This week we will not have a lab-meeting, as I will be in Uppsala, participating in a course about the Open Source-programme "R". As some of you might still want some intellectual input this week anyway, you could always listen to the excellent swedish radio programme "Filosofiska Rummet".
Last Sunday, the theme of this programme were the moralistic and the naturalistic fallacies. I was one of the three participants, together with sociologist Eva Kärfve from Lund University and philosophy professor Per Bauhn from Kalmar. You can listen to the programme here. It is in Swedish, though, but most of you will understand the discussion. Enjoy!
Showing posts with label biology. Show all posts
Showing posts with label biology. Show all posts
Tuesday, October 6, 2009
Thursday, April 9, 2009
Lab meeting in the Darwin room on Wednesday the 15th of April at 10:15am
Hello everybody,
We have picked two papers for the upcoming lab meeting next week. The first one is by Masafumi Nozawaa, Yoshiyuki Suzukia, and Masatoshi Nei and is entitled ‘Reliabilities of identifying positive selection by the branch-site and the site-prediction methods’
Abstract
Natural selection operating in protein-coding genes is often studied by examining the ratio (ω) of the rates of nonsynonymous to synonymous nucleotide substitution. The branch-site method (BSM) based on a likelihood ratio test is one of such tests to detect positive selection for a predetermined branch of a phylogenetic tree. However, because the number of nucleotide substitutions involved is often very small, we conducted a computer simulation to examine the reliability of BSM in comparison with the small-sample method (SSM) based on Fisher's exact test. The results indicate that BSM often generates false positives compared with SSM when the number of nucleotide substitutions is ≈80 or smaller. Because the ω value is also used for predicting positively selected sites, we examined the reliabilities of the site-prediction methods, using nucleotide sequence data for the dim-light and color vision genes in vertebrates. The results showed that the site-prediction methods have a low probability of identifying functional changes of amino acids experimentally determined and often falsely identify other sites where amino acid substitutions are unlikely to be important. This low rate of predictability occurs because most of the current statistical methods are designed to identify codon sites with high ω values, which may not have anything to do with functional changes. The codon sites showing functional changes generally do not show a high ω value. To understand adaptive evolution, some form of experimental confirmation is necessary.
Natural selection operating in protein-coding genes is often studied by examining the ratio (ω) of the rates of nonsynonymous to synonymous nucleotide substitution. The branch-site method (BSM) based on a likelihood ratio test is one of such tests to detect positive selection for a predetermined branch of a phylogenetic tree. However, because the number of nucleotide substitutions involved is often very small, we conducted a computer simulation to examine the reliability of BSM in comparison with the small-sample method (SSM) based on Fisher's exact test. The results indicate that BSM often generates false positives compared with SSM when the number of nucleotide substitutions is ≈80 or smaller. Because the ω value is also used for predicting positively selected sites, we examined the reliabilities of the site-prediction methods, using nucleotide sequence data for the dim-light and color vision genes in vertebrates. The results showed that the site-prediction methods have a low probability of identifying functional changes of amino acids experimentally determined and often falsely identify other sites where amino acid substitutions are unlikely to be important. This low rate of predictability occurs because most of the current statistical methods are designed to identify codon sites with high ω values, which may not have anything to do with functional changes. The codon sites showing functional changes generally do not show a high ω value. To understand adaptive evolution, some form of experimental confirmation is necessary.
And the second paper is by Thomas Lenormand, Denis Roze and François Rousset and is entitled ’Stochasticity in evolution’
Abstract
The debate over the role of stochasticity is central in evolutionary biology, often summarised by whether or not evolution is predictable or repeatable. Here we distinguish three types of stochasticity: stochasticity of mutation and variation, of individual life histories and of environmental change. We then explain when stochasticity matters in evolution, distinguishing four broad situations: stochasticity contributes to maladaptation or limits adaptation; it drives evolution on flat fitness landscapes (evolutionary freedom); it might promote jumps from one fitness peak to another (evolutionary revolutions); and it might shape the selection pressures themselves. We show that stochasticity, by directly steering evolution, has become an essential ingredient of evolutionary theory beyond the classical WrightFisher or neutralistselectionist debates.
You can contact me (Maren.wellenreuther@zooekol.lu.se) if you have problems retrieving the pdf files -and I will send them to you.
All the best and happy reading, Maren
The debate over the role of stochasticity is central in evolutionary biology, often summarised by whether or not evolution is predictable or repeatable. Here we distinguish three types of stochasticity: stochasticity of mutation and variation, of individual life histories and of environmental change. We then explain when stochasticity matters in evolution, distinguishing four broad situations: stochasticity contributes to maladaptation or limits adaptation; it drives evolution on flat fitness landscapes (evolutionary freedom); it might promote jumps from one fitness peak to another (evolutionary revolutions); and it might shape the selection pressures themselves. We show that stochasticity, by directly steering evolution, has become an essential ingredient of evolutionary theory beyond the classical WrightFisher or neutralistselectionist debates.
You can contact me (Maren.wellenreuther@zooekol.lu.se) if you have problems retrieving the pdf files -and I will send them to you.
All the best and happy reading, Maren
PS: Any Fika volunteers? Please send me an email if you are bringing something to the meeting.
Friday, March 20, 2009
"The Biology-Physics Interface": symposium in Lund Wednesday 25 March
We had some excellent discussions with our visiting Finnish guests, and I was hoping that some of you could soon write some bloggpost(-s), where you summarise your thoughts and impressions about Lamarck, species concepts and/or sympatric speciation. Shawn or Maren perhaps? Also, I think we would be interested in a bloggpost from Tina and Josefin, who had a separate discussion about sexual selection/sexual conflict. Please share with the rest of us some of your thoughts and idéas.
For the next week, I would again like to remind about the workshop on "The Biology-Physics Interface", that I am organizing here in Lund together with limnologist Lars-Anders Hansson. This a so-called CAnMOVE-event - "Centre for Animal Movement" - our new "Linnaeus-programme" about animal movement research. I hope that you all can participate and listen to the talks next Wednesday between 13.00 and 18.30 in the "Red Room" (Ecology Building). Below, I have pasted in the programme for the workshop:
13.00-13.15: Welcome! Introductory words - Erik Svensson
13.15-13.30: Presentation of CAnMove - Susanne Åkesson
13.30-14.15: Remote sensing of animal movement – unconventional laser radar possibilities
Sune Svanberg
14.15-14.45: Dragonflies and damselflies as bioinspirators - Erik Svensson
14.45-15.15: Seeing animal flight through the side-wall of a wind tunnel - Anders Hedenström
15.15-15.45: COFFEE BREAK
15.45-16.15: Nanotechnology in biology - Waldemar Hällström
16.15-16.45: Optical Spectroscopy in Animal Appearance and Perception -
Mikkel Brydegaard
16.45-17.15: Magnetic resonance imaging: Morphology and function - Ronnie Wirestam
17-15-17.45: Individual labeling of small animals (Daphnia) - Bengt Danielsson
17.45-18.30: Plenary Discussion: How can methods from physics be of use in biology?
Moderator: Lars-Anders Hansson
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