Author: Mike White

Genomes, Books, and Science Fiction

Beginning of the end of AIDS

This is amazing, given that it has been only 30 years since AIDS first started to have global repercussions, and given how very little we knew about viruses in the early 80’s:

Diane Havlir, M.D., and Chris Beyrer, M.D., M.P.H, The New England Journal of Medicine:

We are at a moment of extraordinary optimism in the response to the human immunodeficiency virus (HIV). A series of scientific breakthroughs, including several trials showing the partial efficacy of oral and topical chemoprophylaxis1,2 and the first evidence of efficacy for an HIV vaccine candidate,3 have the potential to markedly expand the available preventive tools. There is evidence of the first cure of an HIV-infected person. And most important, the finding that early initiation of antiretroviral therapy can both improve individual patient outcomes and reduce the risk of HIV transmission to sexual partners by 96%4 has led many to assert what had so long seemed impossible: that control of the HIV pandemic may be achievable.

Mathematically challenged biology

I can’t decide whether this is sad or hilarious:

PNAS July 17, 2012 vol. 109 no. 29 11735-11739

Heavy use of equations impedes communication among biologists
Tim W. Fawcett1 and Andrew D. Higginson

Most research in biology is empirical, yet empirical studies rely fundamentally on theoretical work for generating testable predictions and interpreting observations. Despite this interdependence, many empirical studies build largely on other empirical studies with little direct reference to relevant theory, suggesting a failure of communication that may hinder scientific progress. To investigate the extent of this problem, we analyzed how the use of mathematical equations affects the scientific impact of studies in ecology and evolution. The density of equations in an article has a significant negative impact on citation rates, with papers receiving 28% fewer citations overall for each additional equation per page in the main text. Long, equation-dense papers tend to be more frequently cited by other theoretical papers, but this increase is outweighed by a sharp drop in citations from nontheoretical papers (35% fewer citations for each additional equation per page in the main text). In contrast, equations presented in an accompanying appendix do not lessen a paper’s impact. Our analysis suggests possible strategies for enhancing the presentation of mathematical models to facilitate progress in disciplines that rely on the tight integration of theoretical and empirical work.

Big SF award, big let-down

Jane Rogers’ The Testament of Jessie Lamb, shortlisted for the Booker, won a big SF award. This was a temptation I couldn’t resist so I checked it out of my library, and damn, this book was a let down.

It certainly qualifies as SF, in the great British, non-pulp tradition. It’s also one more book in the current fad of teenagers in dystopia, and like many teen-dystopias, this book, to its detriment, couldn’t decide whether it was YA or adult fiction.

There is nothing wrong being YA fiction. But if I don’t go in knowing that a book is aimed at young adults, I usually end up unsatisfied – it’s like picking up a cup of hot chocolate that you thought was coffee.

The idea behind this book has potential – a world-wide virus that kills all pregnant women is just one more catastrophe to add to our 21st century list of woes that includes global warming, terrorism, exploitation of animals and the environment, etc. Continue reading “Big SF award, big let-down”

Being a science career realist

Apropos of yesterday’s quote about the science job market, here are some key points that anyone interested in pursuing a science career should keep in mind:

1) The number of independent research positions in academia, industry, and government has always been less than the number of qualified individuals who desire those positions, but the scarcity of such positions is much more severe now than it was 30 years ago, particularly in the biomedical sciences1. Whether we have the right number of independent research positions is a different issue. The purpose of independent research positions in not to provide employment for people who want such positions, and so the fact that many people want independent research positions but don’t have them does not indicate that we need more of these positions. Continue reading “Being a science career realist”

Science jobs gone missing

My 2006 PhD was clearly timed to perfection:

“U.S. pushes for more scientists but the jobs aren’t there”:

A glut of new biomedical scientists that entered the field when the economy was healthier. From 1998 to 2003, the budget of the National Institutes of Health doubled to $30 billion per year. That boost — much of which flows to universities — drew in new, young scientists. The number of new PhDs in the medical and life sciences boomed, nearly doubling from 2003 to 2007, according to the NSF.

But that boom is about to go bust, because an equal number of permanent jobs failed to follow. One big factor: Since 2004, federal research spending across all agencies has stagnated relative to inflation, according to an analysis by the American Association for the Advancement of Science.

Although the injection of $10 billion in federal stimulus funds to the NIH from the American Recovery and Reinvestment Act of 2009 “created or retained” 50,000 science jobs, according to the NIH, that money is running dry, putting those positions at risk.

The lack of permanent jobs leaves many PhD scientists doing routine laboratory work in low-wage positions known as “post-docs,” or postdoctoral fellowships. Post-docs used to last a year or two, but now it’s not unusual to find scientists toiling away for six, seven, even 10 years.

Note the particular accuracy of that quote – post-docs are left doing “routine laboratory work”, as opposed to the oft-made but mistaken claim that a seven year post-doc is about training and gaining new skills that wouldn’t be obtained in any other setting.