Endless Knots

"As networks become more efficient, they become more modular"

Carl Zimmer's National Geographic article, "The Parts of Life," merits reading -- and rereading. The structure of networks, meaning their level of complexity, is difficult to understand but Zimmer moves carefully to lay out an experiment conducted by Jeff Clune (University of Wyoming), Jean-Baptiste Mouret (Pierre and Marie Curie University, Paris), and Hod Lipson (Cornell University). If I've got this right, their experiments indicated that "minimally-linked networks spontaneously produce[s] modules."

Why is this important? Modules are the basis of life -- parts make up wholes, what Jeff Stamps talked about in his book, Holonomy, drawing on Arthur Koestler's elegant term holon, meaning whole-part. As Zimmer says:

We’re made of parts. Our skull is distinct from our spine. Our liver does not grade subtly into our intestines. Of course, the parts have to be connected for us to work as a whole: a skull completely separated from a spine is not much good to anyone.

This is obvious in physical and biological systems, viz. see Herbert Simon's classic, "The Architecture of Complexity." But what about social systems? Do minimally linked networks/organizations spontaneously produce modular groups of mini-networks that can specialize to solve problems?

What is just-the-right-number of links to produce just-the-right-kind of modules to get work done? Complexity scientist Stuart Kauffman has written about this, postulating that there is some apt number of links to create that "place" between order and chaos. See this white paper that we wrote some time ago, "Organizing at the Edge of Chaos," which plays with the tradeoff between too many links and too few in organizations.

A Nobel or "Milner" for Organizational Innovation?

"Cosmic Inflation" by Don Dixon

Best I know, no one awards a prize for breakthroughs in organizational thinking, never mind practice. I can't even remember an author receiving one of the literary crowns (authors don't receive money, remember, the largest bag of bucks being the Nobel for literature -- $1.1M-ish awarded to a mere 100 or so folks in all of the world's existence) to any book about business ideas. Wait. I'm a little uninformed and thinking way too narrowly. A serious foray into search reveals this award from Financial Times and Goldman Sachs, which appears to have been cashing out to business book authors (about $50K, not bad) since 2005.

But a quick skim of awardees indicates their works are predictably, given the grantors, about Wall Street, where of course the way the companies and people they write about are organized is not the point. What they're organized for, obviously, makes quite a good story (follow the money)... which suggests this question: Who's going to get the big advance for the book on what these companies' organizational structures might have to do with why they succeed and fail? Ah-hem.

Why is this on my mind? My personal newswire for interesting stuff around organizations, Tom Stewart, whose feed on Facebook often catches my attention, does so again. Today he posts about the new no-strings (so to speak)-attached-prize in physics -- a cool $3M, awarded to each of nine (9!) physicists working on cosmic "inflation," which arguably could also be given to someone on Wall Street. The awarder is one Yuri Milner, a physicist-turned-social-media entrepreneur (he's no dope). Need I tell you that part of his $12B fortune comes from his early investment in Facebook, where, naturally, I saw Tom's post about this prize?

Here's, in part, how Nature reports it (though they missed the string-theory twist):

“The intention was to say that science is as important as shares trading on Wall Street,” Milner told Nature. The prize money comes with no strings attached, although Milner hopes that the theorists will contribute to a new lecture series for the public. Milner also plans to create an annual $100,000 New Horizons prize for young researchers and an ad hoc version of the Fundamental Physics Prize that can be won at any time “in exceptional cases”, the website says. According to the rules of the prizes, anyone can be nominated, and future prizewinners will be selected by a committee of all previous ones.

So here's my message to the next Sloan/Insead/Said grad in management who figured out how to make something of him/herself. Start a prize for "quantum organizational breakthroughs." Even call it that and it will sound scientific so people will think it's important. There's a lot of it going around these days.

Citizen scientists -- cracking the universe's code

Thanks to Adam Lerner of Solvable, this fabulous article by Gareth Cook in Nov 11, 2011, Boston Globe, "How crowdsourcing is changing science." Remember SETI, which has been around almost since the birth of PCs, when many of us, myself and my hubby included, lent our computers (not literally) to this incredible project to process vast amounts of data about the universe? A similar idea is transforming all manner of scientific investigation.

After a treasure trove of ancient papyrus was found in Egypt, archeologists were perplexed by the maddeningly slow nature of translating it. So, they went to the source of speed: the Internet. Read on from these choice grafs - great reporting by Gareth Cook:

But a few months ago, the papyrologists tried something bold. They put up a website, called Ancient Lives, with a game that allowed members of the public to help transcribe the ancient Greek at home by identifying images from the papyrus. Help began pouring in. In the short time the site has been running, people have contributed 4 million transcriptions. They have helped identify Thucydides, Aristophanes, Plutarch’s “On the Cleverness of Animals,” and more.

Ancient Lives is part of a new approach to the conduct of modern scholarship, called crowd science or citizen science. The idea is to unlock thorny research projects by tapping the time and enthusiasm of the general public. In just the last few years, crowd science projects have generated notable contributions to fields as disparate as ecology, AIDS research, and astronomy. The approach has already accelerated research in a handful of specialized fields. And it may also accomplish something else: breaking down some of the old divisions between the highly educated mandarins of the academy and the curious amateurs out in the world.

 

 

Dr. Walsh: Get your PSA test, fellows

If you're a man - or if you care about men, then you must be following the current controversy over whether men should be regularly screened for rising PSA levels. The US Preventive Services Task Force, whose membership can be found here and which notably has no urologists on it, has recommended that healthy men no longer receive the blood test that measures the prostate specific antigen.

Last night, I had the chance to talk with Dr. Patrick Walsh, who is among the handful of most famous urologists in the world, and whose book, Dr. Patrick Walsh's Guide to Surviving Prostate Cancer, is the go-to resource for any man with prostate cancer. Read up here for Dr. Walsh's contributions to prostate cancer detection and the perfection of nerve-sparing surgical techniques that have vastly improved outcomes for men undergoing prostatectomies.

We first met Dr. Walsh two-and-a-half years ago when my husband was diagnosed with Stage 2A prostate cancer, found as a result of a suddenly rising PSA. Thanks to our friend, Dr. Tom Lamont, who introduced us to Dr. Walsh (they both have served on the editorial board of New England Journal of Medicine), we were able to get detailed advice from Dr. Walsh at that time. (Yes, for those of you following our family's saga, my husband had prostate cancer a year before he was diagnosed with pancreatic cancer.) Just as one tiny example of Dr. Walsh's influence: Dr. Andrew Wagner, the urologist at Beth Israel Deaconess Hospital in Boston who operated on my husband, was trained in Dr. Walsh's lab.

But I'd never met Dr. Walsh face-to-face until last night and so was very pleased to be able to talk to him at a gala this weekend honoring Dr. Lamont's 40 years of contributions to medicine. That tribute deserves a post of its own but suffice to say when 280 people show up from around the world to honor a single doctor, then you know that person has had quite an effect on medicine, in Tom Lamont's case the field of gastroenterology. I am extremely lucky to count Tom and his wife Emily Lamont as among my closest friends.

I digress. As soon as I saw Dr. Walsh last night, I asked him his opinion about the PSA controversy. He was unequivocal. Men should continue to have their PSAs monitored. Here's what he said: "29,000 American men's lives were saved this year because they had their PSAs monitored." He's a urologist. He's been treating prostate cancer for decades. He's now retired so has no vested personal interest in bringing more people into his own practice.

And so, men friends, before you cavalierly forego having your PSA checked, listen to what someone who's been working in the field for his entire career has to say. We don't have any data on how much research the panel saying to skip PSA tests actually did, how detailed the data was that they were looking at, how statistically accurate it was, how trained they were to make their evaluation, and what other factors might have been influencing their decisions.

Having just endured a family member's death from another, albeit incurable, cancer, this is not trivial stuff. As yet another doctor friend told us when my husband was considering whether to have his prostate removed, "You don't want to die from prostate cancer." It's a very difficult cancer to endure. Especially when it's preventable.

 

Dance your PhD

Enough of those dry defenses. Science, the esteemed journal of AAAS, the weekly (or is it a daily) which I, for one, don't normally associate with modern dance (or rap), sponsors an annual "Dance your PhD" contest and I'm rooting for my friend, Mount Sinai Medical School PhD-candidate Kate Collins (scroll down for her bio).

Here's how the brilliant Kate (the lead dancer/cell of the basal nucleus of the amygdala!) explains her submission to the contest (I just like the moves, never mind that my nephew, James Murrough, plays the only male role in the video): 

When first encountering a fear-eliciting stimulus, animals evince innate defensive behaviors, such as freezing. With time, most are able to overcome their automatic fear reactions and regain the capacity for organized, goal-directed action. Rodent research suggests that activity in the central nucleus of the amygdala drives stereotyped, automatic fear responses. Activity in the basal nucleus of the amygdala, conversely, appears to enable flexible and adaptive fear responses. Evidence suggests that the central and basal nuclei compete for dominance during fear, with the "winning" (more active) nucleus determining the behavior expressed.

Do similar patterns of neural activity subsume these behaviors in humans? In Kate Collins' dissertation, she is exploring the neural substrates of both automatic and goal-directed fear responses, and the transition between the two opposing states.

And now, for your enjoyment, neural substrates performing to Finger Eleven's "Paralyzer" and Young MC's "Bust A Move."

Dance Your PhD - Bust A Move: Taking Action in the Face of Fear from Alex Susse on Vimeo.

 

 

The future of computer science -- in one hour

I had the chance to listen to one of the icons of computer science recently. John Hopcroft, IBM Professor of Engineering and Applied Mathematics in Computer Science at Cornell, gave a talk on future directions in theoretical computer science to a standing-room-only crowd at Worcester Polytechnic Institute.

While this is not my field, I was interested to hear how someone who's been in the field -- and received just about every award -- might be thinking about the issues most likely to impact the development of the theory of computer science, especially when addressing a throng of young people who will have to execute against those challenges.

Here are my notes, mainly unedited. I hope they make sense.

The early focus was on making computers useful; now they are useful and as we move forward, we need to develop theory that supports new directions.

While we google quite liberally now, in the future there will be new kinds queries that produce reasonable answers to specific questions, like "which car should I buy?" The "system," knowing all your prior searches (hello, privacy) will be able to cluster results of those searches in "temporal cluster histograms" (which he then showed but which I can't remember and which I'm not now going to google...)

He gave the example of googling Michael Jordan. If you're a sports nut, you'll of course get this Michael Jordan but if you're a computer scientist then you would be looking for this one. The future computer will of course know this -- and know that I wouldn't be looking for either one, to be honest.

Which of course led him to privacy issues, which he parsed nicely in regard to electronic medical records. Your doctor needs your whole record; your insurance company needs only the information pertaining to your last visit; a researcher needs statistical information with no independently identifiable info.

(My next note is one of those that I recorded solely because it sounded like poetry -- "zero knowledge proofs" -- but I have no clue as to what it means.)

His next point was a very good one: in the future (which, I believe is actually right this minute), data sets will be so large that we'll only be able to analyze them by sampling them. As one of the computer scientists at the lecture explained to me, think of Facebook's data on 800 million users. There are no machines large enough to bring that magnitude of data into memory -- thus sampling. Kind of like being in the ice cream store and unable to eat all those gallons as there's not enough room in our tummies -- thus we sample. Well, not exactly, but you get the point.

But before I leave this, a few more thoughts because as we collectively dive more deeply into understanding our vast (and vastly growing social networks, about which more below), we need to better understand the implications of what it takes to fully analyze gigantic amounts of data. Which brings me to the classic large data problem that many may remember: SETI, where many of us gave/have given over our machines to the "search for extraterrestrial intelligence," lending our computers to computationally solve that bigger problem of finding such intelligent life. In that example, the SETI scientists send us a piece of the data along with the algorithm and our computer runs "the package," returning a solution that the SETI folks can then combine with others' solutions.

Graph algorithms, the math by which we analyze network maps (who's connected to you, how many people/degrees are between me and you, what your favorite Facebook group looks like), are different.

Whereas SETI-like data can be partitioned for individual machines to compute pieces of the whole solution, graph algorithms, which is what make up network maps, cannot. Why? Because the graphs only  can be analyzed when the algorithm can see all the links between the nodes, which may not be included in the selected parcel. Thus, we can't parcel out pieces of Facebook's 800 million users' data for analysis on your machine and mine. Notice, for instance, the recent study of how sentiments vary on Twitter -- "Drawing on messages posted by more than two million people in 84 countries..."-- which is to say a mere fraction of the tweets.

Big problem which I'll come back to in later posts but in the meantime, let's return to Dr. Hopcroft's lecture where he...

Then used the word "permute," which I'd never heard before thus recording it. No clue once again. Is this a mathematician-type really meaning permutate? Dunno.

Next example re: privacy had to do with GPS only tracking major roads when minor roads often are the better route. Local drivers always take them but they don't show up when you ask for best routes on your GPS. Getting that info requires sharing back road routes but alas, do you want to be identified everywhere you're driving?

This led to his talking about how to look up weather patterns in your local neighborhood, which he does so that he can figure out whether he can walk home in the rain. Walking is his preferred mode of travel -- and he's figured out how to look at current weather maps and adjust for small time differences so that he knows when to leave his office.

And then he got more fully into some stuff that brushes up against the areas we're all interested in: social networks.

An early measure of the quality of communities was thought to be conductance, a connectivity measure from graph theory that indicates how fast you can go from one part of the graph, er, network, to another. But, it turns out, Dr. Hopcroft says, conductance is not the right model for communities.

Instead, we need to look at overlapping communities, massively overlapping communities with common cores that have very fuzzy boundaries. In fact, we need different algorithms in order to understand different communitites.

We need, he said, a "theory of sparse vectors." (I need a graph theorist for this one.)

He then went on to talk about the need for the new generation to incorporate the "law of large numbers" in their thinking. "When I was grad student," he said, "we analyzed graphs with only 7-8 'edges,'" i.e. the connection/link between two nodes. Now, as he had said earlier, the number of edges is so huge that they don't yet fit into any computer memory known to humans.

"There's something fundamental about giant components," he said, something I took to mean that we still don't understand.

My last note about Dr. Hopcroft's lecture is my favorite line: "We have to upgrade our intuition," i.e. it just plain doesn't work in the new world. What's going on now in understanding patterns of higher dimensions is counter-intuitive. Our intuition, he said, was formed in the world of 2 and 3 dimensions but now we live in a world in which datasets are growing exponentially. Touche.

Assistant professor appointment- our very own Dr. James Murrough

It's hard not to crow about this one. Nephew James Murrough has just been named assistant professor at the Mount Sinai School of Medicine. James's career is quite astonishing at such a young age -- and he's doing unique work in the field of psychopharmacology of mood disorders. For such a Phish fan, it's a noble pursuit. So unbelievably proud of him - and I have a hundred pictures of him from a very young age on that I'll refrain from posting in tribute to his professionalism, opting instead for this one from the Mount Sinai site. Here's an excerpt from the announcement:

We are pleased to announce that Dr. James Murrough has been appointed as Assistant Professor in the Department of Psychiatry as of July 1, 2011.  In this capacity Dr. Murrough will conduct cutting-edge clinical trials and neuroimaging research in the Mood and Anxiety Disorders Program (MAP) under the direction of Dan Iosifescu, M.D.; he will also be seeing patients in the FPA with a focus on psychopharmacology of mood disorders. In parallel, Dr. Murrough has received a secondary appointment as Assistant Professor in the Department of Neuroscience and has been named a member of the Mount Sinai Friedman Brain Institute.
 
Dr. Murrough completed his undergraduate studies at Emory University in Atlanta, GA where he earned a B.S. in neuroscience and behavioral biology. He completed a 1-year NIMH-supported research training program in cognitive neuroimaging at Weill Cornell Medical College in New York prior to obtaining his M.D. from Tufts University Medical School in Boston.
 
Dr. Murrough joined Mount Sinai School of Medicine in 2005 for residency training in psychiatry, where he subsequently excelled in both clinical care and research. Dr. Murrough became the first psychiatry resident to participate in a specialized physician-scientist research track and now serves as a mentor to current psychiatry research-track residents. Following completion of his residency in 2009, he was awarded the MSSM-AstraZeneca Research Fellowship in Experimental Therapeutics and Clinical Neuroscience of Mood Disorders. For the past two years Dr. Murrough was a research fellow in the Mood and Anxiety Disorders Program under the mentorship of Drs. Dennis Charney, Dan Iosifescu, Alex Neumeister and others.
 
Dr. Murrough’s research focuses on biomarker and novel pharmacotherapy discovery in mood disorders with an emphasis on MR imaging and PET technologies to characterize brain systems that regulate emotion and the impact of therapeutics on these systems.  Dr. Murrough has been very productive during his fellowship, publishing multiple articles in prestigious peer-reviewed scientific journals, including Nature Medicine, Archives of General Psychiatry, the American Journal of Psychiatry, and Biological Psychiatry. Dr. Murrough has received independent research funding from NARSAD, the American Foundation for Suicide Prevention and the NIH CTSA-supported KL2 Scholars Program.
 
...Dr. Murrough will continue to develop clinical and translational projects in mood disorders that cut across traditional boundaries in psychiatry and neuroscience in an effort to identify mechanisms of disease and novel therapeutic interventions that are urgently needed for...patients.

Cancer Commons - another open-science initiative

While we're on the subject of cancer, an unfortunately "popular" topic of late in my world, thanks to Patrick McGovern at Lybba (check it out, another great resource for good health and better medicine, especially for the little ones), I've learned about Cancer Commons, which is taking the next step in solving the cancer koan. This cutline carries the gist: "What if the thousands of "N of 1" experiments conducted daily by 30,000 oncologists could be coordinated into a giant adaptive search for better, individualized treatments?"

The move to aggregate data is very popular in medicine these days -- and difficult given the legacy systems of different institutions and the addiction to paper records that leaves the medical field woefully behind industry in its database interoperability.

There are many efforts to address this, e.g. I recently learned about Improve Care Now, which links pediatric GI docs and their data, thus providing them with access to greater research pools than their practices alone can provide. (If you know a child or teen with Crohn's or colitis, check it out--I'm oversimplifying their groundbreaking work here.) And there are the "translational science" awards from NIH that are attempting to accelerate the time between "bench and bedside," typically an astonishing 17 years, this according to a Principal Investigator working on one of these grants.

Comes news now of another approach being tried out in cancer that incorporates data, individualized treatment, and networking. Here's a pull from Cancer Commons' white paper. Having spent so much time online in the past nine months, reading listservs, trying to fathom what clinical trial protocols really hold promise, and whether "our" patient might be a candidate...and feeling, regardless of a very committed circle of friends, alone with the disease nonetheless, I appreciate any effort to pool information and link up researchers, clinicians, and patients. Take a look:

Modern molecular biology supports the hypothesis that cancer is actually hundreds or thousands of rare diseases, and that every patient’s tumor is, to some extent, unique. Although there is a rapidly growing arsenal of targeted cancer therapies that can be highly effective in specific subpopulations, especially when used in rational combinations to block complementary pathways, the pharmaceutical industry continues to rely on large-scale randomized clinical trials that test drugs individually in heterogeneous populations. Such trials are an extremely inefficient strategy for searching the combinational treatment space, and capture only a small portion of the data needed to predict individual treatment responses. On the other hand, an estimated 70% of all cancer drugs are used off-label in cocktails based on each individual physician’s experience, as if the nation's 30,000 oncologists are engaged in a gigantic uncontrolled and unobserved experiment, involving hundreds of thousands of patients suffering from an undetermined number of diseases. These informal experiments could provide the basis for what amounts to a giant adaptive search for better treatments, if only the genomic and outcomes data could be captured and analyzed, and the findings integrated and disseminated.

Toward this end, we are developing Cancer Commons, a family of web-based open-science communities in which physicians, patients, and scientists collaborate on models of cancer subtypes to more accurately predict individual responses to therapy. The goals are to: 1) give each patient the best possible outcome by individualizing their treatment based on their tumor’s genomic subtype; 2) learn as much as possible from each patient’s response, and 3) rapidly disseminate what is learned. The key innovation is to run this adaptive search strategy in "realtime", continuously updating disease and treatment models so that the knowledge learned from one patient is disseminated in time to help the next.

Cancer Commons is being developed one cancer at a time, beginning with melanoma.

Copernicus? Galileo? Einstein? -- just to name some Westerners...

NY Times reports great distress among psychologists today ("Journal's Article on ESP Expected to Prompt Outrage"):

One of psychology’s most respected journals has agreed to publish a paper presenting what its author describes as strong evidence for extrasensory perception, the ability to sense future events.

The paper describes nine unusual lab experiments performed over the past decade by its author, Daryl J. Bem, an emeritus professor at Cornell, testing the ability of college students to accurately sense random events, like whether a computer program will flash a photograph on the left or right side of its screen. The studies include more than 1,000 subjects.

Reporter Benedict Carey does a good job of laying out why this is so upsetting to people - the principal reason being that "[c]laims that defy almost every law of science are by definition extraordinary and thus require extraordinary evidence." According to objectors, the researchers failed to take this into account, plus, for shame, they didn't use "topflight statisticians."

Point: if the scientific community only allows in ideas that do not defy "every law of science," how can any new knowledge, ground-shattering as it might be, become the new laws? Right, Copernicus and friends?

 

Now this is origami

Again, thanks to Ian Lamont, the amazing folds of Brian Chan. With Brian's permission, I'm posting a few here not yet available on his site, and leading off, because we're so close to The 'Tute, this one, the logo of MIT, which is on his site.