Feedback - Week 4 - JOURNAL CLUB Wagner et al. (1997)
I'll leave this post here for those that have comments they want to post about this meeting and/or the reading.
I found the article a little on the esoteric side, and we decided to focus on the review by de Visser
et al. (2003)
at the next Journal Club meeting (week 6) which looks at the whole field and places Wagner
et al. (1997)
in context.
Feedback - Week 3 - BOOK CLUB Kauffman (1993) CH1
[sorry guys, just noticed I've been citing this book as being published in 1992 instead of 1993]
Thought we could test run a weekly feedback post on the readings. If anyone thinks there was a worthwhile point raised during the meeting, they can add a comment to this and future feedback posts.
("Week 3" above refers to the 3rd week of the UQ calendar)
My recollections: John pointed out that Chapter 1 as a historical overview of evolutionary theroy (to set up the backdrop for his ideas in the rest of the book) puts forward an invented history that didn't really happen if you go back and look carefully for yourself (which John appears to have done). Some of the "black and white" differences between pre-Darwin and Darwin that Kauffman talks about are not true representations of history, and though some like Linaeus were more "typological" thinkers, many were not and accepted change could occur within species. John said he still thought Darwin did some great important new stuff, but it didn't pop out of nowhere. Perhaps Duncan or John could correct me there, or add other important points.
Also there's Mitchel's group email that most of us recieved:
- "I have to bail on today's meeting... By way of a token (meta)comment:
It seems hard to say much about Kauffman's work without first
proceeding to the later chapters. In the introduction and chapter 1,
he's stating some intuitions and setting out a research program, and
in chapter 2, one only begins to see his substantive results. My
intuitions may disagree with his - I might think that an organism
would best be viewed as a combinatorial structure *made out of* forms
of spontaneous order, in which the *combination* is a product of
selection - but such disagreement won't count for much until I've
walked with him through the concrete results he wants to present. Only
then would I be in a position to have an informed opinion."
More on Waddington
Nature has a nice review of Waddington's life and ideas you all might be interested in
here. [PDF]
Some forthcoming talks March 10-15
BrisScience: The Secrets of Our Genes with John Mattick, Institute for Molecular Biosciences.
A FREE public talk next Monday evening (Mar 13 at 6.30pm) at the Judith Wright Centre. Professor John Mattick of the Institute for Molecular Bioscience (The University of Queensland) talks about our current understanding of DNA and how it is used to build complex living organisms. Professor Mattick's contributions to science have been recognised with numerous awards, including the Order of Australia. More information: Prof John Mattick: The Secrets of our Genes, Monday, March 13; 6:30pm to 7:30pm (doors open at 6:00pm); complimentary refreshments follow. Judith Wright Centre of Contemporary Arts (420 Brunswick St, Fortitude Valley; www.jwcoca.qld.gov.au). The talk is open to all and there is no need to book. BrisScience (www.BrisScience.org) is a new initiative to bring science to Brisbane. This series of free monthly talks will feature dynamic scientists and science communicators speaking about ideas at the leading edge of science and be accessible to people without any background in science. Questions? Contact Jennifer Dodd (0408 796 357, jdodd@physics.uq.edu.au) or visit the website for further information.
Institute of Molecular Bioscience Seminar Series
Prof Martin Pera, Australian Stem Cell Centre, Monash University, presents Human embryonic stem cells: the past, the present, and the future on Friday 10 March at 12.00pm in Level 3 Auditorium, QBP.
Institute of Molecular Bioscience & Queensland Brain Institute Special Seminar
Professor Masatoshi Takeichi, Riken Institute, Japan presents Cells into organs: how multicellular systems form on Wednesday 15 March at 2.00pm in QBP Auditorium. Please register by contacting s.doig@uq.edu.au .
Call for suggested readings - topics
Discuss Evolution - Suggested Readings:PLEASE ADD TO THESE LISTS BELOW! - by adding a comment here or emailing me at c.glen@uq.edu.auI've started with things I'm interested in and added the suggestions we’ve had so far, but really would appreciate if anyone can add their own interests, with their name next to the topic if its their field of study)... just a starting list, by no means exhaustive.
1) APSECTS/TOPICS OF INTEREST(What we’re looking for)
Aspects of interest:Latest research
Old lines of research that have merit but almost been forgotten
Key papersEssays (SJ Goulds collections may be of interest)
key reviews and books (book sessions)
articles of opposing views on a topic.
Topics of interest:Origin of flight (Chris)
vertebrate palaeontology (Chris)
Speciation events
Phylogeneticsideas from evolution applied in other fields; i.e. linguistics, artificial intelligence, economics. (Duncan's interest)
Optimisation (I here this term used a lot)
developmental biologyfunctional morpholgy (Chris)
Analogy
Other sources of ideas:I've mentioned to some of you that we'll also use the archives of the ANU evolutionary theory discussion group as a source of inspiration when we can't come up with literature ourselves. Duncan's just informed me that they've closed down for 6 months (great timing) but the archives should still be online for the period:
http://mailman.anu.edu.au/mailman/listinfo/evo.theory2) SUGGESTED READINGS:We can discuss these and other suggestions at the meetings so we can plan several meetings ahead. Perhaps I good idea is to bring along papers that you want to suggest so we can flip through them at the tail end of the meeting.
BOOKS:
2 books suggested by Paul Griffiths:
Müller, Gerd B, and Stuart Newman, eds. 2003. Origination of OrganismalForm: Beyond the gene in developmental and evolutionary biology. Cambridge,Mass.: MIT Press.
West-Eberhard, Mary Jane. 2003. Developmental plasticity and evolution.Oxford: Oxford University Press.
PAPERS:
Here's a set of four papers debating the whether "PhyloCode" should replace the Lineaen system (2 for, 2 against), it might be a bit much to read all 4 for one meeting so I suggest we can discuss how to approach this at the meetings.
1. Benton MJ. Stems, Nodes, Crown Clades, and Rank-free Lists: is Linaeus Dead? Biological Review 75: 633-648, 2000.
2. Brochu CA and Sumrall CD. Phylogenetic Nomenclature and Paleontology. Journal of Paleontology 75: 754-757, 2001.
3. Bryant HN and Cantino PD. A Review of Criticisms of Phylogenetic Nomenclature: is Taxonomic Freedom the Fundemental Issue? Biological Review 77: 39-55, 2002.
4. Keller RA, Boyd RN, and Wheeler QD. The Illogical Basis of Phylogenetic Nomenclature. The Botanical Review 69: 93-110, 2003.
Duncan has spotted this one too:
5. Davidson, EH; Erwin, DH (2006) Gene regulatory networks and the evolution of animal body plansSCIENCE, 311 (5762): 796-800; FEB 10 2006
Abstract:
Development of the animal body plan is controlled by large generegulatory networks (GRNs), and hence evolution of body plans mustdepend upon change in the architecture of developmental GRNs. However,these networks are composed of diverse components that evolve atdifferent rates and in different ways. Because of the hierarchicalorganization of developmental GRNs, some kinds of change affectterminal properties of the body plan such as occur in speciation,whereas others affect major aspects of body plan morphology. A notablefeature of the paleontological record of animal evolution is theestablishment by the Early Cambrian of virtually all phylum-level bodyplans. We identify a class of GRN component, the "kernels" of thenetwork, which, because of their developmental rote and theirparticular internal structure, are most impervious to change.Conservation of phyletic body plans may have been due to the retentionsince pre-Cambrian time of GRN kernels, which underlie development of major body parts.
General Information on Mimicry is a simple but rich website on, well, mimicry, specifically Batesian and Mullerian mimicry. It's on
Jim Mallett's web page, a guy who (to my joy) accepts sympatric speciation by host race diversification, but who, to my displeasure, thinks there is a One True Species Definition (although his version is pretty good for many purposes).
Anyway, if you ever wanted to find out anything about mimicry, go here and follow the links.
[Thanks to Perplexed in Peioria from the sci.bio.evolution group for the link]
Draft "Goals"
Here are some draft goals of the group, hopefully I’ll have time to write up a more succinct version (and include input from others!):
Goals of “Discuss Evolution”
The goal is to set it up so it's fairly informal and there's no pressure to attend regularly. A main goal was to help brush up that sort of things we learnt about in undergrad but have forgotten as we become more focussed in our own fields of study.
What it's about.
As biologists, we all end up inevitably with a narrow focus on our own topic, and most of what we know about other aspects of biology is based on fading memories from our undergrad courses, when the key topics and papers were handed to us on a platter. As we become postgrads and academics the time we can't afford the time to keep track of all the other fields as it takes all our time to research our own one. Unfortunately this means that we end up with a less integrated view of biology and crucially some really important information that could benefit from other fields us could fly under the radar. Additionally, we find many new leaps forward and fruitful areas of research stem from links made between other fields of research.
Having some streamlined, simple and efficient way to keep tabs on these other fields of research I think is beneficial, if not imperative for some one who is serious about being a professional biologist. We don't necessarily need to know the details, but at least be aware of the developments, have a handle on the "keywords" to help look them up if we need to, and also know a few names of people who do research or understand these other concepts.
The Discuss Evolution group:
I'm hoping this discussion group can do just that. "Evolution" was the best broad umbrella term I could think of for the group. Despite still being in start up mode those that are participating include postgrads and academics involved or interested in animal genetics and developmental biology, nerve growth, anthropology, forensics, human and animal anatomy, vertebrate palaeontology, functional morphology and biomechanics, philosophy of science (esp. evolution theory) and some with backgrounds in artificial intelligence, maths and computing, and general physics (esp. quantum physics).
So, how is it run? – Fortnightly meetings…
Journal Club meetings (fortnightly 4:30pm, UQ Staff club). These fall on the study weeks with even numbers (see UQ Calendar). Set papers are read prior to the meeting and discussed at the start of the meeting. The discussion should lead on to other topics, and the opportunity should arise for questions on other matters can be asked of members more familiar of particular fields.
Book Club meetings (fortnightly 4:30pm, UQ Staff club). Odd weeks in the UQ Calendar. This is expected to be smaller meetings, where chapters of set books are discussed, but generally follows the same structure as the Journal Club meetings.
There is no pressure to attend every meeting, and though we prefer the readings be read prior to the meetings, we welcome those that haven’t (in fact explaining the reading to a small number to those that haven’t can highlight differences in opinion and interpretation and therefore fuel the discussion).
Contact:
Other than this website, emails will be sent to members with [discuss.evo] in the subject heading (so you can set your email filter to put it into a special folder) that will alert members of suggested readings, news and websites that may be of interest as well as upcoming talks held at UQ. By hitting “Reply all” members can contact all others in the group.
Input:
The idea is to get input from all members across diverse fields that should be of broad interest and importance, so please take the opportunity to put forward a topic or reading at a meeting or via the email list [discus.evo].
Next week's paper
Just thought I'd put the paper for next week up here in case someone hasn't got it via email:
Waddington 1951
Welcome
This blog will be the main site for the discuss.evo reading group at the University of Queensland. We will publish links to articles, relevant reading material, comments and meeting details here.
It is for members of the group only.
Sorry that it gives my details in the sidebar - I'll fix that later. [Already done - that was easy.]
John
