spin 1/2

Numerate in the News

2009-07-03T14:10:00.000-07:00

Numerate, my company, has been getting some press lately.

Our CEO wrote an article about our business model which is in Nature Biotechnology. It is a good read even though the editor transformed it a lot from the original.
A blogger over at PEHub heard about us and wrote an article about who we are and what we are trying to do. She interviewed one of our lead investors Adam Grosser, from Foundation Capital, and our CEO Guido Lanza. In the article, the blogger makes the first public announcement that we were selected to negotiate a DTRA grant worth up to $6.5 million over the next 3 years. We were trying to keep it under wraps until we signed the contract, but it is out now. PEHub may also be the organization that outed our round B financing, causing us to prematurely release our announcement of it. PR can be hard to control.

Also, our CTO, Nigel Duffy, and CSO, John Griffin, will also be presenting talks at the upcoming ACS fall 2009 meeting.

Emerging Research Front Paper

2009-05-31T11:55:00.000-07:00

It seems that the primary paper that came out of my thesis is being recognized as an "Emerging Research Front Paper in the field of Space Science" by Thomson Reuters' Science Watch. They interviewed my thesis advisor, Joel Primack, and me about the paper. Joel always said it was going to be a fundamental paper and I appreciate the recognition of the paper but, I can't get over being a bit irritated at the way the interview is presented. Why am I running afoul of science writers lately? Joel was my PhD advisor, he is a big name in cosmology, and is still working in the field, but it was my thesis work and I was the first author. Why does the article seem to give him first billing? I am trying desperately to understand science writers, but am finding it very difficult as of late. Am I being too critical?

New Computing Pioneers? Not Really!

2009-05-27T20:26:00.000-07:00

I haven't posted anything in a very, very long time (as one can see), because I have been concentrating on getting a company, Numerate, Inc., going with an inspiring group of people. I have been meaning to get back to writing, not because I have any more time now, but because I am starting to feel the need to write, again. Unfortunately, most of the things I would like to write about are things I am working on and can't talk about. However, I just read an article which touches on many things I have been working on in the past two years that I can talk about and one that I think needs to be put into perspective. The article touches on a number of issues I have been dealing with, both within the company and outside. The topics touched on in this article have already inspired the beginnings of a number of blog posts, in my head.

Before I tell you which article it is, let me step back a second and describe a bit (not too much) about what it is we at Numerate do. Numerate is a pharmaceutical company that specializes in very early stage small molecule drug development. Our entire process is an in silico process and we don't have any wet chemistry. We help biotechnology and pharmaceutical companies fill their pipelines by solving the problems that the traditional drug development process fails to solve. By doing this we can make the drug engineering (TM) process, as we like to refer to it, cheaper, faster, and more able to solve difficult problems. A key component to the cheaper and faster bit is enterprise cloud computing (for lack of a better term). We have been using Amazon's Elastic Compute Cloud (EC2) since March of 2007. We developed an on-demand enterprise cloud computing system on EC2 using Sun Grid Engine glued together with a number of custom scripts in late 2007. We use as many as 1000 virtual machines at a time on EC2. We have been too busy to write about it and I personally didn't realize how novel it was until recently.

Today, I read the cover article of Chemical & Engineering News entitled New Computing Pioneers and was overwhelmed at how much the article touched on the many of the things I have been working on and how much credit it pays to (in my honest opinion) undeserving Big Pharma. The author tries to paint a picture of how slow-to-innovate Big Pharma is defying its stereotype by embracing cloud computing. From my perspective, they are just the next big industry to realize some of the potential of cloud computing and are now dipping their proverbial toe in the cloud. What they claim to have done in the article isn't all that innovative. For the most part the article is a big puff piece to make Big Pharma look good. First off, I found it quite odd that in the article J&J and Genentech were given props at the beginning and then were never even mentioned. Why? Lily on the other hand talked about a 64 node virtual cluster working on "bioinformatics sequence information." That is tiny! We have been using over 500 nodes on EC2 since mid 2007. Not only that, Dave Powers is quoted as saying that they "complete[d] the work, and shut it down in 20 minutes", "[i]t cost $6.40", and he seemed pleased with this. Well, if you are familiar with EC2 you will know that he got charged for using all 64 machines for an hour. He only utilized those machines for one-third of the time he was charged. That seems like bad utilization to me. The article also points to a paper written by researchers at the Biotechnology & Bioengineering Center at the Medical College of Wisconsin on the viability of using Amazon's cloud-computing service for low-cost, scalable proteomics data processing. First, the article is published by a gray publisher, meaning it is closed access and the general public can't read it without paying at least $30. The publisher also publishes Chemical & Engineering News. Open access is something for which the folks at the Science Commons, who were interview for the article, and I are fighting. That discussion is however for another post. Second, why are they publishing about the viability? Academically, it seems like a weak topic to publish in a peer reviewed journal unless the purpose of the paper is for it to be place on the stack of papers on which all academics needs to stand in order to be seen. Again, this is a topic for a later post.

In contrast to this bit of foolishness about innovation, the article brings up some very interesting points and highlights some interesting companies and efforts. Some of the interesting ideas and points brought up by the article, all of which I hope to address in more detail in later posts, are:

how does a company deal with securing data in the cloud.

how does a company control, monitor, and audit the costs of the use of the cloud by its researchers.

what are the best tools for operating a research cluster in the cloud.

how does one setup a collaborative environment in the cloud under these other considerations.

how can we as researchers contribute to the ultimate commodification of compute cycles.

There are many people and companies trying to answer these questions and quickly fill these needs. One of these companies is mentioned in the article. BioTeam is partnering with Pfizer "on connecting its work to the cloud." The BioTeam, which based on the results of my Google stalking, was developing very similar cloud infrastructure resources to ours own and it seems to have been doing it at about the same time. They are certainly a group to watch in the space of biotech computing. On the other hand, the fact that Pfizer is working with them reinforces my belief that Pfizer lacks the computational skills internally to really be called innovator.

Another highlight of the article was the mention of the Science Commons. The comment from John Wilbanks, the executive director, about "[w]here the data reside in the discovery process" and how that "will dramatically affect the likelihood that they're ever going to be part of a cloud," is an interesting perspective. The mention of Merck's efforts, assisted by the Science Commons (which was not pointed out in the article), to open much of the data generated by Rosetta through Sage is also an interesting move in getting the data out there. You can hear more about this from both John Wilbanks and Stephen Friend, senior vice president and oncology franchise head at Merck Research Laboratories (soon to be at Sage), in a panel discussion at the Commonwealth Club of California entitled "Making the Web Work for Science" of which, I admit, I am an organizer.

All in, the article and its title are misleading, but it brings up many interesting points and actually does mention innovators (BioTeam & Science Commons), they are just not the articles purported innovators.

All views expressed in this article are those of the author and do not necessarily represent the views of, and should not be attributed to, Numerate, Inc., the Commonwealth Club of California, or anyone else with whom the author may have expressly or implicitly associated himself.

AGILE launch

2007-04-23T10:08:00.000-07:00

AGILE successfully launched today! Congratulations to the whole AGILE team. AGILE is a space based Gamma-Ray observatory, which has sensitivity in the 30Mev - 50Gev range. It also has a very large field of view, 3 steradians. This is the European entry into the Gamma-Ray observation game. I worked on the US competitor at Stanford called GLAST, which is set to launch this fall. GLAST has a much larger range of energy sensitivity, 20Mev - >300Gev and the same field of view. They both have great resolution due to the silicon strip detector technology on both satellites, and will be able to pin point the sources of high energy gamma-rays to 30 arcseconds. This is orders of magnitude more accuracy then we currently have with ground based observatories and with previous space based observatories (EGRET).
These satellites will both be scanning the sky for AGN (Active Galactic Nuclei), Gamma-Ray bursts, and many other gamma-ray sources. Gamma ray sources are the most energetic phenomena in the Universe and it will be interesting to see the science that comes out of both AGILE and GLAST.

The Hollywood Cell Story

2007-04-20T14:06:00.000-07:00

The Inner Life of the Cell is one of the greatest visualization/animations I have ever seen. This beats the best astronomy visualizations I have ever seen. There are some inaccuracies in the movie (e.g. the assembly and disassembly of objects is too ordered to represent the real Brownian motion processes, which would realistically take too long), but it is all done in the name of slick animation and for the glamorization of cellular biology. This is just plain cool!

Nicotine and other cognitive enhancers

2007-04-18T21:41:00.000-07:00

I just read a great blog entry on nicotine and it's effects on the brain written by Madam Fathom. She give a great review of how the nerves in the prefrontal cortex behave and how they are effected by nicotine in both a person that smokes and a nonsmoker. I would love for her to do a similar story on modafinil. The maker, Cephalon, claims there is no negative side effects and information from a resent ongoing study seems to indicate what college kids and silicon valley body hackers already know. It improves memory and seems to have a similar effect to nicotine, in that it "may enhance the signal-to-noise ratio" allowing people to concentrate better.

Teaching Company

2007-04-15T21:44:00.000-07:00

A couple of my simulations appear in a new course put out by the Teaching Company. Prof. Alex Filippenko, UC Berkeley, asked to include the visualizations of two dark matter simulations I did as a graduate student in a course he recorded for the Teaching Company. The course is called Understanding the Universe: An Introduction to Astronomy.

Strange Loops (Part 1)

2007-04-08T19:45:00.000-07:00

I just read a review of the new book from Douglas R. Hofstadter entitled "I am a Strange Loop". This may seem like a bizarre title for a book, but if you have read his other tome, the famous "Goedel, Escher, Bach" (GEB), you will understand the title. I ordered this new book today and will most likely write about it after I have read it. The reason I bring it up today is because I have been meaning to write a review, synopsis, and my thoughts on GEB. This is going to be the first installment of a few short articles I plan to write on this book and subjects contained within. Given the fact that GEB is over 750 pages long and that Hofstadter's rambling narrative covers so many topics all at once it deserves many write ups. One last note before I begin: I must admit it has been about a year since I read GEB, so many of the things I am writing about come from my notoriously bad memory and I, unfortunately, also did not follow my normal practice and mark the book up with a red pencil. So here goes.

In GEB Hofstadter, who actually has a PhD in solid state physics, tries to tie number theory, intelligence, and philosophy together for an admittedly vague purpose through the concept of what he calls the "strange loop". A strange loop is simply a self referential cycle. More on that later. He uses a variety of didactic instruments to communicate his thoughts. One instrument which is employed throughout the book is the use of dialog. Before every chapter Hofstadter presents a dialog between the Homeric hero Achilles, the comical figure of the Tortoise, and other fictional and non-fictional characters in a style mimicking Carroll's remake of the Zeno paradox. The dialogs are meant to illustrate the main focus of the proceeding chapters through the use of humor and situation. Hofstadter's use of such dialogs is difficult to get used to and often breaks the flow of the book up in a very unnatural way. Not to mention, he is only marginally successful at illustrating his points in these dialogs. A number of times I found myself getting bored by the dialogs and skipping them to get to the real chapters. Depending on how one learns, the mileage one gets from these dialogs will vary.

Another instrument Hofstadter uses relates directly to the title of the book. He uses the work of Goedel, Escher, and Bach to illustrate his ideas although all not in the same manner. Goedel's work is used directly as the basis for many of Hofstadter's arguments, where the mentions of Escher and Bach's works have more of an art historian feel. He presents interpretations of their work viewed "through the looking glass" of the arguments he is building. The Escher examples come across easier due to their visual nature, but for one to understand the Bach examples one must familiar with the canon's of his writing. Hofstadter does a good job of explaining and exposing some of the more hard to recognize mathematical aspects to both artist's works. There always seemed to be a mathematical quality to Escher's work which ran deeper than just geometry and Hofstadter exposes some of that in GEB. Besides these two examples Hofstadter successfully uses literary tools such as Zen koans and language translations combined with biological and mathematical ideas to make his points.

It is enjoyable and often useful to interpret science and math concepts from a humanistic point of view and I feel that that is what this book does well. With in mind, this book should then be divided into two books; one teaching number theory and one on the humanistic view of intelligence and number theory. Hofstadter has done himself an injustice by combining the two subjects which in turn has limited his audience to a narrow group of individuals both willing to read a 750 plus page book and explore both the rigorous development of a number theory and it's philosophical consequences. There are many people, I know, that I feel would love to read what Hofstadter has to say about certain subjects, but who would be unwilling to read this book. Overall, I liked this book, but mainly because I felt a personal connection with Hofstadter and what he has to say. I am not so sure many other readers will have or have had same experience, but I may be wrong considering Hofstadter won the Pulitzer prize for GEB in 1980.

In part 2 I will give an overview of the construction of the number theory Hofstadter uses to present the strange loop concept and then in part 3 I will give an overview of the philosophical side of GEB.

Nearly Naked Dark Matter Halo

2006-08-21T21:18:00.000-07:00

In two important papers (paper 1 and 2) put on astro-ph two days ago, a group of astronomers describe the observations and analysis of two colliding galaxy clusters which have temporarily stripped each other of their hot X-ray emitting gaseous cores respectively, leave nearly naked dark matter halos. The most important aspect of this set of papers is their confirmation of a major prediction of Cold Dark Matter theory which is not explainable by alternatively proposed solutions to the missing mass problem.

The holy grail for proving that cold dark matter halos exist, thereby also proving that dark matter exists, is being able to "observe" a naked halo. When baryons are present, there is always a way to modify gravitational theory, albeit rarely self consistently, or propose the existence of more cold (unobservable) baryons around a galaxy or cluster to explain observations of gravitational lensing and other phenomena, which are naturally explained by the presence of a dark matter halo. Because dark matter halos are so massive and most began forming very early in the universe, all of them have had a long enough time and have a large enough gravitational potential to pull in the intergalactic gas around them. Only some small halos are theorized to be truly "empty". And even if large naked halos existed, where would we look to find them? The next best observation would therefore be of a dark matter halo where the baryonic matter and the dark matter are clearly separated by a process that would leave no significant amount of cold baryons at the center of the halo. This is what this observation show.

Using the phenomenon of weak gravitational lensing, an effect well know to observers (easily seen by the Hubble telescope through the presence of the arced galaxies), one can determine the mass along the line of sight needed for such distortions in background galaxies. This method was used to determine the mass and center position of the two colliding dark matter halos. Because both of the galaxies clusters are at the same redshift and are traveling perpendicular to the plane of the sky away from each other they must have just made a pass through one another. The significance of this is that dark matter only interacts gravitationally allowing the halos to pass through each other. Baryons on the other hand collide, shock, and heat up which slows them down relative to the dark matter. The heated gas can be seen in the X-rays and is observed to have formed a bow shock behind the gravitational centers of the halos. It is impossible for much gas (baryonic matter) to have remained at the center of the halos and at the same time remained cold (no X-rays). Therefore, a modification of gravity exerted by baryons can not be used to explain this observation, nor can the presence of a large amount of cold unobservable baryons.

This is a great step in proving the existence of dark matter, but there is a long way to go to truly understanding the nature of dark matter and dark matter halos. It is, however, exactly this combination of weak and strong gravitational lensing observations combined with multi-wavelength observations that will lead the way. I will soon post an explanation of what these kinds of observations can tell us about the nature of dark matter.

BPS - Body Positioning System

2006-08-16T08:52:00.000-07:00

Stanford biologist have just published a paper on the study and discovery of three genes in fibroblasts, which are contained in the deepest epidural layer and in the surface of most organs. They find that the expression of the genes is correlated with location on the body. It is well known that fibroblasts are responsible for embryonic development of limbs and other body parts, but it was thought that they become dormant after the body is fully formed. The working hypothesis of the Stanford scientist is that these and other genes in the fibroblasts are still active and communicate position information to other cells. This allows skin cells to know how much to regenerate in order to heal wounds. It is still unclear as to whether the gene expression is a remnant of the embryonic development stage or if they are continually active and influencing cellular development. If right, the scientist are hopeful that this may lead to the development of organ and limb regeneration by adult cells instead of embryonic stem cells. There is a NYT article on the study here.

Symbiosis and Human Health

2006-08-14T11:23:00.000-07:00

It seems as though the science community is starting to explore the symbiotic side to human health and well being. In an article in the New York Times there is a report about research which is looking at the effect different gut microfauna have on ones ability to extract calories from food, suggesting that this could contribute to obesity in some cases. More information can be found at Obetech, LLC. Another article in the same vein (found here) has even more bizarre implications, suggesting that parasites may effect human behavior on a large scale.