BioMOO Journal Club transcript (LONG!)

[No way! Way!]

The second meeting of the BioMOO Ecology and Evolution Journal Club took
place in the BioMOO Seminar Room on Friday the 17th of February, at 2100
hrs GMT. Thanks to everyone who contributed, and again thanks to Gustavo
Glusman for establishing and maintaining BioMOO, and to the Weizmann
Institute of Science in Israel for providing BioMOO with a real-life home. 

BioMOO's telnet address is:

bioinfo.weizmann.ac.il 8888  or  132.76.55.12 8888

The paper for discussion was:

Sih, A., and R. D. Moore.  1993.  Delayed hatching of salamander
eggs in response to enhanced larval predation risk.  The American
Naturalist 142:947-960.


This transcript of the meeting proceedings will be available via anonymous
ftp or gopher from bioinformatics.weizmann.ac.il. It has been edited to 
improve the formatting, fix spelling mistakes, and cut out 'noise' from 
people entering and leaving the seminar room. Otherwise, the transcript 
reads as it occurred in real time.
 
The following people were present, and either contributed to the 
discussion, or were there just to listen:

Simon Blomberg, School of Biological Sciences, University of Sydney
Helen Rodd, York University
Bill Adlam, Oxford University (St. Peter's College)
Dann Paul Siems, University of Minnesota
Geordie Torr, James Cook University, Townsville, Australia
Mark Belk, Brigham Young University
Victoria McGovern, UNCC
Richard Harbottle, St Mary's Hospital Medical School, Imperial College, 
	University of London.
Michael Richardson, Carleton University, Conservation Ecology project
Jon D. Moulton, Portland State University (Oregon)
John Foster Towell III, Ph.D.,Affiliated (loosely): Northern Illinois 
	University/Argonne National Labs
Dennis Stockert, NASA Lewis Research Center, Cleveland, Ohio, USA
Massimo Pigliucci, University of Connecticut
Tom Salt, London University
L Ramakrishnan, The University of Texas at Austin
Charlotte Borgeson, University of Nevada
Everett Weber, Old Dominion University, Norfolk, Virginia, USA
Marcus Speh, University of Hamburg and DESY (High Energy Physics Lab), 
	Germany
Alon Haberfeld, University of Guelph, Canada
David Michael McKalip, M.D., Division of Neurosurgery, University of North 
	Carolina at Chapel Hill
Kim Dibble, University of Regina
Julio M. Arias, Univ. of Florida - Inst. of Food & Agric. Sciences - Citrus
	Res. & Educ. Ctr.
Gustavo Glusman, Weizmann Institute of Science, Israel
Bob Silva, Avian Disease & Oncology Lab
Todd A. Guillory, The University of Texas Medical Branch
Eugene Buehler, University of Pittsburgh
Mr. Kelly Joseph Salsbery, Syracuse University and Le Moyne College
Scott Brim, Cornell University
Steve Kay
Eric Cabot, NIH, Bethesda, MD, USA
Chris Glenn, DLU, Nashville, TN

Transcript begins...

SimonB turns the Recorder on.
SimonB says, "OK, it's 21:03. Shall we start?"
McVic nods
SimonB says, "Firstly..."
------------------------------SimonB's slide1------------------------------



                       WELCOME TO BioMOO!

               And welcome to the Ecology and Evolution
                        Journal Club II.




------------------------------SimonB's slide1------------------------------
SimonB grins.
MarkB says, "I suggest we forego the usual discussion of statistics and get 
	right to the interesting questions"
SimonB [to MarkB]: OK. You proposed the paper. Care to say a few introductory 
	remarks?
MarkB says, "if all have at least read the summary, I would like to begin by 
	asking the question why should we observe variation in levels of 
	plasticity within a population?"
Sagitta says, "I was interested to see that the graph in fig. 1 A continued 
	below the origin, suggesting that larvae which would have hatched 
	very late actually hatched earlier in the presence of the flatworms."
Sagitta meant below y=0.
MarkB says, "maybe we are not yet to the point that we can discuss that 
	question.  Let me begin with a few comments.  I found this paper to 
	be a rather clear demonstration of adaptive plasticity.  There seem 
	to be a lot of advantages to the particylar system."
Sagitta nods.
SimonB says, "One can tell adaptationist stories..:-)"
MarkB says, "true they may be stories, but there do seem to be good controls 
	(within families), a question once again, why don't all eggs hatch 
	late?  Seems to be that some sibships do."
SimonB says, "The main thing seems to be: if there are flatworms around, stay 
	in the egg and grow a bit. It's the safe harbour hypothesis."
SimonB nods to MarkB.
Rett says, "but you lose the prospect of quick growth after hatching"
Rett says, "and delay reproduction"
Breeder [to MarkB]: Presumably there is some unknown advantage to hatching 
	early.
MarkB [to Rett]: You lose the prospect of quick growth if you do what?"
Alon says, "seems to me that ANY variation is good."
Rett says, "Hatch early. "
Ramki waves to SimonB.
Sagitta says, "If you hatch early you are better protected from some 
	predators (probably) and from dessication if things get desperate."
Sagitta says, "And from diseases..."
Rett says, "if one hatches early one has the possiblility to outcompete ones 
	siblings as well"
Ramki nods to SimonB.
Kim says, "So presumably there will be some kind of cost-benefit relationship 
	between early hatching(predaotr avoidance) and reproductive success?"
MarkB says, "If there is some unknown advantage then why do some families not 
	seem to have the ability to hatch early?"
Rett says, "Correct."
Rett says, "Perhaps ephemeral resources force flexibility."
Sagitta [to the memorandum]: could be a mixed ESS if the more tadpoles hatch 
	early, the bigger the flatworm population.
Breeder [to MarkB]: Maybe there hasn't been strong enough selection on those 
	groups.
Sagitta shakes its head and stares at itself.
SimonB says, "What do people think of Sih and Moores hypothesis that early 
	hatching is a phylogenetic carryover from a recent ancestor?"
SimonB says, "Phylogenetic explanations seem to be 'in' at the moment."
Alon [to SimonB]: As they said, it needs more testing.
Sagitta quotes from the paper: "In some amphibian species, eggs sufdfer heavy 
	mortality due to low oxygen, fungal infection or predation."
Ramki says, "hi"
Pimephales nods greetings to group
MarkB says, "A phylogenetic explanation begs the question of lack of early 
	hatching in some lineages."
Ramki says, "I don't know about phylogenetic inertia, but adaptive plasticity 
	in hatching seems to be found in other groups (tree frogs, for eg)"
MarkB says, "Actually the suggestion that one type of predator can cause 
	adaptive shifts in plasticity in nature seems too simple, aren't there 
	lots of other things that eat little salamanders?"
Breeder [to MarkB]: Quitle likely, and presumably they could cause the same 
	shifts but as yet there is no evidence either way.
Rett says, "Some predators have preferences"
Gustavo says, "How does that change the fact that there is a difference 
	between the control group and the test?"
SimonB says, "Of course. The authors pose the question as to how general the 
	response is. Maybe there is a tendency towards early hatching in the 
	presence of other types of predators."
Kim says, "I'm curious as to how ind in the egg detect the presence of a 
	particular predator. Will a threshold density of predators be 
	necessary? How many will constitue a predation 'threat'"
Ramki says, "to give yet another example (as yet unpublished) a fellow grad 
	student here found that predation by cat-eyed snakes on clutches of 
	tree frogs expediated hatching, and aquatic predation by shrimps 
	delayed hatching.."
SimonB [to Ramki]: Hey, that's neat. That's exactly what I meant.
Ramki says, "So , specific predators can cause responses"
Breeder [to Ramki]: What sort of tree frog?
Rett says, "in response to Kim, it may be a chemical response therefore, it 
	isn't how many but how much indicator is present"
Ramki says, "Agalychnus callydras (spelling?) red eyed tree frog, in Costa 
	Rica."
Breeder thought it might be.
SimonB [to Kim]: There must be some rule of thumb. Threshold concentrations 
	of flatworm slime or something.
Ramki [to Breeder]: How?
Pimephales says, "are there specific responses to specific predators -- this 
	would seems to not be the way to go -- generalized responses seem 
	more likely."
Sagitta says, "Let's not speculate on the neurobiology, as we don't know 
	anything about their sense of smell."
Kim [to Rett]: I realize it is probably a chemical response, but isn't how 
	much indicator present depedent on a number of factors (ie # of preds, 
	distance from eggs etc)
MarkB says, "Could the response to a predator be a general response to 
	anything that chemically "smells" like a predator?"
Ramki says, "depends on which predator exerts strongest selection pressure"
Pimephales says, "whatever a predator smells like:-)"
Breeder [to Ramki]: I know that cat-eyed snakes eat their eggs - what I want 
	to know is how an egg mass knows that a snake has eaten half of it.
Sagitta was also curious about that.
Ramki says, "Apparently, they sense the mechanical disturbance"
SimonB grins to Breeder.
Breeder [to Ramki]: Aren't Agalychnis eggs laid on leaves above the water?
MarkB says, "other work on crucian carp for instance suggests that predators 
	must smell like they have been eating the specific type of prey."
Ramki nods.
Breeder [to Ramki]: Wouldn't wind do that too?
Rett [to Kim]: Yes but the system was developed by the organism to measure that.
Ramki says, "No, but if you rattle the clutch manually, you get the same 
	response."
Breeder is a little dubious.
Ramki says, "read about it in Science... soon"
Sagitta says, "Presumably it's not specific to the snakes but would work for 
	most large terrestrial predators."
SimonB says, "I still think the phylogenetic hypothesis is interesting. Early 
	hatching is the ancestral condition. Late hatching is derived, and 
	exists side-by-side the ancestral trait as a polymorphism."
Pimephales says, "there is similar work on fathead minnows anto northern pike 
	predators -- the predator needs to have consumed other fatheads 
	before it is recognized as a threat"
Breeder looks forward to it.
Kim thinks there has got to be some cost associated with superduper predator 
	detection. Perhaps some prey use 'sloppy' detection techniques and 
	hedge their bets.
MarkB [to Pimephales]: Where is that work on pike and minnows published?"
Breeder [to SimonB]: How can you say 'early hatching' presumably the 
	ancestral condition is 'just right hatching'.
Sagitta [to Breeder]: But `just right' depends on the environment.
Rett says, "Could it be that there are some key super duper indicators and 
	some general and that the super duper indicators are generated with 
	high pre"
Pimephales [to MarkB]: I can't remember the exact location but I can get it 
	for you if you sent me an e-mail request.
SimonB [to Breeder]: OK, pedant. Early relative to the derived condition.
Rett says, "predation risk"
Breeder [to SimonB]: Thank you :)
SimonB grins to Breeder.
Jon-D says, "Sagitta had an interesting early question about why do late 
	hatching sibs hatch earlier in response to predation.  Can anyone 
	tackle that one?"
Pimephales says, "It seems like all of this must somehow be mediated by some 
	sort of generalized stress response""
Pimephales says, "maybe elevated corticosteroid levels accelerate metabolic 
	rates?"
Sagitta [to Pimephales]: "Low oxygen, which makes them hatch earlier, must be 
	a generalised stress, so do you think flatworms desensitise them to 
	stress?
Sagitta [to Pimephales]: Or what?
SimonB [to Jon-D]: That seems really bizarre to me. I don't understand why 
	they would.
Sagitta [to Pimephales]: and a faster metabolism would speed development as 
	well as hatching.
Alon [to Sagitta]: maybe if there are flatworms, the oxigen isn't that 
	important.
Pimephales [tp Sagitta]: I'm not sure -- its just that specific 
	responses to specific predators seems informationally overly expensive.
Rett [to Pimephales]: It depends upon the danger of the predator.
Kim agrees heartily with Pimephales
Ramki says, "Maybe it is a response to a class of cues."
Jon-D [to SimonB]: Note that the regression line crosses the x axis for the 
	PC1 vs hatching stage chart.  Same effect for Fig. 2.
Rett says, "Hasn't someone found a similar response due to a single chemical 
	or group of chemicals?"
MarkB says, "I just finished an experiment with bluegills showing that they 
	delay maturation in the presence of predators.  Visual cues seemed to 
	be unimportant, but chemical cues appeared to explain the shift."
SimonB nods to Jon-D.
SimonB . o O ( weird )
Rett says, "Plants can respond to chemical cues of specific fungal infections."
Sagitta says, "They point out that flatworms could deplete O2 or exude slime 
	& so accelerate hatching, but I doubt that that is the reason."
Rett says, "What do you propose as a mechanism?"
Sagitta  . o O (Who is Rett trying to put on the spot here?)
Rett says, "Sagitta."
MarkB says, "I am working along the lines of a general stress response, 
	elevated stress hormone levels, but haven't finished that yet."
Sagitta . o O (Damn!)
SimonB says, "Well, responding to environmental cues is pretty ubiquitous. 
	What I want to know is: is it adaptive, and is it an adaptation? The 
	salamanders seem to be behaving adaptively most of the time. Doesn't 
	shed light on the selective forces, tho."
Breeder grins to Sagitta.
SimonB laughs to Sagitta.
Sagitta says, "I would guess that a single hormone determines when they hatch."
Rett [to Sagitta]: But what environmental factor is effecting the hormones 
	release?
Pimephales says, "But that hormone is likely to be influenced by many other 
	pathways."
Ramki says, "If predation has historically been a selective force, plasticity 
	would be an adaptation..."
Sagitta [to Pimephales]: That explains why oxygen and flatworms and who knows
	what else has an effect.
Sagitta laughs to Sagitta.
Pimephales says, "Seems plausible to me."
MarkB says, "Actually it seems we need at least two hormones, one that "says" 
	hatch and another that "says" wait until a larger size (cued by the 
	presence of a predator).  When the amount of the first exceeds the 
	second they hatch."
Rett says, "Couldn't a physiological response control the release of a single 
	hormone."
Pimephales says, "It seems that a hormonal heirarchy could accomplish the 
	same thing and do it more economically."
Sagitta says, "I would have thought that one hormone would do, if it is 
	secreted in response to low o2 (etc) and broken down in response to 
	flatworms (etc)."
SimonB . o O ( one hormone, 2,3... Does it matter? )
Pimephales says, "A single hormone would necessitate specific responses to 
	every conceivable environmental factor." 
Sagitta . o O ( I only proposed one new hormone, so Occam's razor is on my 
	side! )
Rett nods
Kim says, "What a about a single hormone with concentration effects? More 
	hormone issued equals earlier hatch date. "
Pimephales says, "I like the idea of concentration effects."
SimonB says, "What amazes me about this paper is that they did some 
	experiments that actually agree with the theory, for the most part, 
	although why late hatching controls will actually hatch earlier in the
	presence of predators has me stumped."
Sagitta says, "Or perhaps hatching depends on the breakdown of the jelly 
	rather than the behaviour of the larva inside. That would open 
	another receptacle of invertebrates."
MarkB says, "Is the earlier hatching of normally late hatchers really a 
	significant difference?  You can't really tell from the figure."
Breeder [to SimonB]: Do late hatching controls hatch earlier in the presence 
	of predators than `normal' animals?
Kim doesn't understand SimonB's confusion. But then she didn't get a copy of 
	the real paper. Why couldn't late hatchers have the same early hatching 
	mechanism but a later default setting?
Sagitta . o O ( in fig. 1 there are 4 points below the line & 5 above. )
SimonB [to MarkB]: I don't know. The sample size is small, too.
Rett [to SimonB]: Do juveniles have a higher survivorship than eggs?
Breeder wishes he could have gotten hold of the paper.
Sagitta [to Kim]: The question is "Why, then, do the late hatchers hatch 
	earlier than the control late hatchers?"
SimonB [to Rett]: In the presence of flatworms, no.
Rett says, "Perhaps due to an intensified 'attention' to predator chemicals."
Kim [to Sagitta]: HMMM? I assume they are hatching earlier in the presence of 
	predators. Am I very confused or what?
Sagitta [to Kim]: yes and probably yes.
SimonB smiles to Kim.
Kim eyes Saggitta 
Sagitta [to Kim]: Mostly they hatch later when with flatworms but those that 
	are expected to hatch very late hatch a bit earlier.
Alon [to SimonB]: What about general survivorship?
Sagitta says, "Looking at the graphs, I'm almost certain it's a real effect."
Sagitta waves its hands.
Breeder says, "Could someone please tell me - do control late hatchers hatch 
	later than early hatchers in the presence of predators?"
SimonB [to Alon]: Not actually having seen a salamander in the field, let 
	alone worked on them, I don't know. But I think that hatchling 
	survival would be low, as for most small herps.
Jon-D [to Sagitta]: It seems that in the presence of flatworms there is an 
	optimal time for hatching.  Both early and late hatchers move toward 
	the optimum.
Breeder . o O ( that's late hatch no pred, early hatch with pred )
Sagitta [to Jon-D]: So why is it important not to be too big in the presence 
	of flatworms.
MarkB says, "I think we are misinterpreting fig. 1A, fig.1B relates to date 
	of hatching (PC2)."
Jon-D says, "Perhaps it is not important to not be too big.  Perhaps it is 
	just a result of moving hatch time toward the optimum.  I have no 
	mechanism for this..."
Sagitta [to MarkB]: They both go below the x-axis, though.
Kim says, "Are flatworms visual predators??"
Rett [to Sagitta]: Perhaps movement in juveniles is advantageous.
MarkB [to Sagitta]: Not in my copy.
Sagitta says, "But _not_ when there are no flatworms around? My guess is 
	that it's nonadaptive."
Sagitta [to MarkB]: Sorry, you're right. I was comparing 1A with 2A!
Jon-D says, "The regression dips below the x axis in fig 1A and 2A, which 
	relate size of hatching and PC1."
SimonB . o O ( Aah. )
MarkB [to JON-D]: Yes size, but not date.
Jon-D nods
Sagitta . o O ( the date depends upon how old the eggs were when they were 
	collected, as well as everything else. )
SimonB says, "So, very late hatching controls produce smaller young in the 
	presence of predators, although they still hatch late when predators 
	are around."
Sagitta nods.
SimonB . o O ( Am I right? Gee I hate PCA's. )
MarkB says, "With respect to why late hatchers hatch at a smaller size in the 
	presence of predators, maybe there is some effect of stress levels on 
	growth, but not on hatch date."
SimonB nods to MarkB.
Sagitta [to MarkB]: It's certainly possible.
SimonB says, "Maybe they use up yolk reserves, making them lighter."
Rett says, "There may be an critical size below which the predator is less 
	likely to notice the organism."
Rett says, "Some zooplankton use this strategy"
Jon-D says, "But aren't these predators no threat to larger salamanders?"
SimonB [to Rett]: From the natural history info they give, I don't think so. 
	The flatworm tries to catch the larva, but the larger larvae can 
	struggle free.
SimonB nods to Jon-D.
Sagitta says, "They never saw larger ones succumbing."
MarkB [to Rett]: Good point.
SimonB says, "It takes more than one flatworm to kill a larva. One flatworm 
	grabs it, and a whole mob descend on it and devour it."
Rett says, "Does remaining in the egg longer give rise to larger or smaller 
	juveniles?" 
MarkB says, "Sorry I must leave right in the middle of everything."
SimonB [to Rett]: Generally larger, which is the main point of the paper. 
	Unless they stay in the egg too long, in which case they seem to be 
	smaller/lighter/less developed (can't say which).
SimonB [to MarkB]: Do you want to sum up?
MarkB has disconnected.
Breeder grins to SimonB.
SimonB . o O ( oops! )
Ramki grins.
SimonB grins.
Sagitta grins.
Breeder grins so much his head falls off.
Pimephales grimaces
Sagitta cheshire cats.
SimonB says, "OK, who wants to sum up instead? Or does anyone want to raise 
	any more points?"
Alon [to the]: green party maybe you would like to sum up.
SimonB says, "OK, it look like it's going to have to be me!"
Alon . o O ( hear hear )
Rett claps
Sagitta listens.
Ramki . o O ( go for it )
SimonB says, "The demonstration that salamander eggs can respond to 
	environmental cues to delay hatching is interesting, but perhaps not 
	surprising, given the structure of the egg masses, and that at the 
	end of incubation, the eggs are basically free swimming larvae inside 
	a capsule..."
SimonB says, "However, that they can respond adaptively to the presence of a 
	predator is kind of neat, although we have also heard about other 
	examples of that today..."
Sagitta agrees to SimonB.
Ramki nods to Breeder.
SimonB says, "And it looks like the authors are right in suggesting that 
	there are lots of neat experiments to be done on systems like this, 
	which are comparatively easy to manipulate. It would be interesting 
	to explore the proximate mechanisms too."
SimonB gets off of his soapbox.
SimonB says, "Has anyone got another paper they would like to propose? I'm 
	stepping down from the organiser role. My thesis is due this 
	semester..."
Sagitta looks around.
Rett says, "Good seminar, lets hear it for SimonB"
Sagitta applauds SimonB.
Ramki claps.
Breeder hip hips a coupla times.
Jon-D says, "What is the mechanism for proposing a seminar? My advisor is 
	interested, but not here now."
Pimephales whoops appreciatively.
SimonB blushes.
Alon joins the applauds.
Kim claps loudly and then crawls under a chair in case of paper selection 
	threats.
Gustavo still has to define the 'mechanism' a bit - but proposals are welcome.
Rett says, "I suggest a paper at least 1 yr old to ensure all have a copy"
SimonB [to Jon-D]: It's easy. You just decide on a paper, and post messages 
	to the appropriate newsgroups. Decide on a time and date, according 
	to who you expect to attend (remember the timezone problem).
Pimephales says, "How about something regarding programmed cell death?"
Sagebunny nods
Gustavo [to SimonB]: And it's best to coordinate with me.
SimonB [to Gustavo]: Of course.
SimonB grins to Gustavo.
Gustavo received a request not to e-mail announcements, so that's off 
	until a better method is found.

...Transcript ends.

Simon Blomberg.



-- 
Simon Blomberg                                   simonb at extro.ucc.su.OZ.AU
School of Biol. Sciences, A08
University of Sydney            We demand the right to stop to look even at
NSW   2006  Australia        lizards, which are nobody's property. -JBS Haldane