Ethical issues in research methods: DOs & DON’Ts

1. Ethical issues in research methods: DOs & DON’Ts The Group 2 M. Holm, F. Postma, S. Reddy Vanga, J. Martijn, H. Agic

2. Ethics of GMO technology in plant breeding Genetically Modified Organisms = genetic characteristics are artificially modified in order to give them a new property http://www.gmo-compass.org http://www.goldenrice.org/ http://ec.europa.eu/food/food/biotechnology/index_en.htm

3. The ethical side of GMO crops • Consequences of GM technology: • Human health risks • Risks on environment • Social-economic constructions • GM technology : • Violates integrity of life http://ec.europa.eu Lammerts van Bueren, E.T. 2010

4. Gainoffunction experiments in pathogenic organisms Theseare experiments in which a pathogen is modified in the laboratorytobecome moredangerous by for instanceincreased transmission from hosttohost. Theyhave so far mostlybeenperformed on viruses, in particularinfluenza. The U.S. governmenthalted all funding for virus gainoffunction research in late 2014

5. Gainoffunction experiments in pathogenic organisms So far the debate is primarilyfocused on biosafety and containmentpractices. ”Ethics” areinvoked by all sides in the debate in a ratherilldefinedmanner. At itscorethis is a questionof potential risk versus potential benefits and whether or not it is acceptable toendangerpeople in the hopethatwemightfindcures for dangerousdiseases.

6. Confirmation bias in phylogenetic reconstruction Reconstruction of evolutionary history ScientificMethod Question What is the evolutionary history? Collect information Collect sequence data Construct hypothesis Reconstruct phylogeny ( hypothesis ) Experiment ( test hypothesis ) The phylogeny is a hypothesis!No real way of testing Accept or Reject hypothesis

7. Confirmation bias in phylogenetic reconstruction Problem: Too many different ways of making phylogenies Different genes give different phylogenies Collect sequence data Different species selections give different phylogenies Align genes Different alignment softwares Trim alignments Different site selections Different phylogenetic softwares Make phylogeny Different models of evolution Which one is the closest to the truth???

8. Its easy to fall into a trap and (subconsciously) select the phylogeny that you like the most Because you published a similar phylogenybefore Because that phylogeny is the most spectacular and gets you into a high impact journal Because this phylogeny fits very well in the story of a paper Etc. Confirmation bias in phylogenetic reconstruction How to make sure not to fall in this trap?

9. Confirmation bias in phylogenetic reconstruction “My thesis advisor is so happy because it confirms his long-held belief in how the phylogenetic tree would look” “It took me seventeen different computer programs, 84 substitution models and 4,000 CPU years of computing, but finally I got the tree I hoped I would get when I started the study”.

10. Bias in the calibration of molecular clocks with the fossil record How does it work? Erwin et al . 2011. Science, 334, 1091.

11. Bias in the calibration of molecular clocks • Problem? • Using material that many workers still dispute • Fitting the data to fit a hypothesis • Consequences? • Producing flawed science • People unaware of the problems use and apply erroneous results • Ethical issues • Bandwaggon research

12. Ethics in Computational Biology • No experiments, animals or no mutational studies. • What’s the problem! - Closed source? “Software company bans competitive users” Nature 429, 231 (20 May 2004) | doi:10.1038/429231a

13. Why? • If you compare • If you implement a code in “competitor” programs. • It’s effect? • Peer review • Restricted freedom …and many! “OPEN FOR DISCUSSION” http://www.bannedbygaussian.org/ http://www.gaussian.com/g_misc/silly.htm