Is metabonomics ready for prime time?
April 19, 2006
Some years ago, I was introduced to the term metabonomics at an ENC conference. It was evident then that using NMR to screen for metabolites was gathering steam, even in the pharma industry, where SAR-by-NMR and NMR structure determination had traditionally been the focus of NMR groups. Among the speakers at the conference that year was Jeremy Nicholson, who has just published a paper in Nature on the potential role of metabonomics in personanlized medicine. Actually in keeping with the halo-ed traditions of the world of biology, he coins a new term pharmaco-metabonomics, which is the combination of pre-dose metabolite profiling and chemometrics to model and predict the response of an individual
. The paper discusses a proof-of-principle, where the authors look at the metabolic effects of paracetamol on rats by studying the urinary drug metabolite profile using NMR.
The authors argue that their technique has advantages over a pharmacogenomics approach, since they take into account critical environmental factors, which are not genotypically controlled. I think the real value will come in combination with genetic approaches, which are (at least I think they are) more predictive than the techniques presented here. I think the real value of such techniques come in pre-clinical and clinical drug testing, where metabolites can be used as markers for drug profiling, either at an inividual patient level or for some form of patient stratification. The most impressive thing about the technique was the number of metabolites they were able to measure and use to build a model. The question I have is about the noise in the data, especially in humans. Would the data be clean enough to identify the appropriate metabolites? Hopefully that question will be answered soon.
Further Reading
Technorati Tags: Personalized Medicine, Metabonomics, Metabolobins, Pharmacogenomics, Biomarkers, NMR
Nanoscaffolds: Papers to read
April 18, 2006
I have talked about this subject before in Blind hamsters in past tense. Nature has a new article talking about this and some other work by Samuel Stupp’s group at Northwestern.
The papers are freely available at PNAS:
Elliis-Behnke et al
Hartgerink et al
Similar work has also been reported by the Institute of Bioengineering and Nanotechnology in Singapore
Technorati Tags: Ellis-Behnke, Nanoscience, Nanotechnology, Bioengineering, Nanobiology, Nanomedicing, Regenerative Medicine
The role of academia
April 15, 2006
This post was inspired by Sandra Porter’s post on teaching ethical issues in biotechnology.
When I started my scientific career, all I wanted to do was work in academia as a researcher. The general belief was that “real” research was done by academics and all industry did was take academic principles, scale them up and commercialize them. That was a very naive 15 years ago. The reality turned out to be rather different.
As things stand, I never worked in academia after finishing grad school, and don’t really do any research anymore My understanding of the role of academic research has also changed. One only needs to look at the number of companies that spin out of academic institutions. Just last week, I was at a symposium where, in about six talks, about 4 or 5 companies were mentioned. The talks were all by academics whose research had resulted in the formation of a company or two. I am sure many purists worry about this, and believe that commercialization takes the essence away from academic research, but I beg to differ. There are some who spend their careers understanding the fundamental principles of physics, chemistry and biology. Others develop new mathematical foundations. However the majority of research is and should be focused on how we can take those principles and do something more tanglible with them. People are trying to indentify better sources of energy, better means of nutrition, improve the environment, alleviate disease, develop better materials, etc. I see nothing wrong with commercializing research that has an end goal in mind, a product as it were. Industry has its own constraints, especially the underlying need for maintaining profitability. In such an environment research usually cannot, especially today, carry the same risk as academic research, and needs to operate on much shorter timelines. In a world where Bell Labs is a relic of the past, academia has a very valuable role in driving innvotion. The role of industry is to foster innovation by maintaining close academic ties and by taking ideas from academia and bringing them to fruition.
The above picture is rather simplistic, but is sufficient for the following argument The relationships and roles of universities/academic institutions and industry have changed. The number of people choosing industrial careers has, I suspect, increased over the years, with increasing opportunities to work in startups, etc. Like Sandra says, perhaps we should rethink what we teach in science courses. It would be very useful to have classes in bioethics and business management, and even a rudimentary knowledge of IP law would probably help a lot of people, especially those who might want to pursue careers as IP attorneys or traverse a more management oriented career. Another change that would greatly benefit young scientists joining industry is some exposure to the kinds of practises one is expected to follow in industry. I will use my own, somewhat related, example. While I had been programming for some time as a graduate student, there were practises that had to learned (and quickly), when I started programming in a more structured environment. I would have been productive faster, if I had been more familiar with some of the “workflows” that need to be used in industry. All the courses I mention should be electives. There are a few people I know, who would never, ever want to endure a course in IP law.
Technorati Tags: Science Education, Industry, Academia
Google Analytics
April 13, 2006
I wrote a few days ago that I would do a wait and see on Google Analytics. The wait is over. Google Analytics is an excellent component of my three-pronged analytics strategy … and it has oh so cool graphs. The Geo Map overlay alone is worth it. Although the Geo map gives you the same information in text form, the map is so much cooler.
Web 2.0 & Science at BioIT World
April 9, 2006
Nascent the nature blog on web technology and science has an article on a session onWeb 2.0 in Science at BioIT World. The speakers included Tim O’Reilly, Jim Ostell and Declan Butler. As a science blogger, I wish I had been there. Nature has taken the lead in taking advantage of web-based technologies (although their RSS feed could use some improvement).
The web has always been a rich avenue for discuss among scientists, through bulletin boards and newsgroups. Modern technologies, especially blogs and semantic web technologies allow us to take the level of interaction to a new level. del.icio.us and Wikipedia should be part of every scientists life. Tools like Backpack from 37signals are ideal for collaborative projects. One does not have to be a computational scientist to take advantage of modern technology. Forget the hype, forget the buzzwords. There is a lot of technology out there that can help scientists collaborate and be more productive. Scientists are by nature skeptics. That is healthy, but at the same time, scientists are usually willing to explore new ground. That has not happened yet with web technologies. Hopefully that will change … soon
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Technorati Tags: Blogging, Web 2.0, Semantic Web, Nature Magazine, Technology, Internet Technologies, Information, Collaboration
