Helen's review of the last paper
Mechanisms for the environmental regulation of gene expression: Ecological aspects of animal development (Gilbert, 2005)
This is the most recent in a series of papers published by Gilbert in which he introduces the concept of ecological developmental biology. Gilbert commences with a historical account of the degree of focus (or neglect) that environmental factors have received in the study of normal development. Throughout much of the 20th century, researchers have focussed on minimising environmental variation to maintain repeatability in the laboratory environment. However, it is becoming clear that the majority of organisms interact directly with the environment during development, and that the correct environmental conditions can have an instructive role in normal development. This paper links environmentally sensitive processes to specific regulatory networks. Gilbert explores three different mechanisms. 1. The neuroendocrine system can monitor the environment and transfer signals to the endocrine system, which can alter gene expression. For example, the butterfly Araschina levana has vastly different wingspot patterns due to seasonal temperatures, which can be reproduced in the laboratory. The titre of the hormone ecdysone is environmentally sensitive, and ecdysone expression directly impacts the expression of patterning genes. This presents a likely explanation for the seasonality of wingspot patterns. Other examples include temperature-driven sex determination in reptiles, and the interaction between the mammalian foetus and mother. 2. Environmental factors can change the methylation pattern of genes, thereby altering their transcriptional capabilities. It has been established in mice that dietary intake of methyl donors (eg. Folate) can influence the methylation state of genes, which can have a subsequent influence on phenotype. 3. Microbial symbionts can directly impact gene expression. The impact of mammalian gut flora on gene expression and gut differentiation was discussed.
This is the most mechanistic paper to date, but some of the earlier ones present a better historical account. Email me if you are interested.
Discuss.evo - Meeting 2 (4:30pm Thursday, 19th April; UQ Staff Club)
The paper for the April meeting was suggested at the last meeting by Helen Gunter after a discussion about various topics such as epigentics and various external effects on heredity. Her summary of the article is below (thanks Helen).
I'll email the PDF to those in the group, but if however you don't get it email me at c.glen@uq.edu.au and I'll get a copy to you.Chris Glen------------------------------------------------------------------------------------------
Gilbert, S.F. (2005) Mechanisms for the environmental regulation of gene expression: Ecological aspects of animal development. J. Biosci. 30(1):65-74 SUMMARY (prepared by Helen Gunter):This is the most recent in a series of papers published by Gilbert in which he introduces the concept of ecological developmental biology. Gilbert commences with a historical account of the degree of focus (or neglect) that environmental factors have received in the study of normal development. Throughout much of the 20th century, researchers have focussed on minimising environmental variation to maintain repeatability in the laboratory environment. However, it is becoming clear that the majority of organisms interact directly with the environment during development, and that the correct environmental conditions can have an instructive role in normal development. This paper links environmentally sensitive processes to specific regulatory networks. Gilbert explores three different mechanisms. 1. The neuroendocrine system can monitor the environment and transfer signals to the endocrine system, which can alter gene expression. For example, the butterfly Araschina levana has vastly different wingspot patterns due to seasonal temperatures, which can be reproduced in the laboratory. The titre of the hormone ecdysone is environmentally sensitive, and ecdysone expression directly impacts the expression of patterning genes. This presents a likely explanation for the seasonality of wingspot patterns. Other examples include temperature-driven sex determination in reptiles, and the interaction between the mammalian foetus and mother. 2. Environmental factors can change the methylation pattern of genes, thereby altering their transcriptional capabilities. It has been established in mice that dietary intake of methyl donors (eg. Folate) can influence the methylation state of genes, which can have a subsequent influence on phenotype. 3. Microbial symbionts can directly impact gene expression. The impact of mammalian gut flora on gene expression and gut differentiation was discussed.
This is the most mechanistic paper to date, but some of the earlier ones present a better historical account. Email me if you are interested. -
Helen Gunter [hgunter@sib.uq.edu.au]
Discuss.evo 2007 - Meeting 1 (15th March)
I'll post the details of the meeting here soon...
Chris Glen
First meeting for 2007
Welcome to the 2007 series of the UQ Evolution Reading Group.
First meeting: 4:30pm Thursday, 15th MarchLawniczak, M. K. N., Barnes, A. I., Linklater, J. R., Boone, J. M., Wigby, S. and Chapman, T. (2007). Mating and immunity in invertebrates. Trends in Ecology & Evolution 22: 48-55. [PDF]
At the meeting I’ll be suggesting that the follow up paper for April could be (and inviting other suggestions of course!):
Losos et al., 2006 – ‘Rapid temporal reversal in predator-driven natural selection’ Science 314:111
It’s a short one page (Brevia) article that predicted changes in limb lengths of small ground island lizards (Anolis) after the introduction of a larger predatory lizard (Leiocephalus). They predicted initial selection for longer legs that allow faster escape on the ground but that a slower shift into the arboreal environment (which helps elude predatory species) would favour shorter legs. They found the first 6 months long legs were selected for and short legs in the next 6 months. I’d be interested to hear what some might have to say about researchers introducing predatory lizards to islands as part of a ‘microevolutionary experiment’!
Another interesting paper is:
Bridle and Vines (2007) ‘Limits to evolution at range margins: when and why does adaptation fail?’
Trends in Ecology & Evolution 22(3): 140-147
We can discuss suitable scheduling and venue for future meetings on the day.
Anyway, look forward to seeing you there.
Cheers,
Chris
Trinkaus and Neandertal difference
Modern Human versus Neandertal Evolutionary Distinctiveness
by Erik Trinkaus
Current Anthropology 47, August 2006
Introduction by John Wilkins: This paper garnered a lot of media interest, but most of it was wrongly phrased (in terms of "genetics", not morphology). This paper asks the question whether modern humans are more derived than Neandertals and if we have over-focussed on Neandertal "deviation" from the "evolutionary norm". It raises what I think are some basic questions about the nature of phylogenetic classification and the role of morphology in evolutionary investigations. The paper is relatively short if you do not spend much time on the tables, and there are a number of useful critical comments by others at the end.
Abstract: Considerations of morphological variation among later Pleistocene human groups have focused principally on the distinctiveness of the Neandertals of western Eurasia relative to their predecessors and to penecontemporaneous and recent modern humans. In this discussion, there has been a dearth of attention of the degree to which modern humans are derived relative to earlier members of the genus Homo. Of 75 cranial, mandibular, dental, axial, and appendicular traits in which the Neandertals and/or modern humans are derived relative to Early and Middle Pleistocene Homo, approximately one-quarter are shared among Neandertals and modern humans, a similar percentage largely unique to the Neandertals, and about half largely unique to modern humans. The results are similar whether the Neandertals are compared with the earliest modern humans or with their Late Pleistocene and more recent modern human successors. Even though these figures could shift modestly through variation in trait selection and/or as a result of a more complete earlier Pleistocene Homo fossil record, it is apparent that modern humans are morphologically more derived than the Neandertals. Our focus should therefore be at least as much on the evolutionary biology of early and recent modern humans as on that of the Neandertals.
The paper can be downloaded from here.
Summary of Tangled Nature discussion
The discussion centred around Christensen et al. and Schwämmle & Brigatti. One problem we identified was that there were no "methods" sections: you have to follow all through the papers to understand what exactly is being simulated. It would have been nice to know, for example, how exactly the linear regressions were done in Figure 2 of Schwämmle & Brigatti; as it is they seem to have been rather cavalierly drawn in, although the error bounds seem to indicate that a statistical method has been employed.
John was particularly happy to see that a non-asexual model was introduced in Christensen
et al., since so much theory gets done on asexuals. At the same time though it was unsatisfactory that the models are so limited, but there has to be a balance struck between sophistication and tractability. Finally we found Figure 1 of Schwämmle & Brigatti fascinating since it demonstrated some species reuniting after some time evolving separately; although it seems to me this would be considerably less likely to occur if the "strategies" were multiple-dimensional rather than one-dimensional.
Tangled Web papers
Readings provided by Martin Hely
These are papers about a model known as "tangled nature". Basically, they consider a large set of potential "species" where every pair of species has some randomly-determined interaction (mutualist, predator-prey, competition, or no interaction at all) AND there are mutations which can transform an individual of one of the species into one of another species. For appropriately chosen parameters, this model exhibits lengthy epochs where the makeup of the community is roughly constant, but with occasional periods of re-organization. In complex systems jargon, it exhibits punctuated equilibrium as an "emergent property".
Christensen et al. is the original presentation of the model. Laird, Lawson & Jensen give a run-down of the basic model and some of the variations that have arisen. Jensen 2004 pushes the model into the physics literature (as part of a memorial issue to Per Bak). Lipowski and Schwämmle & Brigatti are examples from physics journals of models related to tangled nature and I've included them more to stimulate discussion on the phenomenon of apparently rather substantial biological conclusions appearing in physics journals.
http://www.uq.edu.au/biohumanities/readings/christensenetal2002.pdfhttp://www.uq.edu.au/biohumanities/readings/jensen2004.pdfhttp://www.uq.edu.au/biohumanities/readings/lairdlawsonjensen.pdfhttp://www.uq.edu.au/biohumanities/readings/lipowski2005.pdfhttp://www.uq.edu.au/biohumanities/readings/schwaemmlebrigatti.pdf
Fitness papers online
There are two papers for the next journal meeting on 18 May:
Shanahan 2003, "The evolutionary indeterminism thesis" [1.4Mb]
and
Sober 2001, "The two faces of fitness" [5.1Mb]
A reminder that the Gavrilets chapters for this week are up also
here.
Feedback - Week 7B (Midsem break) - JOURNAL CLUB - CANCELLED
We had intended to look at Pigluicci's paper, but postponed it to the Journal Club in week 9.
Feedback - Week 7 - BOOK CLUB - CANCELLED
We had intended to look at Gavrilet's paper, but postponed it to the Book Club in week 8.
Gavrilets again in two weeks
We'll address Sergey in two weeks. Nobody showed up today (fair enough too).
So In a little while I'll do a short summary of my understanding of Gavrilets' views, and then we can discuss them in a fortnight.
Repost Gavrilets 1-2
Sorry for the error in the previous version - only every second page got inserted.
Here is a (12Mb) version with all the pages.
Gavrilets chapters 1 and 2 online
You can download the 8.4Mb PDF of Gavrilets' book
here. You may need to click the Annoying Lawyer's Button disclaiming any responsibility for life, earthquakes, fraud or inadvertent education first.
More on Gavrilets
Due to technical problems with computers (are there any other kind) I haven't been able to post the scanned first two chapters of G's book yet. With luck, I'll have them up soon, but perhaps we can discuss them after we do the paper for Thursday.
If anyone is coming along, let me know - we have two pikers so far (Chris and Duncan) due to some religious holiday or other. If nobody's coming, then I'll drink beer at home instead.
Feedback - Week 6 - JOURNAL CLUB - de Visser et al (2003)
Genetic robustness:
Katrina pointed out some flawed arguments in the review, or instances of lumping concepts together incorrectly. In particular were the concepts of plasticity and varience which were getting confused.
One thing I raised, Which Katrina countered (apologies if my terminology is a bit off), is I've often thought that any genes that are not being fully expressed due to some buffering system as discussed in this paper would be come "deleted", or at least decoupled from the ancestral phenetypic character it is now not actively used for. This is probably because I'm used to seeing the "use it or loose it" effect in functioanl anatomy (eg wings reduced or lost in some animals, where there's no longer natural selection pressures maintaing its normal function). I assumed if the expression of a gene was being buffered over enough generations, the gene is no longer subject to natural selection to maintain its role in a functional workable system, and could become a "non functional intron sequence" from random point mutations, or possibly changes in the parts of the "genetic network" that are buffered with it could end up excluding the gene from is role in effecting the phenotypic character. I can see that through pleiotropy, its possible the gene's role elsewhere in other characters will save it from "deletion" or prevent radical change - so that elsewhere the expresion of the gene is regulated by natural selection. Katrina said that the "use it or loose it" effect wouldn't work like this on genes, as the buffer system is an active integrated part of the system too, and only buffers the products of the "normal gene", and any radical change will sidestep the buffering system, be expressed, and therefore presented to natural selection and mostly likely removed from the population (as most mutations are deleterious).
We decided to go with another paper that Katrina has noticed flaws in for the next JOURNAL CLUB meeting.
Please add comments
Feedback - Week 5 - BOOK CLUB Kauffman (1993) Ch2
The majority generally thought that the author wasn't backing up his ideas with enough data, and was making sweeping statements on a narrow base of observations.
Majority of poeple weren't enthused by the book and we decieded to change to something else - next BOOK CLUB we will start on the work of Gavrilets on fitness landscapes.
On Gavrilets
Since we are reading Gavrilets' on speciation I thought I might offer a few links for those who are interested to follow it up.
Here's his
homepage. He has other papers one can download.
Here's a link to his
book, and a
press release. This is a
paper in
Paleobiology he coauthored with various folk, including Eldredge. And this is a paper on
Adaptive Dynamics.
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
