Tuesday, March 25, 2008

The Economist Speaks on Consumer Created Health

It looks like the argument that consumer created health is "Unsafe" isn't holding water with patients, or less stodgy doctors. Indeed, according to the Economist, mistakes posted online are typically corrected within two hours as a result of the number of people reviewing them. Loyal readers will recognize this principle as Linus' Law named after the man behind the Linux open source movement. The economist also notes that patients today frequently know more about their conditions than their doctor. I would argue that this evidence is quite damning for medical schools, such as Stanford, that STILL teach young med students that fully informing their patients of risks and alternatives is unnecessary and a waste of their time. Indeed, one has to wonder how long before consumer created health care brings the unsoundness of many clinical practices into full public consciousness. The Economist article can be found here.

Monday, March 17, 2008

Three Great Blogs on Consumer Health

Here are three great places to go if you want to hear the future of patient-empowerment. Clearly, accountability for the AMA, pharmaceutical companies, and individual Dr.'s is on its way. With the rise of Google Health and MS Health Vault, it is clear that consumers will finally begin to get the info that they need to demand accountability. The question in my mind is what the backlash will look like once Americans come to see just how corrupt our current medical system actually is. Much of the abuse that hospitals and Dr.'s commit will not stand up to the coming public scrutiny. I think that many currently smug and elitist Dr.s and insiders are about to feel very uncomfortable with the public outrage coming their way.



http://projecthealthdesign.typepad.com/

http://www.ced.org/

http://e-caremanagement.com/



Saturday, March 15, 2008

Great number quantifying Big Pharm's problems


This article from the Chicago Tribune has lots of good stats for the revenue issues facing Big Pharma as a result of patent expirations. One has to wonder why Big Pharma is slow to embrace Systems and Information Theory, given all the incentive to come up with something new in order to increase top line.


Tuesday, March 11, 2008

Great reference for the future of Nanotech

Wow, I've sure been a bum! Actually, I've been busy as heck networking and researching. I met a great guy over at SRI in Menlo Park who is deeply interested in molecular manufacturing. He even got to paper-signing stage for a strat-up, but the VC backed out at the last minute. His point echoes the newsletter author in my last post. Apparently, the VCs were circling around looking for their next kill after the tech bust. Most of them jumped on the Web 2.0 bandwagon and left nanotech. My contact told me that most of the VCs he met had no basis for evaluating technology whatsoever. He said the few very notable exceptions recognized the investment in basic research that remained. My two cents worth: Because there is so much money on Sand Hill Rd, the smart and established money with institutional clients will move into nanotech where the entrepreneurs are eager and the competition is scarce. Why not move out to a five year time horizon given the potential of the innovations and the fact that institutions would have to re-invest the money anyways.

For a great and comprehensive view of the coming Nano-revolution: check out this comprehensive Road Map over at the Foresight Institute.

Thursday, February 28, 2008


I got this newsletter today, and thought I would pass it along. More confirmation that everything nano is coming. The obvious question is when will it arrive. This author says be patient. I think things will move faster than anyone realizes.


What's Bugging Nano?
By Yiannis G. Mostrous and GS Early

A couple weeks ago in my investment letter The Real Nanotech Investor, my colleague--nanotech scientist and consultant Tim Harper--reflected on a keynote address he gave at a nanotech conference six years ago. He was at the same conference this year and realized that the reason there’s consternation in the nanotech sector right now isn’t that the companies aren’t doing the work; it’s that the venture capitalists (VC) are using an outmoded method for funding, promoting and developing nanotechs.

The model came from working with the dot-coms, and the VCs are using the methodology with nanotech. The problem is nanotech doesn’t fit as neatly into that paradigm, much to the current chagrin of the overzealous VCs.

I’ve been mulling over that concept and Tim’s view that nanotech takes about seven to 10 years to get out of the lab and into a product phase. That doesn’t mean we have another decade to wait for companies to start making money from their research; that’s already begun.

We’re at about the point of inflection where many technologies are taking wing in the marketplace. The problems the VCs face is that these technologies don’t always “plug in” like dot-coms did.

Then, last week, my product manager Josh asked me about Tim’s article and about nanotech in computers. It was then that this edition of Nanotech Investing News was born. Well, that and the following news story.

It was this confluence of stories and ideas that clarified the point Tim was making, the question Josh wanted answered and the reality of nanotech in 2008.

Unlike the familiar dot-com tech run, more often than not, nanotech has to build a medium or industry as well as a product to inhabit the medium, as is the case with a recent story regarding one of my favorite big nano companies, Toshiba. There isn’t a nanotech Internet to hook apps into; there isn’t an equivalent major spending boom for fiber-optic networks and a wide, open telecom environment. There’s just the unsexy scientific and strategic work of innovating and adapting technologies for existing and future markets.

For example, there’s been great theoretical promise for carbon nanotubes in developing smaller, faster silicon processors. As the lithography on semiconductors gets more intricate, copper becomes a less-efficient conductor and will soon reach its limits of advantage.

Nanotubes, organic conductors and other next generation options have been less than ideal because, as mentioned earlier, you have to move away from the complementary metal-oxide-semiconductor (CMOS) computing world that now occupies the planet. That means you have to start building niche equipment for niche applications until the world decides all the CMOS stuff we’ve accumulated is passé, and it’s time to go quantum, nano or organic.

Since that day is a long way into the future, the other option is to find a way to make nano go old school, and plug it into CMOS technology. Sure, it’s kind of unexciting evolutionary instead of revolutionary stuff, but that’s the way the world works for the most part. And after building this cutting-edge carbon nanotube and placing it in a CMOS chip, what kind of speed do we get from this new performer? One gigahertz. Yep, one.

But don’t get too upset; this is actually very good news. This is a proof of concept: You can use nanotubes where you once used copper wires. This is a big deal. Now Stanford University and Toshiba researchers will have to expand their efforts and juice these processors up and see what they can do with more nanotube wires, purer nanotubes, etc.

So now we’re here in the nanotech era, and yet we’re looking at years of research and development (R&D) before we likely see nanotubes running in CMOS equipment.

On the other side of the coin, there’s a story today about the work Nokia Oy and the University of Cambridge are doing on the next generation of mobile phones using nanotechnologies. There’s even a Morph exhibit at the New York City Museum of Modern Art (MoMA).

I see both stories as linked because it’s human nature, especially for investors, to look for the next hot thing. And these two stories link the hope to the reality.

The fact is nanotech is already beginning to change the way we build, fly, ski, ride and dress. Soon our medicines, computers and most of our daily lives will be influenced by various nanotechnologies. But that time isn’t here yet.

It’s coming, but it’s not going to slam down like the dot-com revolution; it’s going to be a tidal shift that happens over time. And although the results will be dramatic, they won’t necessarily be perceptible on a quarterly basis.

Investors should certainly get involved—but responsibly and patiently.

Wednesday, February 27, 2008

Wow, things are moving!

I've been following the advice of a wise man lately, "Seek first to understand before you seek to be understood." As such, I've met a bunch of smart people and dove into a bunch of research. I'm terribly behind in all my reading, but eager to keep plowing through it. Also, I'm behind in creating my first discussion tools. I guess I better start burning some midnight oil!

First, any serious student of the changes going on in Life Sciences should read "Information Theory and Evolution" by John Avery. This man has great perspective. Second, I found some great work from the annals of the history of IT management. My thesis is that we can understand and predict the disruption to traditional Life Sciences organizations by understanding the history of the disruption caused by Object Oriented programming.

Alan Kay, the godfather of OO technology (and also its greatest critic) was a mathematician and molecular biologist:


  • "I thought of objects being like biological cells and/or individual computers on a network, only able to communicate with messages..."

  • "In computer terms, Smalltalk is a recursion on the notion of computer itself. Instead of dividing "computer stuff" into things each less strong than the whole--like data structures, procedures, and functions which are the usual paraphernalia of programming languages--each Smalltalk object is a recursion on the entire possibilities of the computer. Thus its semantics are a bit like having thousands and thousands of computer all hooked together by a very fast network."

  • "Object-oriented design is a successful attempt to qualitatively improve the efficiency of modeling the ever more complex dynamic systems and user relationships made possible by the silicon explosion."

  • "I invented the term Object-Oriented, and I can tell you I did not have C++ in mind."


Check out this article on the Lessons learned from an early, large OO development effort at IBM. The team size was about 150, a number thrown around as a common size for teams working on commercial Life Sciences research projects. On the one hand, some of the lessons learned provide insight into why mother nature manages her IT projects the way that she does to eliminate complexity. On the other hand, other lessons apply to the management issues that a Life Sciences CEO might face in managing an early, large scale Systems-based project.


Friday, February 22, 2008

Too Cool Example of Biology Advancing Altenergy


Moth eyes may hold key to more efficient solar cells from PhysOrg.com

One of the difficulties with solar power is that solar cells are notoriously inefficient. Some of that inefficiency, says Peng Jiang, is due to the fact that silicon is reflective. Jiang, an assistant professor at the University of Florida, tells PhysOrg.com that there are “disadvantages to the anti-reflective coating currently used in solar cells.”



Think of the disruptive power of these efficient, yet cheap to produce solar cells. It's like printing money. In remote locations or the developing world, technology like this could have its greatest impact. Half of all hospital beds today are occupied with a patient that contracted a water-borne illness. Imagine the improvement in world health if water could be boiled and sterilized with energy from this technology.



Future preview of upcoming attractions at the NBB: I just got a great book by John Avery called "Information Theory and Evolution". Also, I've got some great articles from the Santa Fe Institute that can inform our understanding of ADD. I hope to get a post together over the weekend.



Check out this movie of an electron filmed by researchers in Sweden. Does that look a Torus?


Thursday, February 21, 2008

BioX at Stanford and a Change in Focus

I attended the BioX symposium yesterday at Stanford. BioX funds initiatives at Stanford that encourage cooperation across disciplines. It was a great opportunity to see first hand many new technologies for diagnostics that dramatically improve health and relieve suffering. From talking to many bright people and hearing what they have to say, I found a few common points.

1. Most people in medicine are really passionate about what they do. (So am I)
2. Most people in medicine are really brilliant and knowledgeable.
3. Most people in medicine really want to advance their practice methods.
4. Doctors are used to being hailed as experts and believe in their own expertise.

The question that I am now trying to focus on is how does one leverage these points above to encourage medical professionals to support change. If we look at the role of technology in all other fields, it has lowered costs and improved accuracy through automation. Not in medicine. Key to the realization of benefits, such as cost reduction, is changing business processes to leverage the new capabilities and cut jobs. Without changing methods, attitudes, and employee streamlining, there can be no benefit from new technology. Thus, technology can be viewed as a replacement for doctors. People don't like the prospect of working themselves out of a job.

The medical community is beginning to slowly embrace the concept of "Personalized" medicine and "Preventative" medicine. The challenge that I have when speaking with doctors and BioTech researchers is that change can easily become threatening or adversarial. Diagnostics mean facts, and facts are better than opinions. Diagnostics inevitably reduce the room for physician judgment and empower people to make their own decisions. They also have the power to reveal physician mistakes.

When one points out that computer science has advanced Systems and Information Theory way beyond medicine, it has the potential to open a pandora's box. Many have heard the arguments, but don't really grasp it. Many sort of get it, but don't recognize that they are witnessing a paradigm shift. Some are busy making it happen. The real key for me to figure out is how does one "Sell" the benefits of radical change on the basis that it will benefit both patients and doctors? I think the keys are to listen and build trust first and to then position new ideas as the extension of existing and accepted ideas.

Personally, I would like to see physicians redeploy their time on improving access and creating healthier populations for the same dollar spent. For example, people may no longer suffer from catastrophic cancer because cancer will be caught early when it is still easy and cheap to treat. As a result, there would be more dollars elsewhere for basic health care for patients currently under-served. If those formerly under-served patients then avoided the ER or themselves got preventative health care, then there would be even more dollars saved to go to the next under-served patient. Just as important, our working population would be more productive without catastrophic illness, and thus pay more taxes or shrink health care as a percentage of the budget. This point is especially important for baby boomers who want or need to stay in the workplace.

As more health care became productized, it could be exported around the world to further increase access and leverage the same R&D cost over a larger patient base. Cost per patient could plummet, easing the burden on families. Through new and more productive research methods (Systems and Info Theory), orphaned illnesses could become economical to treat. Ultimately, physicians and BioTech researchers would still have plenty to do. It's that their jobs have to be eliminated so that they can perform new ones. At the same time, we would get more value for their time and lessen the burden on society. I believe that the greatest threat to this vision is not physicians per se, but their leaders who derive power and wealth from the current system. Ultimately, I believe that the best moral leadership is leadership that accomplishes its purpose. I believe that a thing acquires purpose by its moral rightness. Perhaps there is common ground in that between advocates of new technology and those who must implement it.

Wednesday, February 20, 2008

The Innovation Gap in Medicine

Yesterday was a busy one full of networking and new ideas. In particular, the event that I attended in Palo Alto last night sponsored by MIT was rather enlightening. It was held at an IP law firm. Naturally, the topic of patents and innovation came up. The way the current system works, many companies are fearful of allowing scientists to leverage research patented by other firms for fear of lawsuits. It seemed that the one measure promoting cooperation was the fact that lawsuits are expensive to prosecute. The view was presented that academic institutions and scientists "ultimately do what's right for patients" despite minimal public scrutiny. The NBB View: POWER CORRUPTS.

This quote from the following white paper over at Genstruct characterizes the innovation problem well:

"The FDA defines critical path research as the ability to translate basic research into innovative products, and this deficiency is the focus of the innovation gap. One hypothesis that can explain this gap is that the basic sciences now create new biomedical knowledge at a rate that outpaces the human ability to capture and process the knowledge in ways that lead to new product innovations. Supporting this hypothesis is the current approach in the pharmaceutical industry that suggests that minimum critical mass for a research team is 100–150 scientists, combined with the output of high-throughput screening, combinatorial chemistry, and highthroughput biology (genomics, proteomics,and other panomics technologies)."


Silicon Valley infotech companies don't suffer from a lack of cooperation or ability to keep up with new ideas. Why can't Life Sciences companies and academic research organizations work together to share costs and IP? Silicon Valley VCs have lost much capital over the years by allowing engineers to make business decisions. Why do doctors and scientists get to make these business decisions?

The barriers to entry, from medical licensing to control over public tax dollars, have prevented competition and scrutiny. Recent legislation requiring NIH funded research to be published publicly through Pub Med within 1 year is a good first step. The adoption of Open Source research under GPL needs to be the next step. In my mind, the superior economics and productivity make this model inevitable in medicine too. Dying patients can't wait. Democracies can't tolerate opaque bureaucracies.

I leave readers with this quote from Wikipedia:


Linus's Law according to Eric S. Raymond states that "given enough eyeballs, all bugs are shallow". More formally: "Given a large enough beta-tester and co-developer base, almost every problem will be characterized quickly and the fix will be obvious to someone." The rule was formulated and named by Eric S. Raymond in his essay "The Cathedral and the Bazaar".



On a lighter note, check back tomorrow for a report on Stanford's BioX event that focuses on interdisciplinary research methods.


Monday, February 18, 2008

Check out GenStruct!

I got inspired to check out GenStruct's website based on the article in the prior post. This company gets it! This link provides a number of articles that detail and define Systems Biology from several perspectives. The article on diabetes really speaks to the need for Systems education in our medical schools, given the letter to the editor of the NYT that I posted last week. The article that talked about the innovation gap in Life Sciences really stood out to me, also. I currently plan to attend a conference next week called "Between a rock and a hard place" about the challenges that the industry has faced with the existing model. I have seen the future, and GenStruct is already a first mover in the next BioTech industry. Check it!

Systems Biology Makes The News

The following article appears in the January issue of "Gen: Genetic Engineering and BioTechnology News."

"Systems Biology Alters Drug Development".

This article paints Systems Biology as a new and emerging paradigm. It certainly is new in medical research and medicine. At the same time, the article carefully avoids criticizing the existing reductionist paradigm. It also avoids the question of the safety of drugs developed through reductionism. The burning questions in my mind are:


  • When will these emerging technologies reach a critical mass so that society and our legal system force democratic scrutiny over current medical research budgets?

  • What will be the effect on the medical establishment and its control over research and the practice of medicine once the technologies scale?

  • What will the InfoTech lobby do to get in on the bonanza? Will it become a "Right to innovate" issue if tax dollars are used as a competitive barrier?

  • What will happen to politicians closely aligned to the existing pharmaceutical and medical industry? Will they switch from blaming insurance companies to blaming doctors?


Excerpts from the Article

In this first quote, we see the holy grail of medical research at a company called Genstruct, In Silica Modeling. But why have all prior attempts at using computers in research failed?

"The company combines data from various sources, for example, high-throughput genomic, proteomic, and metabolomic data to create cause-and-effect disease models. It applies artificial intelligence tools to look at all the predicted and observed relationships between the data and puts it into the context of a complex system."


Now that medicine is borrowing Systems know-how from InfoTech, companies like Genstruct can finally automate and eliminate much of the work done by chemists. At the same time, the diagnostics and drug products developed with this approach will eliminate the work currently performed by doctors.


This next quote speaks to how Entelos uses a Systems approach to help eliminate animal testing. Given the audience, it is understandable that neither the writer nor Dr. Friedrich point out that their work provides evidence that the "Bottoms up approach" is not mathematically sound. At what point do these technological advances create legal jeopardy for existing research models? It may well be the lawyers that drive this paradigm shift in the end.

"What makes Entelos’ approach unique, according to Dr. Friedrich, is the company’s top-down method, which synthesizes quantitative data from thousands of peer-reviewed papers into a single framework. “Our model doesn’t contain every piece of biology ever known in a subject, but what it does do is get you to something usable much faster than a more standard bottom-up approach,” explained Dr. Friedrich. The company uses a mathematical method to quantitatively describe the relationship between various biological entities over time, making simulations and predictions possible."



Thursday, February 14, 2008



This quote is from a letter to the editor of the NYT regarding the results of a recent study on diabetes. It is the best perspective from a physician that I have seen on why a lack of Systems education in medical schools drives the medical crisis and harms patients.



To the Editor:

The results of the Accord study are not surprising. Diabetes is not a disease of blood sugar; it is a disease of faulty hormonal signaling, particularly insulin and leptin.

The increased mortality seen in the diabetics in this study is not from lowering the sugar, but from the treatment that neglects and often worsens the underlying cause of insulin resistance.

Until medical “science” begins to recognize the difference between symptoms and disease we will continue to see results such as this and the recent Vytorin (Enhance) cholesterol-lowering study, where the treatment itself becomes the disease.

Ron Rosedale
Denver, Feb. 9, 2008

The writer is a medical doctor.

Wednesday, February 13, 2008

MIT "Brain Fitness Event"

I went to a great event last night in Palo Alto that covered the emerging "Brain Fitness" market. Thanks MIT Alumni and Wilson Sonsini for hosting. Panelists discussed the economics, science, and marketing issues related to this trend. Participants included Physic Ventures, Advanced Brain Technologies, www.Lumosity.com, and www.sharpbrains.com.

I had two big take-aways:

1. The thesis that InfoTech /Life Sciences / Health care will converge is right on target with this blog and Andy Kessler's "The End of Medicine". (write-up in books section). Indeed, panelists struggled to define the market as a resident of any one category. Ultimately, panelists concluded that it is between health care, games, software, and Life Sciences. Convergence in action. These software "Games" have the potential to improve brain function today, as well as delay, treat, or prevent aging diseases, such as Alzheimer's. As a result, fewer physician hours will be spent. This market is an example of technology that can deliver higher quality health care and support prevention rather than cure. Technology like this will ultimately reduce the power of the physician lobby as people seize control over their own health.


WARNING: BEGIN RANT. IF YOU ARE A DOCTOR, LOOK AWAY


2. ADD was presented in purely pathological terms by one of the companies covering that specific market. An unfortunate result of the lack of Systems training in medicine today is that the "Experts" badly misunderstand ADD and how ADD is a benefit to individuals who manage it well. Doctors focus on symptoms, not benefits. Unfortunately, many children and adults suffer because of this Attention Deficit in medical education. Indeed, ADDers are on average highly intelligent, highly creative, and willing to make their own way. ADD professionals misunderstand that ADD is an adaptation that benefits society as as well as individuals. As such it's a feature of the system, not a bug. Anyone who saw "A Beautiful Mind" will remember the concept of a Nash Equilibrium.

For a more positive and accurate view of ADD, check out this book from two Doctors who have ADD.

This blog has already covered the topic of reductionism and how it limits advancements in Neuroscience.



I found some excellent research at the Santa Fe Institute on Nash Equilibria and cooperation. Look for a series of articles soon that contradict the medical industrial complex on ADD. Also, I'm coining a new phrase: "Consumer created health care". It's what happens when people get online and do their own research, whether the AMA likes it or not. (They don't).

Tuesday, February 12, 2008

Congress Guarantees Access to Publicly Funded Research

This article from www.scienceprogress.org discusses landmark legislation that requires public access to studies funded with public dollars. This legislation will spur grass roots efforts to leverage open source to enable collaboration with those inside and outside of medicine. Ultimately, the best way to overcome the inertia and self-interest of the medical establishment is to dis-intermediate it through public scrutiny and participation. With this landmark legislation, the day draws closer when large InfoTech companies and bright individuals will join in next generation research models, like open source. Society will benefit as those outside medicine join forward thinkers within medicine to leverage their knowledge and skills to prevent disease and improve technology products.


Naturally, not everyone is pleased. Excerpt from the article:

"Opponents, led by members of the Association of American Publishers, launched their own coalition—dubbed PRISM, the Partnership for Research Integrity in Science and Medicine—to cast doubts on the provision’s impact on the peer review process and publisher copyrights, even equating public access with government censorship. PRISM in turn drew ridicule from science bloggers, who criticized the group’s statements as Orwellian and the group as astroturf, as PRISM declined to list its own membership."

Monday, February 11, 2008

Thank you to Tom Schneider

I owe a double thanks to Tom Schneider of the NCIFCRF Nano-Biology program. The first thanks is for letting me link to his valuable work applying Shannon Entropy to Life Sciences. Links to his work can be found in the "Deep Research" section of this site. The second thanks is for his valuable perspective on the meaning of truth.



"Different measures have different consequences."




Sunday, February 10, 2008

The Mathematics of Teaching Pigs

The old saying goes:

"Never try to teach a pig to sing. You make the pig mad. You make yourself mad. You still don't end up with a pig that can sing."

But what do Bayesian Statistics have to say about all this?

From Wikipedia


"....Bayesian statisticians argue that even when people have very different prior subjective probabilities, new evidence from repeated observations will tend to bring their posterior subjective probabilities closer together. However, others argue that when people hold widely different prior subjective probabilities their posterior subjective probabilities may never converge even with repeated collection of evidence. These critics argue that worldviews which are completely different initially can remain completely different over time despite a large accumulation of evidence......"

Lindley's paradox describes a counterintuitive situation in statistics in which the Bayesian and frequentist approaches to a hypothesis testing problem give opposite results for certain choices of the prior distribution.

The Net

If a person places a high probability of truth on their initial belief, they may never change their mind no matter what new information arrives.

That Pig Won't Sing! You will make yourself and the pig mad! Run Away!

Thursday, February 7, 2008

iTulip Calls for Alt Energy Bubble



iTulip.com's Eric Janszen sees a looming bubble in Alternative energy. He was very successful in calling both the DotCom bubble and the Housing Bubble.
I generally agree with his arguments. At the same time, I believe that the money made in mortgages is going into a broader Nano-Bubble, of which Alt Energy is one part. For example, next generation solar technologies will use nano materials and alt fuels like methanol from wood pulp will rely on genetically engineered "Super yeast".

FWIW, the Sundeck on Sandhill Rd. was quite crowded yesterday and people are quite busy.



P.S. My informed sources tell me that Amorphous computing is still, well, Amorphous.

P.P.S. I had a thoroughly enjoyable discussion on gray goo.


Wednesday, February 6, 2008

What is Amorphous Computing Anyway?

I found a very cool presentation from Harvard on "Amorphous Computing". The title is "Global-to-Local Programming: Design and Analysis for Amorphous Computers". It can be found at the Harvard website for SOS publications. I've just browsed it so far. This example of computing mimicking biology is quite fascinating. It does raise the following question:

"Are we humans merely cheap, replaceable, and unreliable nano-robots creating a global structure through global to local programming?"

I'll be on Sand Hill Rd later. Maybe they can answer this burning question..............

Monday, February 4, 2008

Cool example of NanoTech and Bio Convergence

This article below highlights research that shows that mother nature is the best originator of source code for the lazy to copy. It highlights numerous future uses--everything from lasers to diagnostics. With advanced Bio/Nano materials replacing stethoscopes and scalpels, can the automation of diagnosis and the arrival of preventative medicine be far behind?





DNA is blueprint, contractor and construction worker for new structures from PhysOrg.com

DNA is the blueprint of all life, giving instruction and function to organisms ranging from simple one-celled bacteria to complex human beings. Now Northwestern University researchers report they have used DNA as the blueprint, contractor and construction worker to build a three-dimensional structure out of gold, a lifeless material.

Hello World: Announcing NBB 1.0 Beta!




Here by popular demand, the Nano Bubble Blog now moves into 1.0 Beta production. Anyone unfortunate enough to stumble onto this blog should take all views with a grain of salt, excuse the numerous errors and omissions, and wear appropriate protective gear. Absolute perfection is not currently scheduled until release (9.4b).*




*Features and schedule subject to change.

Thursday, January 31, 2008

Cool Companies

Hello World! Cool companies coming as soon as I start my networking. Check back soon.

Deep Research



Molecular Information Theory

The Work of Dr. Tom Schneider from the NCIFCRF deserves it's own special section. While Shannon Entropy has been applied in InfoTech and communications for decades, it is relatively unknown amongst today's medical researchers. This field, known as "Molecular Information Theory" is not only key to the next generation of medicine, it is very important to the field of nano-engineering and molecular machines.

  • An important warning on the distinction between Thermodynamic Entropy and Shannon Entopy.

  • A good primer for biologists unfamiliar with Claude Shannon's Information Theory.

  • A good start for computer science people is this article on Claude Shannon and Biology. pdf    full cite

  • This advanced article discusses molecular machines in depth using Molecular Info Theory. pdf    full cite

  • Complete tour of Molecular Information Theory with above articles and more.

  • Dr. Schneider's comprehensive home page is found here.





Systems Theory

Systems Theory has deep history in computer science and its application has been around for decades with such technologies as Object Oriented Programming and Dsitributed Computing. There has been work going on to apply this mature science to medicine. Indeed, the health care crisis will not be resolved until reductionism is replaced with this new (to biology and medicine) paradigm. Many InfoTech people have a difficult time accepting that Systems Theory is largely new to medicine. So, really, let me underscore the point to be prefectly clear. This paradigm is largely obscure to practicing physicians and pharmaceutical researchers. Really.

  1. Self-organization, Emergence and the Architecture of Complexity

    This article is pretty deep, but comprehensible for anyone that has ever designed or programmed an object oriented system. A good bit of math is discussed, but no Greek letters. It does an excellent job of explaining how system becomes emergent. The full cite is below. I highly recommend it to both InfoTech people and open minded Molecular Biologists looking for a deep conceptual explanation of Systems Theory.

    Heylighen F. (1989): "Self-Organization, Emergence and the Architecture of Complexity", in:
    Proceedings of the 1st European Conference on System Science, (AFCET, Paris), p. 23-32.


  2. Emergence Versus Self-Organisation:
    Different Concepts but Promising When Combined


    Tom De Wolf and Tom Holvoet
    Department of Computer Science, Kuleuven,
    Celestijnenlaan 200A, 3001 Leuven, Belgium
    {Tom.DeWolf, Tom.Holvoet}@cs.kuleuven.ac.be

    This article makes some extremely important points about the history of complexity science and the meanings of key terms. These definitions are important indeed to keep straight.

  3. Here is a link to Tom De Wolf's full bibliography of very useful work.



Interviews

Hello World!

Books

This section contains reviews of books related to technology, systems, medical reform, and health.



The End of Medicine. Andy Kessler.

Andy is a Silicon Valley entrepreneur and VC with much success to his credit. His very readable book details how imaging and diagnostics will bring scale, efficiency, and automation to medicine. Best vision that I’ve seen so far, although he only mentions systems in passing.


Introduction to Systems Biology. Dr. Uri Alon.

This book is by far the simplest and most straight forward. Dr. Alon understands the notion of patterns (motifs) that make complex systems simpler. Indeed, his book is the closest to the “Gang of four” pattern book that every OO programmer has on his desk. Not there yet, as Dr. Alon acknowledges, but a really excellent start.



Systems Biology: Properties of Reconstructed Networks. Bernhard O. Palsson.

Palsson does an excellent job at providing historical context for SB and calls for the establishment of standards. He should also be congratulated for calling for an effort to map the hierarchy of the system—its “Enterprise Architecture” if you will. On the down side, he misses a fundamental point on page 23: the amino acid code is not random, but rather, it is optimized for the laws of Shannon Entropy. Also, he is still reluctant to recognize that the system is “designed” to insulate itself from stochastic effects associated with thermodynamics. He emphasizes that the system is “constrained” by the laws of chemistry. Not a useful way to look at it. He also engages in endless arbitrarily complex math regarding optimal states. A dressmaker just uses the pattern book because the patterns are useful. She doesn’t whip out any differential equations to prove it.


Design Patterns: Elements of Reusable Object-Oriented Software.
Erich Gamma, Richard Helm, Ralph Johnson, John M. Vlissides


This book is better known for its authors, the “Gang of four”. If you’ve ever designed software you’ve seen this book. Ultimately, this book has to cover everything in carbon-based systems, too. It has to do with Information entropy. I don’t think that the biologists are generally hip to this fact yet.

Health Care Public Policy

This page contains links to articles, research papers, and blog entries regarding issues of public policy and controversial health practices.




  • This paper published at the CHCF site chronicles the truly disturbing delays and negative attitudes of physicians in adopting urgent reforms. Indeed, our health care delivery system seems to be 15 years behind corporate America in understanding the fundamental truth of change. If you can't change the people, you have to change the people.

    The Science of Spread: How Innovations in Care Become the Norm



  • This article from Yahoo! is crucial to understanding how new medical technology will sharply reduce spending on diabetes and on chronic care in general. Indeed, along with Cancer, heart disease and stroke, diabetes is one of the four top line items in our health care budget. It would be nice if individuals had more help in managing diet and exercise, but our current paradigm is about letting things break. With alternatives like this one for treating obesity, we get the benefits of improved health and reduced cost. Andy Kessler makes this point in his book: "The End of Medicine".


    Obesity surgery seen as diabetes cure



  • This page from the NY Times chronicles the controversy regarding the epidemic of doctors diagnosing young children with bi-polar disorder and treating them with regimens of powerful drugs.

    Troubled Children: A Series



Grass Roots Medical Reform

This page contains links demonstrating that concerned individuals are finding ways to bypass medical bureaucracy and offer creative solutions for developing medical breakthroughs.




  • This article is a good example of how individuals who are diagnosed with life threatening illnesses often find that they are going up against a system that hinders innovation.
    Lab Rat?WSJ



  • I found this article to be enlightening and disturbing at the same time. I see this effort as a good first start to forcing medicine to become more responsive to patients and society. A little entrepreneurship and cooperation never hurt. What is disturbing is that with all the good ideas submitted, the doctors interviewed were skeptical that there could be any good ideas out there that doctors weren't already working on. I guess the guy slept through math class when they discussed Godel's Incompleteness Theorem. Or perhaps he feels that God made special exceptions for doctors that allow them to be all knowing and infallible. Perhaps the guy could check out this site for a few "New" ideas for medicine, like the ones that are in the process of revolutionizing it.

    Will Sharing Ideas Advance Cancer Research?WSJ




  • This blog entry reviews an article discussing new legislation forcing researchers using public dollars to make their research available to the public.


Wednesday, January 30, 2008

Pharm and BioTech News

Academic Research Paper Links



Reductionism and complexity in molecular biology.

This article is a great place for the mildly-scientifically inclined to get started in understanding the challenges with our current medical paradigm. It does a good job of defining reductionism, and why it has limitations in a clear manner with specific examples. It is also blissfully free of Greek letters, strange mathematical symbols, and generally incomprehensible jargon. The author does an excellent job of making the provocative assertion that effort spent on HIV vaccine development has been hindered by reductionism.


Van Regenmortel M.H.V. 2004. Reductionism and complexity in molecular biology. EMBO Reports 5, 1016-1020.

Tuesday, January 29, 2008

The Nano Bubble Blog Rant

Silicon Valley IT companies will accelerate the convergence between Life Sciences and Computer Science in 2008 and beyond. This convergence will ultimately lead to the dis-intermediation of the entrenched pharmaceutical and health care industries and their political lobbies. Ten years from today, most of the diagnosis and treatment decisions currently performed by doctors will be automated. Obsolescence for existing doctors and medical students may be near. At the same time, consumers will make their own decisions based on facts, not physician opinions. Not only will consumers enjoy better health for dramatically lowered costs, they will remove an undemocratic element from our society.

Few realize that roughly half of the 50 United States, including California, allow physicians to make decisions for their patients without fully informing them of risks and alternatives. In the same way, the American Medical Association has placed the blame for our health care crisis on insurance companies while neglecting to mention that our medical and pharmaceutical paradigm is based on junk science that is mathematically impossible. As a result of this lack of disclosure, taxpayers are forced to fund expensive research that has no basis in science, throwing even more good money after bad. Ultimately, taxpayers have no say in stopping the AMA, Universities, and health care providers from wasting their money. The only democratic scrutiny in our medical system is our Byzantine tort system, resulting in the worst outcomes for everyone.

Many BioTech CEOs have long believed that IT people would leverage the valley's continuing education infrastructure to launch new careers in BioTech. Instead, they represent the tip of a wedge that will turn the BioTech Industry upside down. Silicon Valley engineers are learning that the current paradigm must be replaced with computer science based methods. Many of today’s pharmaceutical companies will write-off multi-billion dollar pipelines, or face the wrath of the tort industry. What remains to be seen is whether the CEOs and shareholders will be forced to swallow the loss, or whether we all have to continue to pay for dangerous, ineffective, and toxic drugs through our Medicaid and Medicare dollars. A new industry and a new way of doing business will arise out of the ashes of the old BioTech and Big Pharm model.

Awareness that biological information systems and human designed IT systems converge on the same design principles is increasingly reaching IT executives and VCs. Silicon Valley will pounce on the opportunity to get in on the bonanza. A new tech boom will result as the valley re-deploys existing talent to develop and patent models of biological pathways that will then be licensed to create “System-designed” diagnostics and drugs. Next generation companies will cooperate through open source consortia, forcing pharmaceutical and university researchers to change or face extinction. In addition to the promise of lower health care costs, IT companies will be motivated to participate in open source medical research by the need to acquire new engineering skills. IT companies will learn how to revolutionize their own core markets with nano-based technologies. Health care will become digital, democratized, ubiquitous and cheap. An entirely new product-oriented health care paradigm will displace the existing people and players and create new fortunes for entrepreneurs and savvy executives. Those individuals and companies that successfully make the transition will enjoy unprecedented opportunities for achievement and wealth.


Medicine is Based on Outdated Science


Today, drug development and physician practices are based on the belief that a system is nothing more than the sum of its parts studied in isolation. This ideology is called "Reductionism". According to Doctors and Bio-Chemists, living systems are the products of chemical reactions and nothing more. Based on the laws of chemistry and nothing more, doctors and researchers believe that they can understand a system "bottoms up". Our tax dollars and insurance premiums go to the private and academic medical complex based on these beliefs. The trouble is that science has known that this belief is not mathematically sound since 1931 when Kurt Godel published his Incompleteness Theorem.

Scientists have long accepted that biological systems are complex systems that store, transmit, and process information to successfully compete and adapt in their ecosystems. Information Theory is the branch of physics that governs all information systems in the universe. In accordance with these laws, information systems that must adapt to continually changing parameters take on hierarchical and modular structures for maintainability. These laws govern systems that are implemented in silicon-based chemistry as well as carbon-based chemistry. Living systems and IT systems converge on exactly the same handful of design patterns that have been used by human engineers for decades.