Monthly Archives: March 2007

Bosnian Pyramid Update

I really did not have time to follow up on the whole case, but Alun has so check out his latest…. And you can always be up to date by following the postings on the APWR Central blog. I wish the whole thing was just an April’s Fool joke, but unfortunately, it is just one’s fool’s joke that threatens to destroy some real archeological treasures in the region.

Blogrolling for today

Pursuing praxis

Chaos Theory

Fish Feet

Science After Sunclipse

Barbara’s Blog (Barbara Ehrenreich)

Eleblog

Mass Eyes & Ears

Uri Kalish – Urikalization

Mythusmage Opines

Squid Drawing

Jenna drew a squid. Perhaps if I post it here, PZ will see it and post it as well, and send Jenna a Pharyngulanche of visitors to her blog.
jenna%27s%20squid.JPG

Evo-Devo: what new animal models should we pick?

A review of evo-devo (Jenner, R.A., Wills, M.A. (2007) The choice of model organisms in evo-devo. Nat Rev Genet. 8:311-314. Epub 2007 Mar 6.) is starting to make rounds on the blogs. I cannot access the paper (I’d like to have it if someone wants to e-mail me the PDF), but the press release (also found here) is very vague, so I had to wait for some blogger to at least post a summary.
This is what the press release says (there is more so click on the link):

The subject of evo-devo, which became established almost a decade ago, is particularly dependent on the six main model organisms that have been inherited from developmental biology (fruit fly, nematode worm, frog, zebrafish, chick and mouse).
To help understand how developmental change underpins evolution, evo-devo researchers have, over recent years, selected dozens of new model organisms, ranging from sea anemones to dung beetles, to study.
One of the selection criteria deemed most crucial is the phylogenetic position of prospective model organisms, which reflects their evolutionary relationships.
Phylogenetic position is employed in two common, but problematic, ways, either as a guide to plug holes in unexplored regions of the phylogenetic tree, or as a pointer to species with presumed primitive (ancestral) characteristics.
Drs Ronald Jenner and Matthew Wills from the Department of Biology & Biochemistry at the University of Bath (UK), call for a more judicious approach to selecting organisms, based on the evo-devo themes that the organism can shed light on.

Larry Moran and PZ Myers went into a completely different direction which I find quite uninteresting: evo-devo was and currently is a study of animals and if people who study other organisms want to make their own equivalents, good for them, more the merrier, hi-ho-hi-ho, etc.
I have no problem with the idea that Earth is a planet dominated by bacteria and that the animals are a recent afterthought. I sympathize with those who lament the lack of interest, funding and teaching in the ares of plant, protist and fungal biology. But evo-devo is currently an area of Zoology, so the search for new animal models, as opposed to plant models, is a perfectly appropriate question. We want to know how animals develop and evolve and evo-devo tries to put those two questions together. I am sure botanists, mycologists, microbiologists are working on their own version within their own domains – and hopefully the groups will read each other and learn – but that is outside the realm of this particular review paper.
What bothers me about the press release is its vagueness. Different people have different definitions of the terms “development”, “evolution” and “evo-devo”. Different people have different evo-devo questions they deem important and the review appears to reflect the biases of the authors (and so do posts by Larry and PZ).
Development
Some people focus on the early embryos and things like pattern formation, determination of dorso-ventral axis, or limb development. Others consider the entire life-cycle, including growth, maturation and senescence, to be parts of development. Some focus on patterns of expression of developmental genes. Others are more interested in phenotypes. Some focus entirely on the development of anatomical structures, while others are more interested in the development of biochemical, physiological and behavioral traits and how they evolved. Obviously, people with different focus in development will ask evo-devo to pursue different questions.
Evolution
Again, some people are interested in genotypic evolution. They use the population-genetic definition of evolution as “change in frequency of alleles in a population over time”. Their models can detect some things (e.g, type, strength and direction of selection), but not others (levels/units of selection, effects of population structure, etc.), so they focus on the former and the latter is ignored, or given lip-service, or even deemed unimportant (or even non-existent!).
Others are interested in phenotypic evolution. After all, genes are invisible to selection – it is organisms that get selected and the changes in gene frequences are a downstream result of that process. They have different aims and goals for evo-devo as a discipline.
Using the broadest definitions of both development and evolution, the classical studies of imprinting, developmental ‘windows’ for learning birdsong, and organizing vs. activating effects of hormones are smack in the middle of evo-devo research – the mainstream onto which some genetic stuff has been added lately.
Evo-devo
Evo-devo is short for “evolution of development”. But, it actually asks three distinct questions:
How animal development evolved
Trying to trace and document how various developmental mechanisms evolved over time, in essence building a phylogenetic tree of developmental changes in animals on this here planet Earth since the apperance of first animals until today.
How animal development evolves
Figuring out generalizations, hopefully rules, and perhaps even laws, about the ways different evolutionary mechanisms affect different developmental mechanisms.
How animal development affects animal evolution
Figuring out the way different developmental mechanisms affect the way evolution can proceed, i.e., developmental constraints in the positive sense of ‘funneling’ evolutionary direction by making some directions more likely than others. From the very inception of the field, fueled by the publication of Stephen Jay Gould’s “Ontogeny and Phylogeny” (his by far the most influential book, though ALL the others are more popular), the focus has been on things like allometry, heterochrony, heterotopy, etc. This paper appears to be focused on this goal as all the suggestions appear to have such processes in mind:

Developmental programming. Allometry of horns in the beetle Onthophagus nigriventris.
Developmental bias. Variation in body size in C. elegans.
Developmental constraint. Shell morphology in the gastropod Cerion.
Redundancy. Anterior-posterior axis development in Drosophila melanogaster.
Modularity. Sense organs in the cavefish Astyanax mexicanus.
Evolvability. In silico cell-lineage evolution.
Origin of evolutionary novelties. The sea anemone Nematostella vectensis (bilateral symmetry, triploblasty).
Relationship between micro- and macroevolution. The three-spined stickleback and Heliconius butterfly wing patterns.
Canalization and cryptic genetic variation. D. melanogaster phenotypic variation increase during HSP90 impairment.
Developmental and phenotypic plasticity, polyphenism. Ant caste polyphenism and caste determination by primordial germ cells in the parastic wasp Copidosoma floridanum.

Frankly, ALL of these topics I find immensely exciting and, sure, I’d love to see these ideas implemented and these models adopted, and this research done. But what bothers me is that this list just enlarges the Big Six list into a Big Many list. It does not do what it is purported to do – move from separate studies of devo and evo to an evo-devo research program.
You can study development in an organism, but to study evolution of development you HAVE to do comparative work. This means that choices of single species miss the mark completely. If I have written this paper I would have suggested pairs and groups of species, not single species.
For some questions, one wants to compare closely related species, perhaps all in the same genus, e.g., Drosophila (D. melanogaster, D. pseudoobscura, D. yakuba, etc.). Rudolf Raff made great strides early on in the field of evo-devo by comparative studies of two closely related species of sea-urchins, one of which undergoes metamorphosis (i.e., goes through a larval stage) and the other one skips it and develops directly from an egg to an adult.
For other questions, one may want to look at somewhat less related species that cover a greater spread of evolutionary relationships. Perhaps a bunch of different insects: fruitlies, house flies, mosquitoes, cockroaches, termites, beetles, butterflies, moths, sandflies, wasps, honeybees, etc. (like this paper does, for instance), or a bunch of different fish, e.g., zebrafish, medaka and fugu, or comparing chicken to quail to turkey to ostrich.
For yet other questions, looking at the philogenetic depth is quite fine. It is exciting what we are learning about the origin, evolution and development from the studies of Cnidaria (see this, this and this for an example), or about the origin of Vertebrates from the comparative studies of echinoderms, hemichordates, urochordates, cephalochordates, agnathans and fish (check out this and this).
So, if you had unlimited space, time, manpower, money and freedom, tell me what pairs or groups of animals you’d choose as new evo-devo models, not individual species, and what would you study with them? What for? Which of the defintions of development and evolution you ascribe to? Which of the three evo-devo questions excite you personally?

“Post-human”

The best way to make it easy for the low-brow followers to kill the enemy is to dehumanize it. That is what right-wing talking-heads have been doing for a while. Of course, if someone actually gets killed, they did not do it – they were just telling “jokes” on radio or TV.

When Yes means No.

When I ask a guy for something, I may get Yes as an answer half the time and No half the time. Yes mostly means Yes and No means No. If the answer is “Let me think about it”, that means usually that within 24 hours or so I will get a definitve Yes or No answer.
If I ask a woman for something, I rarely ever get a No. I may get Yes half the time and “Let me think about it” the other half. And moreover, Yes need not necessarily mean Yes, and “Let me think about it” ALWAYS means No – as in: I never hear about it again from that person.
On the surface, that sounds like dishonesty and playing games, and sure is inconvenient not to know what the real answer is. But I am aware of the deeper psychological reasons for not being able to say No to anyone, as I was once like that (and learned through persistence and hard work not to be). It is a matter of politeness mixed with a dose of fear (of being ostracized or something).
And it is certainly much more ingrained in – or inculturated into – women than men. How? Check this post and the 85 comments in the thread under it.

At an IDC conference – Jason reports

Jason drove down to Knoxville and attended an ID-Creationist “conference” and lived to tell about it. And tell he did, in five installments:
One
Two
Three
Four
Five
All the usual suspects were there and all the usual nonsense was spouted, but the most interesting part was the Subway-line conversation Jason had (in Part Four), debating a handful of attendees and noticing age-difference in their thought-processes and debating strategies.