Ruminations on science, technology, computing and the world of hi-tech business

This blog has moved

2006-05-10T07:36:00.000-07:00

In case no one noticed, I am now using Wordpress for my Blog

The future of medicine

2006-01-30T21:45:00.000-08:00

Pharmacogenomics might finally be making its mark. Even if this drug does not pass trials, it is just a sign of the times.

read more | digg story

Moved to WordPress

2006-01-01T08:29:00.000-08:00

For the few who do read this blog, I have moved to WordPress, partly cause I wanted my own domain and partly cause I wanted some of the additional features that WP provides and partly just cause I could.

For future posting, please go to http://mndoci.com

If you subscribe to the feedburner feed, no changes will be required. That feed is at http://feeds.feedburner.com/mndoci

I will be modifying and customizing the new page over time (my command of php is a little limited)

Science magazine achievement of the year

2005-12-28T18:18:00.000-08:00

This has been reported ad nauseum in the blogosphere, so I will add to the list. I am glad that Science chose Evolution as its achievement for 2005. The Chimp sequence is great, but the SNP project and the sequence of the 1918 flu pandemic virus are much more interesting. And despite the misgivings of Bill Joy and Ray Kurzweil (subscription required) about the flu virus, science needs to understand disease and other phenomena. This is just the start. Hopefully the years to come will allow us to learn a lot more about our evolutionary history.

Science's Breakthrough of the Year: Watching evolution in action | Science Blog

Technorati Tags: Evolution, Science, Biology

Moving

2005-12-25T22:28:00.000-08:00

I am in the process of moving my blog to wordpress and my own site. Watch this space

I have also shut off comments for now while I try and get things moved over

Technorati Tags: Blog

Geoffrey Moore, strategy and business models

2005-12-23T14:26:00.000-08:00

In the December issue of Harvard Business Review, Geoffrey Moore has an article entitled Strategy and the Stronger Hand where he talks about two distinct models of businesses. While I generally agree with some of what Geoffrey has to say in this article, it brought to mind another set of articles by Chris Anderson at Wired, where he talks about "The Long Tail". In Geoffrey's view there are two kinds of company: those with a complex systems model (IBM comes to mind) and those with a volume model, e.g. Dell. The rest of the article focuses on the differences in the value chain for each type of business and the potential pitfalls of one business model merging with the other. In "The Long Tail" fit into this scenario, Chris talks about the many niche markets that can be very profitable. Where does this fit into the Moore article? Well it does not fit in directly, since Chris talks more about companies that fit the volume model. But it got me thinking about the smaller niche companies that fit the "complex systems" model. Companies that do not do billion dollar deals but form part of a complex system in the Moore model. Does the success of such a company depend on finding the right alliances so that it can be part of a complete solution? Is there a place for a smaller specialized company to be highly profitable on its own? My opinion is that in todays market, such a company can fill the following two roles:

A disruptive role, where the company throws a wrench into the entire fabric of the value chain that Moore describes. Under this model for the parts of the process that the company fills the customer will be willing to pay a premium for the product. The end-to-end solution provider then has two choices (1) to either understand that for a particular niche they can't provide the solution or (2) work with the disruptive force to ensure that the customer has the best user experience. This would be the ideal situation for the niche company, but a potentially risky one
A collaborative role where the company builds itself up to be part of an end-to-end solution. This would require a product that easily fits into existing end-to-end solutions and, very likely, an alignment with a complex systems provider. This is a lower risk solution and one that many companies probably aspire to.

Technorati Tags: Geoffrey Moore, Strategy, Business Models

The "Live Forever" crowd

2005-12-23T12:41:00.000-08:00

Ah the "Live Forever" crowd. I have never understood the obsession with extending life. It is one thing to beat disease and illness. It is another to want to reverse or slow down aging to an extent that we live for a couple of hundred years. I strongly believe that those technologists that spend a large portion of their thought process on this subject would be doing society a service by channeling their thoughts elsewhere. I know many of them already do that, but I would spend a lot more time thinking about energy, healthcare, communication and the means of building a world which does not have to worry about making ends meet. There are aspects of anti-aging that fall within the above topics, which are very relevant.

What confuses me is how absolutely brilliant people like Ray Kurzweil, for whom I have a lot of respect, focus on the regenerative aspects and medicine. Question becomes: Do we want to alter our natural aging process, or do we want to live healthy, disease free lives. Longevity will be a natural offshoot of the latter, but IMHO, that's where our focus should be. Science and technology are meant to be leveraged to improve how we live and what we know. Lets use them responsibly and for the right reasons ("right" being VERY subjective)

Further Reading
The Impact of Emerging Technologies: Fictional Science
I am going to live forever
Immortality
Beyond Human

Cell-based nano machine

2005-12-21T10:50:00.000-08:00

From the Whitehead Institute

Cell-based nano machine breaks record | Science Blog

Tackling brain cancer with nanotechnology

2005-12-20T12:48:00.000-08:00

One of the more significant potential applications of nanotechnology is the early diagnosis and treatment of cancer. The possibility of targeted cancer treatments, pre-symptomatic detection and diagnosis. The national cancer institute is one of the leading advocates of nanotechnology in the battle against cancer. Their cancer nanotechnology website is highly recommended

read more | digg story

A small victory for evolution

2005-12-20T10:01:00.000-08:00

A court ruled that ID cannot be taught in classes in PA. In general I do not blog about this debate, since this such an irrelevant argument that I do not want to bgive it any airtime, but one can always make exceptions!!. Why am I happy about the decision? The biggest problem with ID is that it is limited to essentially one religion, which automatically assumes that one religion is correct and the others are not. That alone makes the concept unpalatable and a that belongs to classes in theology or science philosophy.

Biotech entrepreneurs

2005-12-19T16:03:00.000-08:00

As someone who has been on the business side of biotech for a few years, I found the following article rather interesting. Can a dual-degree in biotech and business really achieve its intended purpose? I would suggest that in general, such a degree is not going to change the career path of the enrolled students. A better solution might be to allow biology/bioinformatics/chemistry grads to pursue elective courses in finance and marketing. That would allow the more business-oriented lot to learn some of the technical aspects of business and choose to follow that path if they need to.

I strongly believe that any success I have had (or am likely to have) on the business end of biotech/nanotech has been driven by my strong scientific background (undiluted by business studies) and by learning the business end the hard way; in the trenches. I would say that the majority of biotech-inclined graduate students are more apt to be interested in the scientific aspects and those who tend to drift towards the business end do so gradually. The more entrepreneurial would probably have gone down that route anyway, regardless of degree.

Google and Personalized Medicine?

2005-12-09T07:21:00.000-08:00

All I will say is "Hmmm ... very interesting"

Sergey Brin on Google and personalized medicine. Of course, this is under the assumption that the quote is correct.

Thoughts on grid computing

2005-12-02T10:32:00.000-08:00

For many years people have talked about grid computing. In the scientific computing business, grid computing has been considered by many to be a panacea for various computing problems and there a number of projects are that try and tap into the power of grids. Examples include the world community grid from IBM and United Devices or the efforts from BOINC.

While community grids probably work well for the kinds of projects listed above, I have always wondered how useful they will be for more specific applications, e.g. a drug discovery effort at a pharma company. There are companies that are running grids, to they really give better results than a cluster. IMO, cluster computing has certain advantages for an IT group and in terms of efficiency that a grid cannot achieve in reality. While Prof. Charles Brooks via Predictor@home has demonstrated how multiscale modeling efforts can be applied to grids, I am still somewhat uncertain about the success in a commercial setting. Cluster computing, for now, would be my preference if I was an IT manager. Certainly there are applications, such as lower-priority, long term projects where a grid solution would be optimal (e.g. a routine, version controlled genome annotation project) as it can keep humming along in the background when resources are found within an organization. On the other hand, for a mission critical project (e.g. virtual screening for a specific kinase target), I would prefer to deploy a cluster, i.e. resources that I can control.

What do others think?

Further Reading

Sun's Grid Flop
Cluster Computing
Clusters better than grids

Biology and Computing

2005-12-01T08:04:00.000-08:00

When I got involved in computational science many years ago, the power, or lack thereof, of computing was one of the most frustrating parts of doing research. Getting time on centralized supercomputing resources was never easy and to solve problems, one had to make many approximations, just to make the solutions computationally feasible. Things started changing in the late 90's when Linux clusters started becoming feasible, robust and cheap. Suddenly, large computational resources were available to almost anyone and without that the whole genomics/bioinformatics boom would never have happened. I think the field is ready for the next "big thing". Routine calculations on large systems can now be done on commodity machines. With Microsoft jumping into the fray with their CCS beta, it is evident that HPC has firmly arrived. Specialized hardware (e.g. blue gene) is being used for complex calculations on living and non-living systems. That said, I think the industry is ready for either the next big leap in computing architectures that will allow the complex calculations that require a blue gene to become more accessible, or a change in usage paradigm, which will allow improved, easier access to these specialized resources. On-demand computing for scientific and technical applications is a hitherto untapped paradigm that can, in theory, bring high-performance computing to a larger set of users. As we seek to unlock the mysteries of cellular machinery, regulatory networks, nanotechnology and many other fascinating fields, a radical change in how computing is accessed or the hardware that we use is needed, and hopefully not too far away.

Science and growing up

2005-12-01T06:40:00.000-08:00

I wonder how children percieve science these days? When I was growing up, I had a fascination for the world around me and how it worked. As I started learning more about gravity and the reason the sky was blue, I remember being absolutely awestruck by the simple elegance of some of the science (qualitatively at least) and that early interest is probably why I ended up becoming a scientist. I remember what a big deal the first in vitro fertilization was back in the day. Today I have a feeling people will not even notice. Somehow, and I could be completely wrong, people and as a result children have started taking things for granted. Science is driven by curiosity, by the need to learn more, to understand, and in this world of fast food and instant rice, I am not sure we have the time. The funny thing is that the information revolution has given us tools that can make finding the information (good and bad) a lot easier. All one has to do is go to Wikipedia or use our good friend Google.

Maybe I am just being unnecessarily pessimistic. Maybe kids are using the information available to find out more about what makes nature tick, and just maybe enough of them will learn to respect and understand it to go on and actually make it a career.

Further Reading
2 cents worth. A post that echoes a sentiment I feel. People are not that interested in "why" anymore.

Blog editorial note

2005-11-28T22:54:00.000-08:00

I have been running this blog on and off for a while now and have come to the inevitable conclusion that this blog needed better focus. The blog was already evolving into one focused almost exclusively on science and technology and that is what it will be henceforth. Any political discussion will be restricted to science and technology aspects.

One area that I hope to blog more about is the business of technology since that is what I do for a living.

Futurists

2005-11-26T11:49:00.000-08:00

I found this interview with a "futurist" and it got me thinking about something that has been rankling me for a while. What are the criteria that define a futurist? Shouldn't every scientist working on problems that might have an impact 10-15 years down the road be called one? Or is it someone who talks about how our life is going to change? Most of the futurists I have run into are neo-Luddites (Bill Joy's classic wired article comes to mind), or AI evangelists like Ray Kurzweil. I have great respect for both Joy and Kurzweil, but I do think that while it is wonderful to have thinkers looking far into the future, I wonder if there is a disconnect from reality. In a way, I think some of the conclusions that futurists come to are in a way quite simplistic, while the underlying assumptions are often very complex.

Further reading:

Law of accelerating returns

What is the Singularity?

Krauss and String Theory

2005-11-26T07:59:00.000-08:00

String theory as a science is something I have not spent much time trying to understand. I am still a firm believer in the capabilities of Newtonian mechanics and quantum mechanics, but this article in Slate about Krauss' latest book makes an interesting read. Do you believe in String Theory? I am going to safely sit on the fence till I actually understand the concept properly. That said count me as a cautious skeptic. It's difficult to dismiss something that could be an answer to "every question", but my experience with string theorists makes it very hard not to be a skeptic. Someday I will actually sit down with a book and try and understand it properly.

read more | digg story

RNAi

2005-11-23T09:35:00.000-08:00

I heard about RNAi for the first time about 4 years ago and didn't quite appreciate the elegance and beauty behind the technique at the time. As time has gone on, I have strongly come to believe that RNA interference is likely to play a significant therapeutic role in modern medicine. The idea that small pieces of RNA can shut off the expression of certain genes is remarkable not only in its simple elegance, but in the fact that it eluded researchers for such a long time. RNAi-based treatments and therapies are likely to find general usage a lot faster than other forms of gene therapy that we are used to hearing about.

Further Reading:
Delivering Interference RNA

Communication in the 21st century

2005-11-21T22:05:00.000-08:00

I wonder how many forms of communication people use today. One of my frustrations is that there are so many options and to keep in touch with friends and family I have to use a variety of options. These days, I use the following (in decreasing order of usage)

Cell Phone

Google Talk

Skype

Yahoo Messenger

Good ole land line

I don't use msn messenger much anymore in my efforts to keep some handle on what I use.

In a perfect world, I would use a cell phone for work-related calls or calls on the run, google talk would communicate with other traditional IM apps (why can't everyone use jabber as the communication standard) and Skype would fulfil my VOIP needs (or maybe gizmo someday) for calls to friends and family.

Related Articles:
One login to bind them all
My hard disk on the web

Native Instruments B4 II now available

2005-11-19T17:52:00.000-08:00

The B4 from Native Instruments redefined computer-based music when it was originally released with the quality of its sound, so much so that it has to be included in any serious discussion of clonewheels. After a significant gap (in a world where updates are frequent), the B4 II was released recently (the demo is available too)

read more | digg story

Technorati Tags: Music

Tribute to Bob Moog

2005-11-06T06:08:00.000-08:00

I realized that there had been no mention of the passing of Bob Moog in my blog. I don't think I can ever provide the historical perspective that Ray Kurzweil does in an article for Wired. Bob Moog was the synthesizer. The Moog Modular is still my favorite synth of all time, and his creations have launch many a wonderful (and many really bad) careers. Every Keith Emerson lick I hear, every Klaus Schulze sequence reminds me of the genius of a techie who changed music forever. Now the day of the analog might well be behind us, but as technology moves on to its next phase, the warm, punchy sound of the Moog most people probably first heard on "Switched on Bach" will live forever as the holy grail.

Nanotechnology and Life

2005-11-06T01:07:00.000-08:00

One of the conversations I follow closely (and occasionally with some amusement) is the definition of nanotechnology. As someone in the field, it is useful to know how people define nanotechnology and what makes nanotech special. A recent article by futurist Jeffrey Harrow (a discussion on the word “futurist” will follow some other day) makes interesting reading in this context. He talks about moving away from “tear down” manufacturing, and trying to learn from machines that know how to do that, i.e. the human body. I strongly believe what we learn from biology/life sciences will play a very important part in realizing those dreams. Proteins, DNA, viruses and other biological machines have already mastered “bottom up” design and can provide the template by which molecular manufacturing may some day be possible. But I would like to add a note of warning: the body is extremely complex and blindly mimicking biomolecular machinery is unlikely to work.

Technorati Tags: nanotechnology, biology

Richard Smalley - RIP

2005-10-30T10:47:00.000-08:00

Nobel Laureate Richard Smalley passed away last week. He had been suffering from Cancer for a while, so the death was not a complete surprise, although it was a little sudden.

Smalley got his Nobel prize for discovering fullerenes, and while many were not convinced at the time of the use of fullerenes, I think today there is no argument that the kinds carbon-based nanotechnologies that he pioneered are here to stay. Smalley was also an opponent of "Drexlerian" nanotechnology, which focus on molecular nanomachines (I think Smalley called this "dry" nanotechnology).

Technorati Tags: richard smalley

Jonathan Schwartz

2005-10-29T22:07:00.000-07:00

For those who don't know, Jonathan Schwartz is President and COO at Sun Microsystems. While I tend to disagree with a lot of what Sun has done in recent years, and about 80% of what Jonathan writes in his blog, I must admit it is one of the better reads out there. I like his style and at some level I take perverse pleasure in some of his opinions, which are often very different from what mine would be. One thing I would love to tell him: "Jonathan, Solaris is done. Get over it"

Technorati Tags: Jonathan Schwartz, Sun Microsystems Blogs

Technology and our world

2005-10-29T10:26:00.000-07:00

One of my favorite magazines is Technology Review, the technology magazine out of MIT. The magazine routinely covers the state of the art in biotechnology, electronics, nanotechnology and other technology areas. The focus is not only on what the latest technologies are, but also which ones are commercially viable and those that are currently receiving an influx of funding. It is amazing what consititutes technology today. Some of us have been fortunate to be at the cutting edge of technology and see their growth over time as they become pervasive in our daily lives.

I strongly believe that the adoption of technology, and more importantly making it available to the general public in a way that is most beneficial is very important for the continued success of society. Many people find technology intimidating, and perhaps it is the fault of us techies, as we tend to make technology sound like science fiction at times (certainly a lot of the tech media does that). If the average person understood technology better, or perhaps was shielded as much as possible, then a lot of the apprehension that I have seen may be overcome. This is especially true for biotechnology and nanotechnology. One rather nice solution: appropriate education.

Technorati Tags: Technology

The Vioxx verdict

2005-08-20T13:27:00.000-07:00

Call me biased, but I agree with the Merck lawyers that the burden of proof was not met in Texas. The precedent is very dangerous, and the problem in such cases is that the jury does not understand the scientific details, and often will go with their emotions. I hope that future decisions are made on clear cut technical grounds. The last thing one would want to see is copycat lawsuits against other companies.

Some things are very scary

2005-08-05T06:29:00.000-07:00

Newsday.com: Bush re-ignites evolution debate

I often want to ask politicians a number of questions on any number of issues, as I am quite certain, they lack the intellect to provide lucid answers. When the president of the USA steps into a debate that I am quite positive he does not understand, it is very scary. The thing that is most scary is that while Evolution is universal, Intelligent Design is very Christian in its very concept, so calling it an alternative scientific theory demonstrates a serious lack of thinking. It essentially assumes that the doctrine of one faith is superior to the others. If every faith or the majority of religions supported Intelligent Design, then the argument had some credence. Until then, it is akin to teaching one religion in schools and there is no place for that in a good education, especially in a science curriculum. Coming from the President, that is a frightening thought, but sadly, I am not surprised. President Bush has never stepped back and thought things through rationally.

There is an article about some responses in Technology Review.

Science and hardware

2004-11-01T21:55:00.000-08:00

I would be the first person to admit that I have an affinity for Linux. While I am not the "Linux bigot" that I used to be, I still think that for most scientific use, it is by far the most effective OS. Linux machines are fast, the Unix-style OS efficient, familiar and convenient, and the graphical capabilities, as issue in years past, are excellent. At least where I am concerned, I still can't do any serious modeling on Windows. The latter is great for certan applications, including scientific applications, but a 5 ns MD simulation is something best left to a Linux box or better still a cluster. Proprietary UNIX OS' have niche applications, but have probably seen their best days. I have fond memories of AIX and IRIX, two OS' that have served me well over the years, but today, I would pick Linux over those 9 times out of 10.

Where does leave the Mac, especially OSX. For many scientists, OSX and Apple can do no wrong. It is definitely an intriguing OS, with the front-end classic apple and behind the scenes, a UNIX box. I suspect that in academia and in some bioinformatics circle the Mac OS will always be the OS of choice, but I see some XServers being deployed in a number of places over the next few years. Scientists are a funny bunch. When they like something, they tend to hold on to it like their lives depended on that act, even when the object of their affection has long past its zenith. Then there are the IT groups that dictate hardware choices, pissing off many a research scientist in the process. With all the choices available, and a new generation of scientists, the hardware/OS wars are only just beginning.

Subverting Science

2004-10-31T11:58:00.000-08:00

The New York Times > Opinion > Editorial: Subverting Science

I am not sure the article is accessible to everyone, since the NY Times requires registration, but reinforces what many in the scientific community have come to fear. The lack of respect for good science by the current administration has been galling to say the least. When the world's leader in science and technology does not take the lead in such matters something is very wrong indeed. Climate change is but one of the many issues. The inability of foreign students and scholars to get visas on rather flimsy grounds, the whole stem cell debate, etc proves, to me at least, that those in power are not rational thinkers, and generally distrust good science. This is very troubling. As it is the average American has no clue what science is all about, and when the government does not do its bit to promote free thinking and scientific endeavour it is not surprise that some think that the US' pre-eminence in science could be threatened. I hope that is not the case, but it is something to worry about.