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