Statistics and the Search for Scientific Truth

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1 Statistics and the Search for Scientific Truth Martin Hazelton 1 Institute of Fundamental Sciences Massey University 11 November Presenter: U3A, November / 30

2 Science in a World of Infinite Variety The World is full of variation. A lot of Science is about explaining variations and differences. U3A, November / 30

3 Designed Experiments Experiments provide a powerful approach to explaining differences. The goal is to relate variations in a response to changes in experimental factors. U3A, November / 30

4 Statistical Analysis of Experimental Data Typically there are multiple sources of variation beyond experimental factors. The result is noisy experimental data. This can make it difficult to attribute changes in response to the treatment. Statistics provides the tools to objectively assess the evidence for an association between treatment and response. Statistics makes use of probability models to represent alternative sources of variation. U3A, November / 30

5 The Lady Tasting Tea Muriel Bristol ( The Lady ) was a scientist working at Rothamsted Experimental Station in She claimed to be able to tell whether the milk or the tea was poured into a cup first. Co-worker Ronald Fisher devised experiment to test this. U3A, November / 30

6 The Lady Tasting Tea The Experiment 8 cups of tea 4 have milk poured first, then tea have tea poured first, then milk. Cups presented in random order to The Lady. She had to identify each one as milk or tea first. U3A, November / 30

7 The Lady Tasting Tea Analysis of Results The Lady correctly identified milk/tea pouring order for all 8 cups. Does this provide evidence of her discernment or could it have been lucky guesswork? Can assess the evidence using probability. U3A, November / 30

8 The Lady Tasting Tea A Simplified Case Suppose there had been just two cups of tea: One with milk first. One with tea first. Cups presented in random order so two equally likely possibilities. 1 M T 2 T M 50% chance of selecting correct one by chance. Even if the Lady did guess the correct order, cannot distinguish between discernment and guesswork. U3A, November / 30

9 The Lady Tasting Tea Possibilities from Full Experiment MMMMTTTT MMMTMTTT MMMTTTTM MMMTTTMT MMMTTMTT MMTMTTTM MMTMTTMT MMTMTMTT MMTMMTTT MMTTTTMM MMTTTMTM MMTTTMMT MMTTMTTM MMTTMTMT MMTTMMTT MTMTMMTT MTMTMTMT MTMTMTTM MTMTTMMT MTMTTMTM MTMTTTMM MTMMTMTT MTMMTTMT MTMMTTTM MTMMMTTT MTTMMTTM MTTMMTMT MTTMMMTT MTTMTMMT MTTMTMTM MTTMTTMM MTTTMMMT MTTTMMTM MTTTMTMM MTTTTMMM TMMTMMTT TMMTMTMT TMMTMTTM TMMTTMMT TMMTTMTM TMMTTTMM TMMMTTMT TMMMTTTM TMMMTMTT TMMMMTTT TMTTTMMM TMTTMMTM TMTTMMMT TMTTMTMM TMTMTTMM TMTMTMTM TMTMTMMT TMTMMTTM TMTMMTMT TMTMMMTT TTMMMMTT TTMMMTMT TTMMMTTM TTMMTMMT TTMMTMTM TTMMTTMM TTMTMMMT TTMTMMTM TTMTMTMM TTMTTMMM TTTMMMTM TTTMMMMT TTTMMTMM TTTMTMMM TTTTMMMM U3A, November / 30

10 The Lady Tasting Tea Possibilities from Full Experiment MMMMTTTT MMMTMTTT MMMTTTTM MMMTTTMT MMMTTMTT MMTMTTTM MMTMTTMT MMTMTMTT MMTMMTTT MMTTTTMM MMTTTMTM MMTTTMMT MMTTMTTM MMTTMTMT MMTTMMTT MTMTMMTT MTMTMTMT MTMTMTTM MTMTTMMT MTMTTMTM MTMTTTMM MTMMTMTT MTMMTTMT MTMMTTTM MTMMMTTT MTTMMTTM MTTMMTMT MTTMMMTT MTTMTMMT MTTMTMTM MTTMTTMM MTTTMMMT MTTTMMTM MTTTMTMM MTTTTMMM TMMTMMTT TMMTMTMT TMMTMTTM TMMTTMMT TMMTTMTM TMMTTTMM TMMMTTMT TMMMTTTM TMMMTMTT TMMMMTTT TMTTTMMM TMTTMMTM TMTTMMMT TMTTMTMM TMTMTTMM TMTMTMTM TMTMTMMT TMTMMTTM TMTMMTMT TMTMMMTT TTMMMMTT TTMMMTMT TTMMMTTM TTMMTMMT TTMMTMTM TTMMTTMM TTMTMMMT TTMTMMTM TTMTMTMM TTMTTMMM TTTMMMTM TTTMMMMT TTTMMTMM TTTMTMMM TTTTMMMM U3A, November / 30

11 The Lady Tasting Tea Conclusions Recall, the Lady correctly identified milk/tea pouring order for all 8 cups. Two possible explanations. 1 The Lady truly can detect whether tea or milk was poured first. 2 The Lady made a very lucky 1/70 1.4% guess. Since guess is rather improbable, explanation 1 is plausible. U3A, November / 30

12 Probability Valid statistical analysis of experimental data requires probability models. Unfortunately, humans don t seem to be intuitively good at probability. U3A, November / 30

13 The Monty Hall Problem Probability Challenge #1 Based on a U.S. game show. Contestant must choose one of three doors. Behind two are goats; behind the other is a car. After initial choice, game show host identifies one of the other doors as hiding a goat. Contestant may either stick with original choice, or switch to another door. U3A, November / 30

14 The Monty Hall Problem Example Contestant picks door 1. Host indicates that door 3 hides a goat. Contestant can now stick with door 1, or change to door 2. What is the best strategy? What is the probability of winning the car if contestant sticks with door 1? U3A, November / 30

15 The Monty Hall Problem Explanation U3A, November / 30

16 Patterns in Coin Tossing Data The Audience Gets Another Go Pattern 1: H Pattern 2: T U3A, November / 30

17 Patterns in Coin Tossing Data The Audience Gets Another Go Pattern 1: HTH Pattern 2: HTT U3A, November / 30

18 Patterns in Coin Tossing Data The Audience Gets Another Go Repeated Pattern 1: HTHTH Repeated Pattern 2: HTTHTT U3A, November / 30

19 Probability Models for Genetic Data can be really tricky U3A, November / 30

20 Mistakes in the Statistical Analysis of Scientific Data Mistakes in the statistical analysis of scientific data are not uncommon. These can occur through incorrect probability calculations and also when simply processing and manipulating the raw data. Modern datasets can be of huge size and complexity. Genetic data is a case in point. Require careful computer processing. A single error in a line of code can have profound effects. U3A, November / 30

21 Lies, Damn Lies and Statistics The Problem of Scientific Fraud The complexity and scale of the analysis of many modern datasets provides plenty of opportunity for well disguised scientific fraud. U3A, November / 30

22 The Duke University Cancer Research Scandal Advances in human genetics have the potential to revolutionize medicine. A major long term goal is the development of effective personalized treatments for cancer. Progress had been slower than hoped but a major breakthrough was announced in 2006 by researchers at Duke University. U3A, November / 30

23 The Duke University Cancer Research Scandal Claimed Research Breakthrough Duke researchers examined drug sensitivity of a standard panel of cell lines derived from 9 types of human tumours. Then looked at genetic profiles of most resistant and most susceptible cell lines using microarrays. In theory, these results provide means of selecting best chemotherapy treatment based on genetic profile of a patient s tumour. U3A, November / 30

24 The Duke University Cancer Research Scandal Fame and Fortune (Science Style) The research was widely regarded as a remarkable breakthrough. The paper by the Duke research team that first described the results was hailed as one of the top publications of Subsequent papers appeared in several leading journals. The researcher primarily responsible for the work was Anil Potti (picture above). He became something of a poster boy for Duke University. U3A, November / 30

25 The Duke University Cancer Research Scandal Houston, We Have a Problem. There was great interest in Potti s work from research groups worldwide. One such group was in the famous M. D. Anderson Cancer Center, Houston, Texas. U3A, November / 30

26 The Duke University Cancer Research Scandal Statisticians take centre stage Keith Baggerly (above left) and Kevin Coombes were statisticians working at the M. D. Anderson Cancer Center. At the request of medical research colleagues, Baggerly and Coombes sought to learn more about the remarkable findings of Potti and co. Baggerly and Coombes requested the data and computer code for the statistical analysis from Duke University. U3A, November / 30

27 The Duke University Cancer Research Scandal Irreproducibility Baggerly and Coombes first step was to try and reproduce the data analysis done at Duke. They ran into problems almost straight away. There were issues with data integrity. Some nominally resistant cell lines appeared more sensitive than some sensitive ones, and vice-versa. Data were also mis-labelled in other ways. Some of the data processing had been done by hand, producing results that Baggerly and Coombes could not replicate. Based on their best understanding of the data and the labelling techniques employed, Baggerly and Coombes found that experimental results for genetic effects were no better than pure chance. U3A, November / 30

28 The Duke University Cancer Research Scandal Is anybody listening? Baggerly and Coombes raised their concerns through a variety of avenues. Duke University conducted a perfunctory internal review, which found no significant problems with Potti s work. Potti and colleagues were allowed to continue their research. By 2007, 109 patients were enrolled in a clinical trial based on Potti s findings. Baggerly and Coombes also sent letters to journals that had published Potti s work, but with limited success. U3A, November / 30

29 The Duke University Cancer Research Scandal Can you hear us now? Eventually Baggerly and Coombes resorted to publishing their own interpretation of the Duke data, in a top statistics journal. U3A, November / 30

30 The Duke University Cancer Research Scandal Denouement The evidence of scientific fraud became overwhelming: 1 Baggerly and Coombes research paper; 2 Several international research groups had tried and failed to replicate Potti s findings senior statisticians, epidemiologists and medical researchers wrote to the senior management of Duke University to express concerns; 4 Paul Goldberg, editor of The Cancer Letter, found that Anil Potti had lied of his curriculum vitae. Anil Potti eventually admitted to problems with the data, and subsequently resigned. Almost all the published papers on Potti s research were retracted. U3A, November / 30

31 Not the End of the Story (Unfortunately) Grant Steen showed that over period , about 80,000 patients had participated in clinical trials based on research that was incorrect and for which papers were retracted. Steen, R. G. (2011). Retractions in the medical literature: how many patients are put at risk by flawed research? Journal of Medical Ethics, jme U3A, November / 30

32 Hope for the Future Growing recognition in the scientific community of pivotal importance of reproducibility in data processing and analysis. Journals increasingly will only publish work for which data and computer code are supplied. Statisticians play a central role in the search for scientific truth. U3A, November / 30

33 Thank You for Listening U3A, November / 30

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