Space travel calculator
Screenshot from Space travel calculator webpage.
Evolution of non-lethal agonistic behaviour
Why don't dangerous animals like King cobras or black mambas kill each other when competing for mates? Instead they engage in a non-lethal competition to pin each other down. To understand this a little better, I put together a simulation which tries to see how non-lethal behaviour is selected for.
Screenshot from mating simulation webpage.
Partner matching algorithms
This is some preliminary work for my PhD research.
Screenshot from my work on partner matching algorithms.
Graphical visualisation of Prisoner's Dilemna
Screenshot of Cooperation, an implementation of the Prisoner's Dilemna game.
The programme is written in C++. It's easily extended with new competitor strategies. It can be run from the command line (for fastest results), but it also has a GUI that uses Qt. The GUI shows how the competitors are doing relative to each other, as shown in the screenshot above.
- Debunking Delusions tells the story of how the Treatment Action Campaign struggled against state-supported AIDS denialism and quackery in South Africa. Buy it from Kalahari or Amazon
- Witness to AIDS by Edwin Cameron was the joint winner, with Adam Levin's AIDSafari, of the 2006 Sunday Times/Alan Paton Prize, South Africa's premier literary award for non-fiction. I co-authored two chapters.
GroundUp is a community journalist project that reports stories from South Africa's townships. Most of our stories are about health --especially HIV, TB and sanitation--, education, women's rights and immigrants' rights. Most of my work time is spent on GroundUp at present.
Quackdown exposed nonsense health claims. My colleagues and I also tried to write helpful information about difficult health questions. Unfortunately due to lack of time I seldom update it anymore.
TB Online is a website for activists, patients, health workers and researchers to learn more about TB so that we can work to alleviate and ultimately end the worldwide epidemic. I started working on this in 2010. In 2014 I handed maintenance of the site over to the Treatment Action Group.
This is a selection of articles I've written or co-written since 1997.
Johnson L, and Geffen N. 2016. A Comparison of Two Mathematical Modeling Frameworks for Evaluating Sexually Transmitted Infection Epidemiology. Sex Transm Dis. 2016 Mar;43(3):139-46. doi: 10.1097/OLQ.0000000000000412.
Geffen N. 2016. Clearing up two Mbeki misconceptions. GroundUp. 20 March 2016.
Geffen N. 2016. Mbeki confirms he's an AIDS denialist. GroundUp. 7 March 2016.
Geffen N. 2016. Mbeki's reputation is not in tatters because he was aloof. GroundUp. 1 February 2016.
Geffen N. 2015. The banal evil of drug pricing. GroundUp. 23 September 2015.
Geffen N. 2015. Gays and sin: In limited defence of Zizipho Pae. GroundUp. 30 July 2015.
Geffen N. 2015. Anything to Stay Alive: The Challenges of a Campaign for an Experimental Drug. Dev World Bioeth. May 15. doi: 10.1111/dewb.12084.
Geffen N and Elliott K. 2015. UCT and transformation. GroundUp, April-May 2015.
Geffen N. et al. 2015. Community perspective on the INSIGHT Strategic Timing of AntiRetroviral Treatment (START) trial. HIV Med. 2015 Apr;16 Suppl 1:10-3. doi: 10.1111/hiv.12228.
Geffen N, Robinson M, Venter F and Low M. 2014. One Size Doesn’t Fit All: Tailoring Adult Antiretroviral Treatment. Southern African Journal of HIV Medicine 15, no. 3 (1 September 2014): 77–78.
Collins S. and Geffen N. 2014. Community Views: Balancing the Public Health Benefits of Earlier Antiretroviral Treatment with the Implications for Individual Patients - Perspectives from the Community. Current Opinion in HIV and AIDS 9, no. 1 (January 2014): 4–10. doi:10.1097/COH.0000000000000024.
Johnson L. and Geffen N. 2013. A comparison of microsimulation and deterministic approaches to modelling of sexually transmitted infection dynamics. Poster presented at the STI and AIDS World Congress, Vienna, Austria, 14-17 July 2013. [Abstract P3.227]
Geffen, N. 2013. World Health Organization guidelines should not change the CD4 count threshold for antiretroviral therapy initiation. Southern African Journal of HIV Medicine, Vol 14, No 1.
Geffen, N. 2013. South Africans are living longer: antiretroviral treatment vindicated. HIV Treatment Bulletin, April 2013 Issue.
Venter, F. et al. 2012. The medical proof doesn't get much better than VMMC.S Afr Med J. 2012 Feb 23;102(3 Pt 1):124-5.
Geffen, N, Venter, F and Conradie, F. Epstein is wrong about South Africa's AIDS response Quackdown. 1 August 2012.
Geffen, N. Medicines Control Council needs new leaders Business Day. 12 July 2012. (Originally published as Time for fresh leaders at medicines council in Business Day with a sub-editing error that is corrected on Quackdown.)
Geffen, N. Getting circumcision science right in the media Quackdown. 10 July 2012
Geffen, N. Getting Cape Town's transport right GroundUp. 4 July 2012.
Geffen, N. How the asylum seeking process can be improved GroundUp. 29 May 2012.
Geffen, N. Dignity, free speech and art GroundUp. 21 May 2012.
Gater, R and Geffen, N. 2012. Why norms and standards for school infrastructure are critical Cape Times. 16 May 2012.
Geffen, N. 2012. An unfortunate judgment. Quackdown. 29 March 2012.
Geffen, N. 2012. The Tara KLamp scandal deepens: Premier Mkhize must be held accountable. Quackdown. 20 March 2012.
Geffen, N. 2012. A court case and a mathematical model expose the risk of TB in South African prisons Quackdown. 29 February 2012.
Geffen, N. 2012. Monessa Shapiro's selective citations and extraordinary justifications for racism Politicsweb. 29 February 2012.
Geffen, N. 2012. Why is Israel singled out? Cape Times. 24 February 2012.
Geffen, N. 2012. What do we know about AIDS deaths in South Africa? Quackdown. 16 January 2012.
Geffen, N. 2012. What does science show about incentives in HIV testing? Quackdown. 16 January 2012.
Geffen, N. 2011. Premier's views not supported by science. Cape Times. 22 November 2011.
Silber, G and Geffen, N. 2011. Premier Helen Zille's views on HIV are misinformed and unscientific. Quackdown. 15 November 2011.
Geffen, N. 2011. How medicines are tested. Quackdown. 9 November 2011.
Geffen, N. 2011. Why is the SAJBD rejecting a two-state solution? Politicsweb. 30 October 2011.
Geffen, N. 2011. The health-care choices of Steve Jobs and Winstone Zulu Quackdown. 19 October 2011.
Low, M and Geffen, N. 2011. The king, the car and the clamp. Quackdown. 11 October 2011.
Sonderup, M, Spearman, W and Geffen, N. 2011. When the private health sector falls short. Business Day. 3 October 2011.
Geffen, N. 2011. When to start ART in adults: the results of HPTN 052 move us closer to a 'test-and-treat' policy. The Southern African Journal of HIV Medicine. September 2011.
Geffen, N. 2011. Battling the white plague: A brief history of Tuberculosis TB Online. 29 June 2011.
Geffen, N. 2011. A deadly deception. The Times. 30 May 2011.
Low, M and Geffen, N. 2010. The Tara KLamp Story. Published in several places in various forms including The Witness, PoliticsWeb and the TAC website. 25 April 2011 and other dates.
Geffen, N. 2010. Debunking Delusions: The Inside Story of the Treatment Action Campaign. Jacana.
Silber, G. and Geffen, N. 2010. On race and crime: A reply to a reply. 28 January 2010. http://writingrights.org/2010/02/01/race-class-violent-crime-update/
Geffen, N. 2009. The state of HIV in several sub-Saharan African countries: Briefing for African Judges Conference on HIV and the Law. (December 2009)
Geffen, N. 2009. The backlash against HIV funding: Briefing for African Judges Conference on HIV and the Law. (December 2009)
Silber, G. and Geffen, N. 2009. Race, class & violent crime in South Africa: Dispelling the 'Huntley Thesis'. SA Crime Quarterly 30 (December 2009)
Geffen, N. and Cameron, E. 2009. The deadly hand of denial: Governance and politically-instigated AIDS denialism in South Africa. CSSR Working Paper 257. http://www.cssr.uct.ac.za/publications/working-paper/2009/257
Geffen, N. 2009. Beyond HAART: scientists and activists need to work together. Lancet. Oct 31;374(9700):1501.
Geffen, N. 2009. AIDS and Mortality in South Africa. http://www.politicsweb.co.za/politicsweb/view/politicsweb/en/page71619?oid=151162&sn=Detail
Geffen, N. 2009. TMC207 reduces time to sputum conversion in phase II trial on patients with drug-resistant TB. HIV Treatment Bulletin, July/August 2009.
Geffen, N. and Isaacs, D. 2009. Israeli soldiers testify to rights violations in Gaza. Cape Times. 17 July 2009.
Geffen, N. and Clayden, P. 2009. HIV-related medical interventions needed in Southern Africa. HIV Treatment Bulletin South April - June 2009.
Geffen, N. and Collins, S. Assessing the cardiovascular impact of HIV, abacavir, and new signals for lopinavir/r. HIV Treatment Bulletin. May – June 2009.
Geffen, N. and Cameron, E. 2009. The deadly hand of denial: Governance and politically-instigated AIDS denialism in South Africa. CSSR working paper 257. http://www.cssr.uct.ac.za/publications/working-paper/2009/257
Geffen, N. 2009. Justice after AIDS denialism: Should there be prosecutions and compensation? J Acquir Immune Defic Syndr. 2009 Aug 1;51(4):454-5.
Geffen, N. 2009. Response to Jack Bloom's comments on the Pope and Condoms. Politicsweb. http://www.politicsweb.co.za/politicsweb/view/politicsweb/en/page71619?oid=123908&sn=Detail
Geffen, N. Zethu Cakata, Renay Pillay and Paymon Ebrahimzadeh. 2009. Mobilising gay and lesbian organisations to respond to the political challenges of the South African HIV epidemic. In From Social Science to Social Silence: Same-sex Sexuality, HIV & AIDS and Gender in South Africa. HSRC.
Geffen, N. 2008. We have a duty to speak out. Cape Times, 5 August 2008. http://www.capetimes.co.za/index.php?fArticleId=4542327. Last accessed 4 September 2008.
Geffen, N. and Gonsalves, G. 2008. In defence of rational AIDS activism. How the irrationality of Act Up-Paris and others is risking the health of people with HIV or at risk of HIV infection. Southern African Journal of HIV Medicine. Issue 30. Autumn 2008. pp. 12-17.
Geffen, N. 2008. Shattered Myths: a blog in three parts. http://healthblogs.24.com/ViewBlog.aspx?blogid=647460cd-a406-4ec7-aed0-7f292af7a444. Last accessed 4 September 2008.
Geffen, N. 2007. Maternal health and mother-to-child HIV transmission: ongoing crises. Used as part of the documentation at SANAC Civil Society meeting, November 2007. http://www.tac.org.za/nl20071129.html#briefing. Last accessed 21 March 2008.
Geffen, N. Clayden, P. Berger, J., Gonsalves, G. and Kardas- Nelson , M. 2007. Accessing life-saving medical technologies for HIV. Submission to South African Human Rights Commission and presented at the South African AIDS Conference 2007. http://www.tac.org.za/documents/AccessingEssentialMedicalTechnologiesFINAL-20070625.pdf. Last accessed 6 September 2007.
Geffen, N. 2007. Encouraging deadly choices: AIDS pseudo-science in the media. Centre for Social Science Research, UCT. http://www.cssr.uct.ac.za/papers/wp182.zip. Last accessed 6 September 2007.
Geffen N. 2007. Climate change is not hot air. Business Day, 16 January 2006. http://www.businessday.co.za/articles/opinion.aspx?ID=BD4A359789. Last accessed 16 January 2007.
Geffen N. 2006. Why TAC is protesting: A health system in crisis and without leadership: A TAC briefing sheet. 23 August 2006. http://www.tac.org.za/protest.html. Last accessed 5 September 2006.
Geffen N. 2006. What do South Africa's AIDS statistics mean? A TAC briefing paper. 7 August 2006. http://www.tac.org.za/aidsstats.html. Last accessed 5 September 2006.
Geffen N., Berger J., Golombeski C. 2006. Why prisoners with AIDS must be treated. Cape Argus, 29 June 2006. http://tac.org.za/argus20060629.html. Last accessed 21 March 2008.
Geffen N., Nattrass N., Gray G. 2006. HIV denialists ignore large gap in the study they cite. Nature 441, 406 (25 May 2006)
Geffen N., Isaacs D., Berger J. 2006. Submission to African Union Peer Review Mechanism. http://www.tac.org.za/Documents/AfricanPeerReviewMechanismReportFinal-20060217.pdf. Last accessed 5 September 2006.
Geffen N. 2006. Echoes of Lysenko: State-sponsored pseudo-science in South Africa. Social Dynamics. 31(2), pp. 183-210.
Geffen N. 2005. Founding Affidavit, TAC v. Rath and Others. http://www.tac.org.za/Documents/Court_Cases/Rath/Interdict/Geffen-1.pdf. Last accessed 5 September 2006 (with extensive editing by Geoff Budlender).
Nattrass N, Geffen N. 2005. The impact of reduced drug prices on the cost-effectiveness of HAART in South Africa. African Journal of AIDS Research. 4(1). 65-67.
Gallo R, Geffen N, Gonsalves G, Jefferys R, Kuritzkes DR, Mirken B, Moore JP, Safrit JT. 2006. Errors in Celia Farber’s March 2006 article in Harper’s Magazine. http://www.aegis.org/files/tac/2006/errorsinfarberarticle.html. Last accessed 11 May 2006. (Authors listed in alphabetical order.)
Cameron E., Geffen N. 2005. Witness to AIDS. Tafelberg.
Geffen N., Achmat A. 2004. Is Geoff Budlender still dangerous? Business Day, 8 November 2004. http://www.tac.org.za/newsletter/2004/ns03_12_2004.htm#budlender.
Geffen N. 2004. Democracy helps HIV/AIDS advocacy. Harm Reduction News, Summer 2004, 5(2). pp. 10-11. Open Society Institute.
Geffen, N and Grebe, E. 2004. Adding up the Aids toll on 'my traitor's calculator'. Mail & Guardian, 3 February 2004. http://ww1.aegis.org/news/dmg/2004/MG040201.html
Geffen N. 2004. Rian Malan spreads confusion about AIDS statistics. http://www.tac.org.za/newsletter/2004/ns20_01_2004.htm.
Geffen N. 2003. HIV/AIDS: Making drug patent laws consistent with the right to health. Humanus. 4(1). 79-83.
Nattrass N, Geffen N. 2003. Providing Antiretroviral Treatment for All Who Need it in South Africa. Centre for Social Science Research Working Paper No. 42 , UCT.
Geffen N, Nattrass N, Raubenheimer C. 2003. The Cost of HIV Prevention and Treatment Interventions in South Africa. Centre for Social Science Research Working Paper No. 28, UCT.
Soul City. 2002. AIDS Know the Facts. Soul City. (written by Nathan Geffen – distributed in Sunday Times and City Press)
Geffen N. 2002. Costs and benefits of treatment and prevention strategies . HIV/AIDS, Economics and Governance in South Africa: Key Issues in Understanding Response: A Literature Review, pp. 135-150. Centre for AIDS Research, Development and Evaluation.
Geffen, N. 2001. Treatment Action Campaign (TAC) Response to the International Intellectual Property Institute (IIPI) Report: Patent Protection and Access to HIV/AIDS Pharmaceuticals in Sub-Saharan Africa (IIPI, 2000). www.tac.org.za/newsletter/2001/ns010206.txt. Last accessed 5 September 2006.
Geffen, N. 2001. Pharmaceutical Patents, Human Rights and the HIV epidemic. Presented to the World Business Council on Sustainable Development.
Geffen, N. 2001. Applying Human Rights to the HIV/AIDS Crisis. Human Rights Dialogue. Series 2, No. 6 (Spring/Summer 2001): Rights and the Struggle for Health.
Geffen, N. 1998. Pattern Recognition and the Nondeterminable Affine Parameter Problem. Computer Science Masters Thesis, UCT Library.
Mason S et al. 1997. Information Management System for Affordable Housing Provision. South African Journal of Surveying & Mapping Vol.24, Part 3 (No.145), December, pp. 129-138.