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

Ethics of GMO technology in plant breeding Genetically Modified Organisms = genetic characteristics are artificially modified in order to give them a new property

Consequences of GM technology: – Human health risks – Risks on environment – Social-economic constructions GM technology : – Violates integrity of life The ethical side of GMO crops Lammerts van Bueren, E.T. 2010

Gain of function experiments in pathogenic organisms These are experiments in which a pathogen is modified in the laboratory to become more dangerous by for instance increased transmission from host to host. They have so far mostly been performed on viruses, in particular influenza. The U.S. government halted all funding for virus gain of function research in late 2014

So far the debate is primarily focused on biosafety and containment practices. ”Ethics” are invoked by all sides in the debate in a rather ill defined manner. At its core this is a question of potential risk versus potential benefits and whether or not it is acceptable to endanger people in the hope that we might find cures for dangerous diseases. Gain of function experiments in pathogenic organisms

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

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

Confirmation bias in phylogenetic reconstruction Its easy to fall into a trap and (subconsciously) select the phylogeny that you like the most Because you published a similar phylogeny before 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. How to make sure not to fall in this trap?

“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”. 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”

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

Bias in the calibration of molecular clocks Ethical issues -Bandwaggon research 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

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: /429231a

Why? – If you compare – If you implement a code in “competitor” programs. It’s effect? – Peer review – Restricted freedom …and many! “OPEN FOR DISCUSSION”