This is the old version, but gives more information on some areas.

Research Interests: Evolution, Biochemistry, and Human Genetics (old version)

This page will be more specific about my research when I am far enough along to have some results to present publically (including publishing the software needed for said work - I discuss this further below). In general terms, it involves the intersection of (protein) biochemistry/biophysics (e.g., protein structure) with evolutionary biology, using a combination of 'wet' lab and computer (e.g., phylogenetic) work.

As I state on my politics page, I am particularly insistent on that anyone who writes software for scientific work should place said software under an open-source license, and indeed avoid using software for scientific work (as in under conditions in which I will be ethically obliged to cite said software's use) that is not under such a license (when possible - I am not sure as yet whether I will be practically able to do this completely in my work). Furthermore, I believe that this should be a requirement for publications in any legitimate journal or for a publication to be otherwise considered valid for purposes of tenure, gaining grants, etcetera. I do not see how a work can be properly peer-reviewed if the source is not available:

Are the algorithms claimed to be in use in a publication actually those in use in the software?
How can an experiment be repeated by others and the results confirmed without full publication of methodology?
How can whether a theory is generally correct, or only correct in a particular instance, be explored without being able to modify the methodology used in a experiment for other circumstances (which again requires the full publication of said methodology)?

If I am asked to review a paper involving the use of software written by an author of said paper, and the software is not made available under an open-source license (or placed in the public domain with the source code likewise made available and in the public domain), I will make it plain that I do not consider the work in the paper in question to be adequately well-explained and verifiable by others. Moreover, the purpose of publication is so that others can base their work off of said publication - something that is hindered or made impossible if all details of methodology, e.g., source code in this instance, are not made available including so that others may publish their own work based on that work (something made impossible by source code made available only under a non-disclosure agreement). In regard to non-software copyrights, I approve of the policy of journals to not publish anything regarding a protein structure unless it is in the PDB, or involving a gene unless it is in Genbank or a similar database (and I have problems with the attempts of Swissprot et al to copyright their databases - not that factual data, as opposed to the collection of said data put together, is copyrightable under present laws in any event). Similarly, I approve of journals that make papers available to all (usually after some period of time - I understand their need to recoup costs via subscriptions, although I would prefer this to be done via page charges and advertisements), and of scientists publishing their papers via their own websites (and plan to avoid submitting work to journals that do not either make work available for free after a year or so, or allow free publication by authors online; this also should increase my "Impact Factor" of citations of my work - I certainly prefer to cite material which is freely available!). For some resources which are (usually) thus freely available, see:

http://citeseer.nj.nec.com/cs or http://www.citeseer.org - Citeseer
http://highwire.stanford.edu/lists/freeart.dtl - Highwire Press
http://www.pubmedcentral.gov - PubMed Central

Note that links to journal articles via the latter two are also available via PubMed, and the first is a search index of articles freely available online.

My ultimate area of interest is the application of molecular genetics (genetic engineering) to human beings. This includes gene therapy and genetic enhancement, such as via nuclear transplantation (aka therapeutic cloning) to produce genetically-altered embryonic stem cells, fetal tissues, and fetal organs for implantation. (This area of research is opposed by many religious organizations. While I do not have a problem with their preaching what they feel is right, so long as they are tolerant of other viewpoints, many of them are not only intolerant but are unfortunately attempting - and often succeeding - in forcing their views upon others via the political process. It is possible that I will need to go outside of the US (probably to Canada or the UK) in order to do this research; I hope that this will not be the case. Incidentally, while some may question the propriety of mentions of religion and politics on a page dealing with my scientific research interests... if you believe that, for instance, evolutionary biology can be separated from politics and religion, try talking to a Creationist. Religion and politics also have quite a bit to do with why and, for the former, how I do research in the first place. (In regard to the latter, the scientific method does not specify how one comes up with initial hypotheses for testing, except that optimally as much already-available data as possible should be taken into account. The story of how the structure of carbon rings was initially hypothesized is a clear example of how means (in that case dreaming) other than normally acknowledged conscious rational thought can help in this.)

Below are some (more) links related to this, in semi-alphabetical order; note that I do not necessarily agree with any viewpoints (on scientific or other topics) expressed by the below pages. I also discourage the use of any software available by the below links which is not Open Source, at least for published scientific research. (The algorithms used in scientific work need to be published just as much as laboratory methods and results need to be. These algorithms include, given possible coding errors and heuristic shortcuts, the full source code of all such programs. We only use Biosym/MSI/Accelrys' InsightII software here for lack of good open-source alternatives.)

This is viewable in Any Browser and is Valid HTML 4.01.

Page written by Allen Smith (send mail to meatcan2@beatrice.rutgers.edu, substituting easmith for meatcan2 - see my antispam page(s)for why).

I am not responsible for any pages linked from these, except for those that I have written. Neither is the Structural Biology Computational Laboratory, the Department of Biochemistry and Microbiology, Cook College, or Rutgers Universityresponsible for (or have any copyright on) pages that I have written. My webpages are not official Rutgers webpages.