.

Register here.

Friday, May 21

BTWW: Cyclists’ Breakfast at RTP HQ

7:00am – 9:00am

Cyclists can mingle and enjoy free breakfast
courtesy of the Research Triangle Foundation.

Saturday, May 22

ProductCamp RTP: Share In The Innovation!

8:00am – 6:00pm

Cambria Suites @RDU Airport, 300 Airgate Drive, Morrisville, NC‎

In the spirit of BarCamp, ProductCamp is a collaborative, user organized unconference, focused on Product Management and Marketing.

Register online here.

Ongoing (All Week)**

Bike to Work Week

All around the Triangle!

Sponsored by GoTriangle.

Find out more here.

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To view a complete calendar of RTP community events, please visit the Science in the Triangle calendar.