Ethical issues in research methods: DOs & DON’Ts The Group 2 M. Holm, F. Postma, S. Reddy Vanga,...
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Transcript of Ethical issues in research methods: DOs & DON’Ts The Group 2 M. Holm, F. Postma, S. Reddy Vanga,...
Ethical issues in research methods: DOs & DON’Ts
The Group 2M. 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
http://ec.europa.eu/food/food/biotechnology/index_en.htm
http://www.goldenrice.org/http://www.gmo-compass.org
• 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
http://ec.europa.euLammerts 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 fordangerous diseases.
Gain of function experiments in pathogenic organisms
Confirmation bias in phylogenetic reconstruction
Question
Collect information
Constructhypothesis
Experiment ( test hypothesis )
Accept or Reject hypothesis
What is the evolutionary history?
Collect sequence data
Reconstruct phylogeny ( hypothesis )
ScientificMethod
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 . 2011. 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:10.1038/429231a
• Why?– If you compare – If you implement a code in “competitor” programs.
• It’s effect?– Peer review– Restricted freedom…and many!
“OPEN FOR DISCUSSION”
http://www.bannedbygaussian.org/http://www.gaussian.com/g_misc/silly.htm