The Rules of Contagion

by Adam Kucharski

  12. Background on sequence availability: Gire S.K. et al., ‘Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak’, Science, 2014; Yozwiak N.L., ‘Data sharing: Make outbreak research open access’, Nature, 2015; Gytis Dudas, https://twitter.com/evogytis/status/1065157012261126145

  13. Sample I., ‘Thousands of lives put at risk by clinical trials system that is “not fit for purpose”’, The Guardian, 31 March 2014.

  14. Callaway E., ‘Zika-microcephaly paper sparks data-sharing confusion’, Nature, 12 February 2016; Maxmen, A., ‘Two Ebola drugs show promise amid ongoing outbreak,’ Nature, 12 August 2019; Johansson M.A. et al., ‘Preprints: An underutilized mechanism to accelerate outbreak science’, PLOS Medicine, 2018; https://nextstrain.org/community/inrb-drc/ebola-nord-kivu

  15. Sabeti P., ‘How we’ll fight the next deadly virus’, TEDWomen 2015.

  16. Hadfield J. et al., ‘Nextstrain: real-time tracking of pathogen evolution’, Bioinformatics, 2018.

  17. Owlcation, ‘The History Behind the Story of Goldilocks’, 22 February 2018, https://owlcation.com/humanities/goldilocks-and-three-bears

  18. Background and quotes from author interview with Jamie Tehrani, October 2017.

  19. Tehrani J.J., ‘The Phylogeny of Little Red Riding Hood’, PLOS ONE, 2013.

  20. Van Wyhe J., ‘The descent of words: evolutionary thinking 1780–1880’, Endeavour, 2005.

  21. Luu C., ‘The Fairytale Language of the Brothers Grimm’, JSTOR Daily, 2 May 2018.

  22. Da Silva S.G. and Tehrani J.J., ‘Comparative phylogenetic analyses uncover the ancient roots of Indo-European folktales’, Royal Society Open Science, 2015.

  23. Smith D. et al., ‘Cooperation and the evolution of hunter-gatherer storytelling’, Nature Communications, 2017.

  24. Background from: Stubbersfield J.M. et al., ‘Serial killers, spiders and cybersex: social and survival information bias in the transmission of urban legends’, British Journal of Psychology, 2015. A similar result pattern has been found in other telephone studies, with social information seemingly having an advantage when it comes to transmission.

  25. Background on counter-intuitive elements from: Mesoudi A. and Whiten A., ‘The multiple roles of cultural transmission experiments in understanding human cultural evolution’, Philosphical Transactions of the Royal Society B, 2008; Stubbersfield J. and Tehrani J., ‘Expect the Unexpected? Testing for Minimally Counterintuitive (MCI) Bias in the Transmission of Contemporary Legends: A Computational Phylogenetic Approach’, Social Science Computer Review, 2013.

  26. Dlugan A., ‘How to Use the Rule of Three in Your Speeches’, 27 May 2009. http://sixminutes.dlugan.com/rule-of-three-speeches-

  public-speaking

  27. The rule of three is also common in comedy, where an unexpected third item creates the punchline.

  28. Newberry M.G. et al., ‘Detecting evolutionary forces in language change’, Nature, 2017.

  29. Valverde S. and Sole R.V., ‘Punctuated equilibrium in the large-scale evolution of programming languages’, Journal of the Royal Society Interface, 2015.

  30. Svinti V. et al., ‘New approaches for unravelling reassortment pathways’, BMC Evolutionary Biology, 2013.

  31. Sample I., ‘Evolution: Charles Darwin was wrong about the tree of life’, The Guardian, 21 January 2009.

  32. Background on sponging from: Krützen M. et al., ‘Cultural transmission of tool use in bottlenose dolphins’, PNAS, 2005; Morell V., ‘Why Dolphins Wear Sponges’, Science, 20 July 2011.

  33. Background and quotes from author interview with Lucy Aplin, August 2017.

  34. Baker K.S. et al., ‘Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species’, Nature Communications, 2018; McCarthy A.J. et al., ‘Extensive Horizontal Gene Transfer during Staphylococcus aureus Co-colonization In Vivo’, Genome Biology and Evolution, 2014; Alirol E. et al., ‘Multidrug-resistant gonorrhea: A research and development roadmap to discover new medicines’, PLOS Medicine, 2017.

  35. Gallagher J., ‘Man has “world’s worst” super-gonorrhoea’, BBC News Online, 28 March 2018; Gallagher J., ‘Super-gonorrhoea spread causes “deep concern”’, BBC News Online, 9 January 2019.

  36. Alzheimer’s Society’s view on genetic testing. April 2015. https://www.alzheimers.org.uk/about-us/policy-and-influencing/what-we-think/genetic-testing; Genetic testing for cancer risk. Cancer Research UK. https://www.cancerresearchuk.org/about-cancer/causes-of-cancer/inherited-cancer-genes-and-increased-cancer-risk/genetic-testing-for-cancer-risk

  37. Middleton A., ‘Attention The Times: Prince William’s DNA is not a toy’, The Conversation, 14 June 2013. Researchers have also criticised the scientific analysis behind the story. Source: Kennett D.A, ‘The Rise and Fall of Britain’s DNA: A Tale of Misleading Claims, Media Manipulation and Threats to Academic Freedom’, Genealogy, 2018.

  38. Ash L., ‘The Christmas present that could tear your family apart’, BBC News Online, 20 December 2018.

  39. Clark K., ‘Scoop: 23andMe is raising up to $300M’, PitchBook, 24 July 2018; Rutherford A., ‘DNA ancestry tests may look cheap. But your data is the price’, The Guardian, 10 August 2018.

  40. Cox N., ‘UK Biobank shares the promise of big data’, Nature, 10 October 2018.

  41. Based on 1990 census data, Sweeney estimated 87 per cent of people could be identified. Subsequent studies revised this down to 61–63 per cent based on 1990 and 2000 data. Background: Sweeney L., ‘Simple Demographics Often Identify People Uniquely’, Carnegie Mellon University, Data Privacy Working Paper, 2000; Ohm P., ‘Broken Promises of Privacy: Responding to the Surprising Failure of Anonymization’, UCLA Law Review, 2010; Sweeney L., ‘Only You, Your Doctor, and Many Others May Know’, Technology Science, 2015.

  42. Sweeney L., ‘Only You, Your Doctor, and Many Others May Know’, Technology Science, 2015.

  43. Smith S., ‘Data and privacy’, Significance, 3 October 2014.

  44. Background on taxi data from: Whong C., ‘FOILing NYC’s Taxi Trip Data’, 18 March 2014. https://chriswhong.com; Pandurangan V., ‘On Taxis and Rainbows’, 21 June 2014. https://tech.vijayp.ca

  45. Background and quotes from: Tockar A., ‘Riding with the Stars: Passenger Privacy in the NYC Taxicab Dataset’, 15 September 2014. https://research.neustar.biz.

  46. De Montjoye Y.A., ‘Unique in the Crowd: The privacy bounds of human mobility’, Scientific Reports, 2013.

  47. Shahani A., ‘Smartphones Are Used To Stalk, Control Domestic Abuse Victims’, National Public Radio, 15 September 2014.

  48. Hern A., ‘Fitness tracking app Strava gives away location of secret US army bases’, The Guardian, 28 January 2014.

  49. Watts A.G. et al., ‘Potential Zika virus spread within and beyond India’, Journal of Travel Medicine, 2018; Bengtsson L. et al., ‘Improved Response to Disasters and Outbreaks by Tracking Population Movements with Mobile Phone Network Data: A Post-Earthquake Geospatial Study in Haiti’, PLOS Medicine, 2011; Santi P. et al., ‘Quantifying the benefits of vehicle pooling with shareability networks’, PNAS, 2014.

  50. Chen M.K. and Rohla R., ‘The effect of partisanship and political advertising on close family ties’, Science, 2018; Silm S. et al., ‘Are younger age groups less segregated? Measuring ethnic segregation in activity spaces using mobile phone data’, Journal of Ethnic and Migration Studies, 2017; Xiao Y. et al., ‘Exploring the disparities in park access through mobile phone data: Evidence from Shanghai, China’, Landscape and Urban Planning, 2019; Atlas of Inequality, https://inequality.media.mit.edu.

  51. Conlan A.J.K. et al., ‘Measuring social networks in British primary schools through scientific engagement’, Proceedings of the Royal Society B, 2010.

  52. Background on GPS brokers from: Harris R., ‘Your Apps Know Where You Were Last Night, and They’re Not Keeping It Secret’, New York Times, 10 December 2018; Signoret P., Teemo, ‘la start-up qui traque 10 millions de Français en continu’, L’Express L’Expa
nsion, 25 August 2018; ‘Is Geospatial Data a $100 Billion Business for SafeGraph?’ Nanalyze, 22 April 2017.

  53. Importantly, the target gave permission for their phone to be tracked. Source: Cox J., ‘I Gave a Bounty Hunter $300. Then He Located Our Phone’, Motherboard, 8 January 2019.

  54. Scam alert: Speeding ticket email scam. Tredyffrin Police Department. 23 March 2016.

  55. Background on SARS introduction from: ‘SARS Commission Final Report’, Government of Ontario, 2005; Tsang K.W. et al., ‘A Cluster of Cases of Severe Acute Respiratory Syndrome in Hong Kong’, The NEJM, 2003.

  56. Donnelly C.A. et al., ‘Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong’, The Lancet, 2003.

  57. WHO Ebola Response Team, ‘Ebola Virus Disease in West Africa – The First 9 Months of the Epidemic and Forward Projections’, NEJM, 2014; Assiri A. et al., ‘Hospital Outbreak of Middle East Respiratory Syndrome Coronavirus’, NEJM, 2013; WHO Consultation on Clinical Aspects of Pandemic (H1N1) 2009 Influenza, ‘Clinical Aspects of Pandemic 2009 Influenza A (H1N1) Virus Infection’, NEJM, 2010.

  58. Background on Willowbrook from: Rothman D.J., The Willowbrook Wars: Bringing the Mentally Disabled into the Community (Aldine Transaction, 2005); Fansiwala K., ‘The Duality of Medicine: The Willowbrook State School Experiments’, Medical Dialogue Review, 20 February 2016; Watts G., ‘Robert Wayne McCollum’, The Lancet, 2010.

  59. Quoted in: Offit P., Vaccinated: One Man’s Quest to Defeat the World’s Deadliest Diseases (Harper Perennial, 2008).

  60. Goldby S., ‘Experiments at the Willowbrook state school’, The Lancet, 1971.

  61. Gordon R.M., The Infamous Burke and Hare: Serial Killers and Resurrectionists of Nineteenth Century Edinburgh (McFarland, 2009).

  62. Transcript for NMT 1: Medical Case, 9 January 1947. Harvard Law School Library Nuremberg Trials Project.

  63. Waddington C.S. et al., ‘Advancing the management and control of typhoid fever: A review of the historical role of human challenge studies’, Journal of Infection, 2014.

  64. Background on modern challenge studies: Cohen J., ‘Studies that intentionally infect people with disease-causing bugs are on the rise’, Science, 18 May 2016; https://clinicaltrials.gov; Nordling L., ‘The Ethical Quandary of Human Infection Studies’, Undark, 19 November 2018.

  8. A spot of trouble

  1. Peterson Hill N., A Very Private Public Citizen: The Life of Grenville Clark (University of Missouri, 2016).

  2. Ham P., ‘As Hiroshima Smouldered, Our Atom Bomb Scientists Suffered Remorse’, Newsweek, 5 August 2015.

  3. Ito S., ‘Einstein’s pacifist dilemma revealed’, The Guardian, 5 July 2005; ‘The Einstein Letter That Started It All; A message to President Roosevelt 25 Years ago launched the atom bomb and the Atomic Age’, New York Times, 2 August 1964.

  4. Clark G., Letters to the Times, New York Times, 22 April 1955.

  5. Harris E.D. et al., ‘Governance of Dual-Use Technologies: Theory and Practice’, American Academy of Arts & Sciences, 2016.

  6. Santi P. et al., ‘Quantifying the benefits of vehicle pooling with shareability networks’, PNAS, 2014; other references covered in earlier chapters.

  7. Cadwalladr C. et al., ‘Revealed: 50 million Facebook profiles harvested for Cambridge Analytica in major data breach’, The Guardian, 17 March 2018.

  8. Sumpter S., Outnumbered: From Facebook and Google to Fake News and Filter-bubbles – The Algorithms That Control Our Lives (Bloomsbury Sigma, 2018); Chen A. et al., ‘Cambridge Analytica’s Facebook data abuse shouldn’t get credit for Trump’, The Verge, 20 March 2018.

  9. Zunger Y., ‘Computer science faces an ethics crisis. The Cambridge Analytica scandal proves it’, Boston Globe, 22 March 2018.

  10. Harkin J., ‘“Big Data”, “Who Owns the Future?” and “To Save Everything, Click Here”’, Financial Times, 1 March 2013; Harford T., ‘Big data: A big mistake?’, Significance, 1 December 2014; McAfee A. et al., ‘Big Data: The Management Revolution’, Harvard Business Review, October 2012.

  11. Ginsberg J. et al., ‘Detecting influenza epidemics using search engine query data’, Nature, 2009.

  12. Olson D.R. et al., ‘Reassessing Google Flu Trends Data for Detection of Seasonal and Pandemic Influenza: A Comparative Epidemiological Study at Three Geographic Scales’, PLOS Computational Biology, 2013.

  13. Lazer D. et al., ‘The Parable of Google Flu: Traps in Big Data Analysis,’ Science, 2014.

  14. World Health Organization, ‘Pandemic influenza vaccine manufacturing process and timeline’, WHO Briefing Note, 2009.

  15. Petrova V.N. et al., ‘The evolution of seasonal influenza viruses’, Nature Reviews Microbiology, 2017; Chakraborty P. et al., ‘What to know before forecasting the flu’, PLOS Computational Biology, 2018.

  16. Buckee C., ‘Sorry, Silicon Valley, but “disruption” isn’t a cure-all’, Boston Globe, 22 January 2017.

  17. Farrar J., ‘The key to fighting the next “Ebola” outbreak is in your pocket’, Wired, 4 December 2016; other references covered in earlier chapters.

  18. World Health Organisation, ‘Ebola outbreak in the Democratic Republic of the Congo declared a Public Health Emergency of International Concern’, WHO newsroom, 17 July 2019; Silberner J., ‘Congo’s fight against Ebola stalls after epidemiologist is shot dead’, British Medical Journal, 2019.

  19. Ginsberg M. et al., ’Swine Influenza A (H1N1) Infection in Two Children – Southern California, March–April 2009, Morbidity and Mortality Weekly Report, 2009.

  20. Cohen J., ‘As massive Zika vaccine trial struggles, researchers revive plan to intentionally infect humans’, Science, 12 September 2018; Koopmans M. et al., ‘Familiar barriers still unresolved – a perspective on the Zika virus outbreak research response’, The Lancet Infectious Diseases, 2018.

  21. Gordon A. et al., ‘Prior dengue virus infection and risk of Zika: A pediatric cohort in Nicaragua’, PLOS Medicine, 2019.

  22. Grinberg N. et al., ‘Fake news on Twitter during the 2016 U.S. presidential election’, Science, 2019; Guess A. et al., ‘Less than you think: Prevalence and predictors of fake news dissemination on Facebook’, Science Advances, 2019; Lazer D.M.J. et al., ‘The science of fake news’, Science, 2018; Wagner K., ‘Inside Twitter’s ambitious plan to change the way we tweet’, Recode, 8 March 2019; McCarthy K., ‘Facebook, Twitter slammed for deleting evidence of Russia’s US election mischief’, The Register, 13 October 2017.

  23. Haldane A.G., ‘Rethinking the Financial Network’, Bank of England speech, 28 April 2009; Editorial Board, ‘A fractured reporting system stymies public-safety research’, Bloomberg, 25 October 2018.

  24. Greene G., The Woman Who Knew Too Much: Alice Stewart and the Secrets of Radiation (University of Michigan Press, 2001).

  25. Presentation at Epidemics[6] conference, 2017.

  26. Kosinski M. et al., ‘Private traits and attributes are predictable from digital records of human behavior’, PNAS, 2013.

  27. Cadwalladr C. et al., ‘Revealed: 50 million Facebook profiles harvested for Cambridge Analytica in major data breach’, The Guardian, 17 March 2018. Note that despite the apparent similarity in methods, Cambridge Analytica did not work with Kosinki.

  28. Alaimo K., ‘Twitter’s Misguided Barriers for Researchers’, Bloomberg, 16 October 2018.

  29. Godlee F., ‘What can we salvage from care.data?’, British Medical Journal, 2016.

  30. Kucharski A.J. et al., ‘School’s out: seasonal variation in the movement patterns of school children’, PLOS ONE, 2015; Kucharski A.J. et al., ‘Structure and consistency of self-reported social contact networks in British secondary schools’, PLOS ONE, 2018.

  31. http://www.bbc.co.uk/pandemic.

  32. Information Commissioner’s Office, ‘Investigation into the use of data analytics in political campaigns’, ICO report, 11 July 2018.

  33. Rifkind H., TV review, The Times, 24 March 2018.

  34. Assuming a six-h
our reading time (i.e. 225 words per minute). Data: World Health Organization. http://www.who.int, 2018; Dance D.A. et al., ‘Global Burden and Challenges of Melioidosis’, Tropical Medicine and Infectious Disease, 2018.

  35. Declined from 291 per 100,000 in 1990 to 154 per 100,000 in 2016. Source: Ritchie H. et al., ‘Causes of Death’, Our World in Data, 2018.

  36. UK Government, Health profile for England: 2017. https://www.gov.uk.

  37. Harper-Jemison D.M. et al., ‘Leading causes of death in Chicago’, Chicago Department of Public Health Office of Epidemiology, 2006; ‘Illinois State Fact Sheet’, National Injury and Violence Prevention Resource Center, 2015.

  38. Information Commissioner’s Office, ‘Investigation into the use of data analytics in political campaigns’, ICO report, 11 July 2018; DiResta R. et al., ‘The Tactics & Tropes of the Internet Research Agency’, New Knowledge, 2018.

  Further reading

  If you want to know more about the topics covered in this book, additional suggestions for articles, papers and books are given below. To ensure reproducibility, all data and code required to generate the figures in the book are available from: https://github.com/adamkucharski/rules-of-contagion/

  Chapter 1

  A trio of papers by Paul Fine has more information on the theory of mechanistic modelling and resulting concepts like herd immunity: ‘Ross’s A Priori Pathometry – A Perspective’ (Proceedings of the Royal Society of Medicine, 1975); ‘John Brownlee and the measurement of infectiousness: an historical study in epidemic theory’ (Journal of the Royal Statistical Society: Series A, 1979); ‘Herd Immunity: History, Theory, Practice’ (Epidemiological Reviews, 1993). For a more technical description of Ross’s analysis and its legacy, see David Smith and colleagues’ paper ‘Ross, Macdonald, and a Theory for the Dynamics and Control of Mosquito-Transmitted Pathogens’ (PLOS Pathogens, 2012).

  Chapter 2

  Donald MacKenzie and Taylor Spears’s paper ‘“The Formula That Killed Wall Street”?: The Gaussian Copula and the Material Cultures of Modelling’ (2012) provides a useful oral history of the models behind CDOs. Liar’s Poker: Rising Through the Wreckage on Wall Street (W. W. Norton & Company, 1989) and The Big Short: Inside the Doomsday Machine (W. W. Norton & Company, 2010) by Michael Lewis, written twenty years apart, explain how mortgage trading started and the chaos it would later cause. When Genius Failed: The Rise and Fall of Long-Term Capital Management by Roger Lowenstein (Random House, 2000) covers the collapse of the titular hedge fund.